code stringlengths 3 1.18M | language stringclasses 1
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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.mpg.mpiz.koeln.anna.step.common.lsf.LSF;
import de.mpg.mpiz.koeln.anna.step.conrad.common.ConradConstants;
import de.mpg.mpiz.koeln.anna.step.conrad.predict.comm... | 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 de.bioutils.gff3.element.GFF3ElementGroup;
import de.bioutils.gff3.element.GFF3ElementGroupImpl;
import de.bioutils.gff3.file.GFF3FileImpl;
import de.kerner.commons.file.FileUtils;
import de.mpg.mpiz.koeln.anna.abs... | 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.kerner.commons.logging.Log;
import de.mpg.m... | 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.commons.logging.Log;
import d... | Java |
package de.mpg.mpiz.koeln.anna.listener.statistics.prediction;
import java.util.Collection;
import java.util.concurrent.TimeUnit;
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.listener.abstractlistener.... | Java |
package de.mpg.mpiz.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 fin... | Java |
package de.mpg.mpiz.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 {
privat... | Java |
package de.mpg.mpiz.koeln.anna.core.events;
import java.util.EventListener;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface AnnaEventListener extends EventListener {
void eventOccoured(AnnaEvent event);
}
| 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);
void shutdown();
}
| 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.impl;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-09-22
* @thradSave custom
*
*/
class ImmediateStepSheduler extends StepSheduler {
ImmediateStepSheduler(AnnaStep step, EventHandler handler) {
super(step, handler);
... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
import java.util.ArrayList;
import java.util.Collection;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.step.Anna... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
/**
*
* @author Alexander Kerner
* @lastVisit 2009-11-12
*
*/
public abstract class StepSheduler imp... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
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.server.impl;
import de.kerner.commons.logging.Log;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.step.AnnaStep;
import de.mpg... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
import de.kerner.commons.logging.Log;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEventListener;
import de.mpg.mpiz.koeln.anna.core.events.StepStateChangeEvent;
import de.mpg.mpiz.koeln.anna.step.ObservableStep.State;
/... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
import java.util.Hashtable;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import org.osgi.framework.ServiceReference;
import de.kerner.commons.logging.Log;
import de.mpg.mpiz.koeln.anna.server.AnnaServer;
/**
* @lastVisit 2009-11-12
... | Java |
package de.mpg.mpiz.koeln.anna.server.impl;
import java.util.concurrent.Callable;
import de.kerner.commons.logging.Log;
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.step.StepExecutionException... | Java |
package de.mpg.mpiz.koeln.anna.server;
import java.util.Properties;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEventListener;
/**
*
* @lastVisit 2009-09-22
* @author Alexander Kerner
*
*/
public interface Server {
Properties getServerProperties();
// TODO: AnnaEventListener does not match this interfac... | Java |
package de.mpg.mpiz.koeln.anna.step;
public class StepExecutionException extends Exception {
private static final long serialVersionUID = 5683856650378220175L;
private final ExecutableStep step;
public StepExecutionException(ExecutableStep step) {
this.step = step;
}
public StepExecutionException(Executable... | 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;
public interface ExecutableStep {
boolean requirementsSatisfied() throws StepExecutionException;
boolean canBeSkipped() throws StepExecutionException;
boolean run() throws StepExecutionException;
Properties getStepProperties();
boolean isC... | Java |
package de.mpg.mpiz.koeln.anna.step;
import java.util.Collection;
import java.util.List;
public interface ObservableStep {
public enum State {
LOOSE,
// active steps
REGISTERED, CHECK_NEED_TO_RUN, RUNNING,
// well... might wait forever.
WAIT_FOR_REQ,
// finished steps
DONE, ERROR, SKIPPED;... | Java |
package de.mpg.mpiz.koeln.anna.step.conrad.predict.common;
import java.io.File;
import java.io.Serializable;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff3.GFF3Utils;
import de.bioutils.gff3.element.GFF3Element;
import de.bioutils.gff3.element.GFF3ElementB... | 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.mpg.mpiz.koeln.anna.step.common.lsf.LSF;
import de.mpg.mpiz.koeln.anna.step.repeatmasker.common.AbstractStepRepeatMasker;
import de.mpg.mpiz.koeln.anna.step.repeat... | 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.step.conrad.train.common;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import de.bioutils.fasta.FASTAElementGroup;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff3.element.GFF... | Java |
package de.mpg.mpiz.koeln.anna.listener.annafinishedlistener;
import java.util.Collection;
import de.kerner.commons.logging.Log;
import de.kerner.commons.osgi.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.core.events.AnnaEvent;
import de.mpg.mpiz.koeln.anna.listener.abstractlistener.AbstractEventLi... | 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 de.bioutils.AbstractSequence;
import de.bioutils.DNABasicAlphabet;
import de.bioutils.fasta.FASTAElement;
import de.bioutils.fasta.FASTAElementGroup;
import de.bioutils.fasta.FASTAElementGroupImpl;
import de.bioutils.fasta.FASTAEleme... | 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;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
public class RepeatMaskerConstants {
private RepeatMaskerConstants(){}
public final static String WORKING_DIR_KEY = "anna.step.repeatMasker.workingDir... | 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 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.repeatmasker.common;
import java.io.File;
import java.util.ArrayList;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.fasta.NewFASTAFileImpl;
import de.bioutils.gff3.GFF3Utils;
import de.bioutils.gff3.Type;
import de.bioutils.gff3.element.GFF3Ele... | 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 |
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.step.conrad.dataadapter.Adapter;
import java.util.ArrayList;
import java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.DNABasicAlphabet;
import de.bioutils.fasta.FastaUtils;
import de.bioutils.fasta.NewFASTAFile;
import de.bioutils.fasta.NewFASTAFileImpl;
impor... | 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.listener.statistics.runtime;
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.kerner.commons.logging.Log;
import de.mpg.m... | Java |
package de.mpg.mpiz.koeln.anna.listener.statistics.runtime;
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.commons.logging.Log;
import d... | Java |
package de.mpg.mpiz.koeln.anna.core;
public class AnnaConstants {
public static String IDENT = "Anna";
}
| 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.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.mpg.mpiz.koeln.anna.step.common.lsf.LSF;
import de.mpg.mpiz.koeln.anna.step.conrad.common.ConradConstants;
import de.mpg.mpiz.koeln.anna.step.conrad.train.common.AbstractTrain;
/**
*... | 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.util.List;
import de.kerner.commons.CommandStringBuilder;
/**
*
* @cleaned 2009-07-28
* @author Alexander Kerner
*
*/
public class ConradConstants {
private ConradConstants(){}
public final static List<String> getConradCmdString(){
return n... | 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.util.List;
import de.kerner.commons.CommandStringBuilder;
import de.mpg.mpiz.koeln.anna.step.conrad.common.ConradConstants;
import de.mpg.mpiz.koeln.anna.step.conrad.train.common.AbstractTrain;
public class TrainLocal extends AbstractTrain {
// Im... | 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.commons.osgi.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.data.DataProxy;
import de.mpg.mpiz.k... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import de.mpg.mpiz.koeln.anna.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.data.DataProxy;
import de.mpg.mpiz.koeln.anna.step.StepExecutionException;
class DummyStep extends AbstractGFF3AnnaStep {
private final String name;
DummyStep(String name){
this.n... | 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.commons.logging.Log;
/**
* @lastVisit 2009-... | Java |
package de.mpg.mpiz.koeln.anna.abstractstep;
import java.io.File;
import org.osgi.framework.BundleContext;
import org.osgi.util.tracker.ServiceTracker;
import de.kerner.commons.osgi.utils.ServiceNotAvailabeException;
import de.mpg.mpiz.koeln.anna.data.GFF3DataBean;
import de.mpg.mpiz.koeln.anna.server.data.DataProxy... | 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 java.util.List;
import org.osgi.framework.BundleContext;
import de.bioutils.AbstractSequence;
import de.bioutils.DNABasicAlphabet;
import de.biout... | 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.mpg.mpiz.koeln.anna.step.conrad.common.ConradConstants;
import de.mpg.mpiz.koeln.anna.step.conrad.predict.common.AbstractPredict;
/**
* @author Alexander Ker... | 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 |
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