code stringlengths 3 1.18M | language stringclasses 1
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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.conrad.predict.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.com... | Java |
package de.mpg.mpiz.koeln.anna.step.common.lsf;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*
* @author Alexander Kerner
* @ThreadSave stateless
* @lastVisit 2009-08-12
* @Exceptions nothing to do
*
*/
public class LSF {
public ... | Java |
package de.mpg.mpiz.koeln.anna.step.getresults;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
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;
public class GetResults e... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.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.inputsequencereader;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import de.mpg.mpiz.koeln.anna.server... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
public class RepeatMaskerConstants {
private RepeatMaskerConstants(){}
public final static String WORKING_DIR_KEY = "anna.step.repeatMasker.workingDir";
public final static String EXE_DIR_KEY = "anna.step.repeatMasker.exeDir";
public final static String ... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff.GFFFormatErrorException;
import de.bioutils.gff.element.NewGFFElement;
impor... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
public interface DataModifier<V> {
void modifiyData(V v);
}
| Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
import de.mpg.mpiz.koeln.anna.server.data.DataBeanAccessException;
public interface DataProxy<V> {
/**
*
* <p>
* Atomar operation on data. Data will be synchronized bevor and after this
* operation.
* </p>
*
* @param v
* Type of Data, tha... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.EOFException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStre... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Properties;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatcher.ConsoleLogger;
import de.ke... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.impl.GFF3DataBeanImpl;
public class GFF3DiskSerialisation extends AbstractDiskSerialisation {
protected ... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
public class SimpleDiskSerialisation extends GFF3DiskSerialisation {
public SimpleDiskSerialisation() {
super();
}
public SimpleDiskSerialisation(LogDispatcher logger) {
super(logger);
}
... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.ko... | Java |
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.osgi.commons.logger.dispatcher.LogDispatcher;
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... | 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.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.common;
public class StepExecutionException extends Exception {
private static final long serialVersionUID = 5683856650378220175L;
public StepExecutionException() {
}
public StepExecutionException(String arg0) {
super(arg0);
}
public StepExecutionException(Throwable arg0... | Java |
package de.mpg.mpiz.koeln.anna.step.common;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
/**
* @lastVisit 2009-08-12
* @ThreadSave stateless
* @author Alexander Kerner
* @Exceptions good
*
*/
public class StepUtils {
private StepUtils() {}
public static void handleException(Object cause, ... | Java |
package de.mpg.mpiz.koeln.anna.step.common;
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.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.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.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.step.getresults.repeatmasker;
import java.io.File;
import java.util.ArrayList;
import org.osgi.framework.BundleContext;
import de.bioutils.gff.element.NewGFFElement;
import de.bioutils.gff.file.NewGFFFile;
import de.bioutils.gff.file.NewGFFFileImpl;
import de.kerner.osgi.commons.logger... | 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.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.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.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.getresults.predictedgenes;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import de.bioutils.gff.element.NewGFFElement;
import de.bioutils.gff.file.NewGF... | Java |
package de.mpg.mpiz.koeln.anna.step.estreader;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import ... | 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.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.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.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractStepProcessBuilder;
import de.mpg.mpiz.koeln.anna.step.re... | 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 |
package de.mpg.mpiz.koeln.anna.step.conrad.data.adapter;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import de.bioutils.Strand;
import de.bioutils.gff3.Type;
import de.bioutils.gff3.attribute.Attribute;
imp... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.data.adapter;
import de.bioutils.gff.file.NewGFFFile;
import de.bioutils.gff3.file.GFF3File;
public interface GFF3Converter {
NewGFFFile convert(GFF3File file);
}
| Java |
package de.mpg.mpiz.koeln.anna.step.conrad.predict.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.com... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.predict.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.co... | Java |
package de.mpg.mpiz.koeln.anna.step.common.lsf;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*
* @author Alexander Kerner
* @ThreadSave stateless
* @lastVisit 2009-08-12
* @Exceptions nothing to do
*
*/
public class LSF {
public ... | Java |
package de.mpg.mpiz.koeln.anna.step.common.lsf;
import java.io.File;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
*
* @author Alexander Kerner
* @ThreadSave stateless
* @lastVisit 2009-08-12
* @Exceptions nothing to do
*
*/
public class LSF {
public ... | Java |
package de.mpg.mpiz.koeln.anna.step.getresults;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
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;
public class GetResults e... | Java |
package de.mpg.mpiz.koeln.anna.step.getresults;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import de.bioutils.gff3.element.GFF3Element;
import de.bioutils.gff3.file.GFF3FileImpl;
import de.kerner.commons.file.FileUtils;
import de.mpg.mpiz.koeln.anna.abstr... | Java |
package de.mpg.mpiz.koeln.anna.listener.runtime.statistics;
import java.util.Collection;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
import de.kerner.commons.file.FileUtils;
import de.mpg.koeln.anna.core.events.AnnaEvent;
impor... | Java |
package de.mpg.mpiz.koeln.anna.listener.runtime.statistics;
import java.util.Map;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.TimeUnit;
import de.kerner.commons.StopWatch;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatche... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.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.repeatmasker.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.exonerate.lsf;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.mpg.mpiz.koeln.anna.step.common.lsf.LSF;
import de.mpg.mpiz.koeln.anna.step.exonerate.common.AbstractStepExonerate;
import de.mpg.mpiz.koeln.anna.step.exonerate.commo... | Java |
package de.mpg.mpiz.koeln.anna.listener.annafinishedlistener;
import java.util.Collection;
import de.mpg.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.listener.abstractlistener.AbstractEventListener;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg.mpiz.koeln.anna.step.ObservableStep.State... | Java |
package de.mpg.mpiz.koeln.anna.step.inputsequencereader;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import de.mpg.mpiz.koeln.anna.server... | Java |
package de.mpg.mpiz.koeln.anna.step.inputsequencereader;
import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.mpg.mpiz.koeln.anna.abstractstep.AbstractGFF3AnnaStep;
import de.mpg.mpiz.koeln.anna.server... | Java |
package de.mpg.mpiz.koeln.anna.step.exonerate.local;
import java.io.File;
import java.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.mpg.mpiz.koeln.anna.step.exonerate.common.AbstractStepExonerate;
import de.mpg.mpiz.koeln.anna.step.exonerate.common.ExonerateConstants;
public class ExonerateLoca... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
public class RepeatMaskerConstants {
private RepeatMaskerConstants(){}
public final static String WORKING_DIR_KEY = "anna.step.repeatMasker.workingDir";
public final static String EXE_DIR_KEY = "anna.step.repeatMasker.exeDir";
public final static String ... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff.GFFFormatErrorException;
import de.bioutils.gff.element.NewGFFElement;
impor... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
public class RepeatMaskerConstants {
private RepeatMaskerConstants(){}
public final static String WORKING_DIR_KEY = "anna.step.repeatMasker.workingDir";
public final static String EXE_DIR_KEY = "anna.step.repeatMasker.exeDir";
public final static String ... | Java |
package de.mpg.mpiz.koeln.anna.step.repeatmasker.common;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff.GFFFormatErrorException;
import de.bioutils.gff3.elem... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
public interface DataModifier<V> {
void modifiyData(V v);
}
| Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
import de.mpg.mpiz.koeln.anna.server.data.DataBeanAccessException;
public interface DataProxy<V> {
/**
*
* <p>
* Atomar operation on data. Data will be synchronized bevor and after this
* operation.
* </p>
*
* @param v
* Type of Data, tha... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.EOFException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStre... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Properties;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatcher.ConsoleLogger;
import de.ke... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.impl.GFF3DataBeanImpl;
public class GFF3DiskSerialisation extends AbstractDiskSerialisation {
protected ... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
public class SimpleDiskSerialisation extends GFF3DiskSerialisation {
public SimpleDiskSerialisation() {
super();
}
public SimpleDiskSerialisation(LogDispatcher logger) {
super(logger);
}
... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.ko... | Java |
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.osgi.commons.logger.dispatcher.LogDispatcher;
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... | 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.server.dataproxy;
public interface DataModifier<V> {
void modifiyData(V v);
}
| Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy;
import de.mpg.mpiz.koeln.anna.server.data.DataBeanAccessException;
// TODO: should be <V extends DataBean>
public interface DataProxy<V> {
/**
*
* <p>
* Atomar operation on data. Data will be synchronized bevor and after this
* operation.
* </p>
*
* @... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.EOFException;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.OutputStre... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Properties;
import de.kerner.commons.file.FileUtils;
import de.kerner.osgi.commons.logger.dispatcher.ConsoleLogger;
import de.ke... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.impl.GFF3DataBeanImpl;
public class GFF3DiskSerialisation extends AbstractDiskSerialisation {
protected ... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
import de.kerner.osgi.commons.logger.dispatcher.LogDispatcher;
public class SimpleDiskSerialisation extends GFF3DiskSerialisation {
public SimpleDiskSerialisation() {
super();
}
public SimpleDiskSerialisation(LogDispatcher logger) {
super(logger);
}
... | Java |
package de.mpg.mpiz.koeln.anna.server.dataproxy.impl;
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.ko... | Java |
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