code stringlengths 3 1.18M | language stringclasses 1
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package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.File;
import de.mpg.mpiz.koeln.anna.server.data.DataBean;
import de.mpg.mpiz.koeln.anna.server.data.DataBeanAccessException;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-09-21
*
*/
interface SerialisationStrategy {
<V extends DataBean... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.File;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.server.data.DataBean;
import de.mpg.mpiz.koeln.anna.server.data.DataBeanAccessException;
import de.mpg.mpiz.k... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
public interface GFF3DataProxy extends DataProxy<GFF3DataBean>{
}
| Java |
package de.mpg.mpiz.koeln.anna.core.starter;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import org.osgi.fram... | Java |
package de.mpg.mpiz.koeln.anna.core.starter;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import org.osgi.fram... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.adapter;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import de.kerner.commons.file.AbstractLineByLineReader;
import de.kerner.commons.file.FileUtils;... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.train.lsf;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.common.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.commo... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.train.lsf;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.comm... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff.GFFFormatErrorE... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFAST... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
/**
*
* @cleaned 2009-07-28
* @author Alexander Kerner
*
*/
public class ConradConstants {
private ConradConstants(){}
public final static String PROPERTIES_KEY_PREFIX = "anna.step.conrad.";
public final static String CONRAD_DIR_KEY = PROPERTIES_KEY_PREFI... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import org.osgi.framework.BundleContext;
import de.kerner.commons.StringUtils;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import de.mpg.mpiz.koeln.anna.step.common.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.s... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.biout... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
/**
*
* @cleaned 2009-07-28
* @author Alexander Kerner
*
*/
public class ConradConstants {
private ConradConstants(){}
public final static String PROPERTIES_KEY_PREFIX = "anna.step.conrad.";
public final static String CONRAD_DIR_KEY = PROPERTIES_KEY_PREFI... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.common;
import java.io.File;
import org.osgi.framework.BundleContext;
import de.kerner.commons.StringUtils;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.train.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.common.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.con... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.train.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.co... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Properties;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;
import de.kerner.commons.StringUt... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;
import de.kerner.osgi.commons.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.dataproxy.DataProxy;
import d... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.dataproxy.DataProxy;
import de.mpg.mpiz.koeln.anna.step.common.StepExecutionException;
class DummyStep extends AbstractGFF3AnnaStep {
private final String name;
DummyStep(Str... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Properties;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;
import de.kerner.osgi.commons.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.dataproxy.DataProxy;
import d... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.dataproxy.DataProxy;
import de.mpg.mpiz.koeln.anna.step.common.StepExecutionException;
class DummyStep extends AbstractGFF3AnnaStep {
private final String name;
DummyStep(Str... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import java.io.File;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import de.kerner.commons.file.FileUtils;
import de... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import java.io.File;
import java.io.OutputStream;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatcher.ConsoleLogger;... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;
import de.kerner.osgi.commons.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.dataproxy.DataProxy;
import d... | Java |
package de.mpg.mpiz.koeln.anna.step.verifiedgenes.reader;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAF... | Java |
package de.mpg.mpiz.koeln.anna.step.verifiedgenes.reader;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAF... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.predict.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.common.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.c... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.predict.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.... | Java |
package de.mpg.koeln.anna.core.events;
import java.util.Collection;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg.mpiz.koeln.anna.step.ObservableStep.State;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public class StepStateChangeEvent extends AnnaEvent {
private static final lo... | Java |
package de.mpg.koeln.anna.core.events;
import java.util.Collection;
import java.util.EventObject;
import java.util.HashSet;
import java.util.Set;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public class AnnaEvent extends EventObject {
private sta... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-09-22
* @thradSave custom
*
*/
class ImmediateStepSheduler extends StepSheduler {
ImmediateStepSheduler(An... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.AnnaEventListener;
import de.mpg.mpiz.koeln.anna... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.concurrent.Callable;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-09-22
*
*/
public abstract class StepSheduler implements Callable<Void>... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Properties;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.Hashtable;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcherImpl;
import de.mpg.mpiz.koeln.anna.se... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.concurrent.Callable;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.Server;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg.mpiz.koeln.... | Java |
package de.mpg.mpiz.koeln.anna.server;
import de.mpg.mpiz.koeln.anna.step.ExecutableStep;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface ExecutorServer extends Server {
void registerStep(ExecutableStep step);
void unregisterStep(ExecutableStep step);
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
import java.util.EventListener;
import de.mpg.koeln.anna.core.events.AnnaEvent;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface AnnaEventListener extends EventListener {
void eventOccoured(AnnaEvent event);
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface AnnaServer extends ExecutorServer {
final static String PROPERTIES_KEY_PREFIX = "anna.server.";
final static String WORKING_DIR_KEY = PROPERTIES_KEY_PREFIX
+ "workingdir";
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
import java.util.Properties;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface Server {
Properties getServerProperties();
void addEventListener(AnnaEventListener observer);
void removeEventListener(AnnaEventListener observer);
}
| Java |
package de.mpg.mpiz.koeln.anna.step;
public interface AnnaStep extends ExecutableStep, ObservableStep {
}
| Java |
package de.mpg.mpiz.koeln.anna.step;
import java.util.Properties;
import de.mpg.mpiz.koeln.anna.step.common.StepExecutionException;
public interface ExecutableStep {
boolean requirementsSatisfied() throws StepExecutionException;
boolean canBeSkipped() throws StepExecutionException;
boolean run() throws StepExe... | Java |
package de.mpg.mpiz.koeln.anna.step;
public interface ObservableStep {
public enum State {
LOOSE, REGISTERED, CHECK_NEED_TO_RUN, WAIT_FOR_REQ, RUNNING, DONE,
ERROR, SKIPPED
}
State getState();
void setState(State state);
}
| Java |
package de.mpg.koeln.anna.core.events;
import java.util.Collection;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg.mpiz.koeln.anna.step.ObservableStep.State;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public class StepStateChangeEvent extends AnnaEvent {
private static final lo... | Java |
package de.mpg.koeln.anna.core.events;
import java.util.Collection;
import java.util.EventObject;
import java.util.HashSet;
import java.util.Set;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public class AnnaEvent extends EventObject {
private sta... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-09-22
* @thradSave custom
*
*/
class ImmediateStepSheduler extends StepSheduler {
ImmediateStepSheduler(An... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.ArrayList;
import java.util.Collection;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
* <p... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @last... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Properties;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
impor... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.server.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.step.ObservableStep.... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.Hashtable;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcherImpl;
import de.mpg.mpiz.koeln.anna.se... | Java |
package de.mpg.mpiz.koeln.anna.serverimpl;
import java.util.concurrent.Callable;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.server.Server;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg.mpiz.koeln.anna.step.ObservableStep;
import de.mpg.mpiz.koeln.anna.ste... | Java |
package de.mpg.mpiz.koeln.anna.server;
import de.mpg.mpiz.koeln.anna.step.ExecutableStep;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface ExecutorServer extends Server {
void registerStep(ExecutableStep step);
void unregisterStep(ExecutableStep step);
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
import java.util.EventListener;
import de.mpg.koeln.anna.core.events.AnnaEvent;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface AnnaEventListener extends EventListener {
void eventOccoured(AnnaEvent event);
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface AnnaServer extends ExecutorServer {
final static String PROPERTIES_KEY_PREFIX = "anna.server.";
final static String WORKING_DIR_KEY = PROPERTIES_KEY_PREFIX
+ "workingdir";
}
| Java |
package de.mpg.mpiz.koeln.anna.server;
import java.util.Properties;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface Server {
Properties getServerProperties();
// TODO: AnnaEventListener does not match this interface abstraction
void addEventListener(AnnaEventListener observe... | Java |
package de.mpg.mpiz.koeln.anna.step;
public interface AnnaStep extends ExecutableStep, ObservableStep {
}
| Java |
package de.mpg.mpiz.koeln.anna.step;
import java.util.Properties;
import de.mpg.mpiz.koeln.anna.step.common.StepExecutionException;
public interface ExecutableStep {
boolean requirementsSatisfied() throws StepExecutionException;
boolean canBeSkipped() throws StepExecutionException;
boolean run() throws StepExe... | Java |
package de.mpg.mpiz.koeln.anna.step;
import java.util.List;
public interface ObservableStep {
public enum State {
// non-finished steps
LOOSE, REGISTERED, CHECK_NEED_TO_RUN, WAIT_FOR_REQ, RUNNING,
// finished steps
DONE, ERROR, SKIPPED;
public boolean isFinished(){
switch (this) {
case DONE:
... | Java |
package de.mpg.mpiz.koeln.anna.step.common;
import de.mpg.mpiz.koeln.anna.step.ExecutableStep;
public class StepExecutionException extends Exception {
private static final long serialVersionUID = 5683856650378220175L;
private final ExecutableStep step;
public StepExecutionException(ExecutableStep step) {
this.... | Java |
package de.mpg.mpiz.koeln.anna.step.common;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.ExecutableStep;
/**
* @lastVisit 2009-08-12
* @ThreadSave stateless
* @author Alexander Kerner
* @Exceptions good
*
*/
public class StepUtils {
private StepUtils() {}
... | Java |
package de.mpg.mpiz.koeln.anna.server.data;
public class DataBeanAccessException extends Exception {
private static final long serialVersionUID = 4002480662305683330L;
public DataBeanAccessException() {
}
public DataBeanAccessException(String arg0) {
super(arg0);
}
public DataBeanAccessException(Throwable ... | Java |
package de.mpg.mpiz.koeln.anna.server.data;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Map;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.gff.element.NewGFFElement;
public interface GFF3DataBean extends DataBean{
public ArrayList<FASTAElement> getInputSequence();
publ... | Java |
package de.mpg.mpiz.koeln.anna.server.data.impl;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.gff.element.NewGFFElement;
import de.mpg.mpiz.koeln.anna.server.data.GFF3DataBean;
public class GFF3DataB... | Java |
package de.mpg.mpiz.koeln.anna.server.data;
import java.io.Serializable;
import java.util.Map;
public interface DataBean extends Serializable {
public Map<String, Serializable> getCustom();
public void setCustom(Map<String, Serializable> custom);
}
| Java |
package de.mpg.mpiz.koeln.anna.server.data;
public class DataBeanAccessException extends Exception {
private static final long serialVersionUID = 4002480662305683330L;
public DataBeanAccessException() {
}
public DataBeanAccessException(String arg0) {
super(arg0);
}
public DataBeanAccessException(Throwable ... | Java |
package de.mpg.mpiz.koeln.anna.server.data;
import java.util.Collection;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.gff3.element.GFF3Element;
public interface GFF3DataBean extends DataBean {
public Collection<FASTAElement> getInputSequence();
public void setInputSequence(Collection<FASTAElement>... | Java |
package de.mpg.mpiz.koeln.anna.server.data.impl;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.gff3.element.GFF3Element;
import de.mpg.mpiz.koeln.anna.... | Java |
package de.mpg.mpiz.koeln.anna.server.data;
import java.io.Serializable;
public interface DataBean extends Serializable {
public Serializable getCustom(String ident);
public void addCustom(String ident, Serializable custom);
}
| Java |
package de.mpg.mpiz.koeln.anna.listener.abstractlistener;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcherImpl;
import de.kerner.osgi.commons.utils.ServiceRet... | Java |
package de.mpg.mpiz.koeln.anna.listener.abstractlistener;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcherImpl;
import de.kerner.osgi.commons.utils.ServiceRet... | Java |
package de.mpg.mpiz.koeln.anna.step.exonerate.common;
public class ExonerateConstants {
private ExonerateConstants(){}
public final static String WORKING_DIR_KEY = "anna.step.exonerate.workingDir";
public final static String EXE_DIR_KEY = "anna.step.exonerate.exeDir";
public final static String EXE = "exonerate... | Java |
package de.mpg.mpiz.koeln.anna.step.exonerate.common;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.b... | Java |
package de.mpg.mpiz.koeln.anna;
import java.util.ArrayList;
import de.kerner.commons.workflow.WorkFlow;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class ExecutionWorkflow implements WorkFlow {
private final ArrayList<WorkFlowElement> elements = n... | Java |
package de.mpg.mpiz.koeln.anna;
import org.apache.myfaces.custom.fileupload.UploadedFile;
import de.kerner.commons.file.HumanReadableFileSizePrinter;
import de.kerner.commons.logging.Log;
public class UploadBacking {
/**
* <p> For example "#{userBean}" </p>
*/
public static String getIdentString(){
return ... | Java |
package de.mpg.mpiz.koeln.anna;
import javax.faces.application.FacesMessage;
import javax.faces.context.FacesContext;
import de.kerner.commons.workflow.WorkFlowException;
public class InformByFacesMessageWorkFlowException extends WorkFlowException {
private static final long serialVersionUID = -6001010151572002001... | Java |
package de.mpg.mpiz.koeln.anna;
public class ArabidobsisBean extends TrainingSpeciesBean {
ArabidobsisBean(){
super();
setName("arabidopsis-thaliana");
setPath("/home/proj/kerner/diplom/anna/page/trainingFiles/arabidopsis-thaliana");
}
}
| Java |
package de.mpg.mpiz.koeln.anna;
public class FusariumBean extends TrainingSpeciesBean {
FusariumBean(){
super();
setName("fusarium-graminearum");
setPath("/home/proj/kerner/diplom/anna/page/trainingFiles/fusarium-graminearum");
}
}
| Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import de.kerner.commons.eee.JSFUtil;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
import de.kerner.commons.zip.ZipUtils;
public class Extractor implements WorkFlowElement {
private final File dir;
p... | Java |
package de.mpg.mpiz.koeln.anna;
public class ConfigBean {
/**
* <p> For example "#{userBean}" </p>
*/
public static String getIdentString(){
return "#{configBean}";
}
private String workingDir;
private String zipName;
private String trainingFileName;;
public String getWorkingDir() {
return work... | Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import de.kerner.commons.eee.JSFUtil;
import de.kerner.commons.logging.Log;
import de.kerner.commons.workflow.WorkFlowException;
public class RunBacking {
private final static Log log = new Log(RunBacking.class);
private volatile File sessionDir = null;
publ... | Java |
package de.mpg.mpiz.koeln.anna;
import java.util.ArrayList;
import java.util.List;
import javax.faces.model.SelectItem;
public class SelectTrainingSpeciesBacking {
private List<SelectItem> list = new ArrayList<SelectItem>();
// Constructor //
public SelectTrainingSpeciesBacking(){
list.add(getSelectItemFr... | Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import java.io.IOException;
import de.kerner.commons.eee.JSFUtil;
import de.kerner.commons.file.FileUtils;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class CreateInputSequence implements WorkFlowE... | Java |
package de.mpg.mpiz.koeln.anna;
import javax.faces.component.UIComponent;
import javax.faces.context.FacesContext;
import javax.faces.convert.Converter;
import javax.faces.convert.ConverterException;
import javax.faces.model.SelectItem;
public class TrainingSpeciesConverter implements Converter {
public Object getA... | Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import java.io.IOException;
import de.kerner.commons.file.FileUtils;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class TrainingFileCopier implements WorkFlowElement {
private final File sessionDi... | Java |
package de.mpg.mpiz.koeln.anna;
public class TrainingSpeciesBean {
private String name;
private String path;
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getPath() {
return path;
}
public void setPath(String path) {
this.path = p... | Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import de.kerner.commons.eee.JSFUtil;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class SessionDirCreator implements WorkFlowElement {
public void work() throws WorkFlowException {
final Config... | Java |
package de.mpg.mpiz.koeln.anna;
import de.kerner.commons.eee.JSFUtil;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class CheckIfFileWasUploaded implements WorkFlowElement {
public void work() throws WorkFlowException {
final UploadBacking u = JSFUt... | Java |
package de.mpg.mpiz.koeln.anna;
import java.io.File;
import java.util.Properties;
import de.kerner.commons.file.FileUtils;
import de.kerner.commons.workflow.WorkFlowElement;
import de.kerner.commons.workflow.WorkFlowException;
public class PropertiesAssigner implements WorkFlowElement {
private final File sessionD... | Java |
package de.mpg.mpiz.koeln.anna.step.estreader;
import java.io.File;
import de.bioutils.DNABasicAlphabet;
import de.bioutils.fasta.FASTAElementGroup;
import de.bioutils.fasta.FASTAElementGroupImpl;
import de.bioutils.fasta.FastaUtils;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAFileImpl;
im... | Java |
package de.mpg.mpiz.koeln.anna.listener.progresslistener;
import java.util.Collection;
import java.util.Formatter;
import de.kerner.commons.file.FileUtils;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.listener.abstractlistener... | Java |
package de.mpg.mpiz.koeln.anna.listener.progresslistener;
import java.util.Collection;
import java.util.Formatter;
import de.kerner.commons.file.FileUtils;
import de.kerner.commons.logging.Log;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.core.events.StepStateChangeEvent;
import ... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.step.common.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.rep... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.mpg.mpiz.koeln.anna.step.repeatmasker.common.AbstractStepRepeatMasker;
import de.mpg.mpiz.koeln.anna.step.repeatmasker.common.RepeatMaskerConstants;
public clas... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.data.adapter;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import de.bioutils.gff.GFFFormatErrorException;
import de.bioutils.gff.element.NewGFFElement;
import de.bioutils.gff.element.NewGFFEleme... | Java |
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