[med-svn] [rambo-k] 03/06: New upstream version 1.21+r5
Andreas Tille
tille at debian.org
Thu Oct 27 14:39:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rambo-k.
commit c988c5c9ba404c105152d5f1b950756b521ea283
Author: Andreas Tille <tille at debian.org>
Date: Tue Oct 25 19:16:11 2016 +0200
New upstream version 1.21+r5
---
RAMBO-K-plugin_eclipse/.classpath | 9 -
RAMBO-K-plugin_eclipse/.project | 17 --
.../RAMBO-K Indexer (32 bit).launch | 27 ---
.../RAMBO-K indexer (64 bit).launch | 27 ---
RAMBO-K-plugin_eclipse/RAMBO-K-Indexer.iml | 13 --
RAMBO-K-plugin_eclipse/plugin.properties | 11 --
.../org/rki/rambok/indexer/GeneiousDataReader.java | 56 ------
.../org/rki/rambok/indexer/GeneiousDataWriter.java | 73 --------
.../src/org/rki/rambok/indexer/GeneiousReader.java | 82 --------
.../src/org/rki/rambok/indexer/GeneiousWriter.java | 53 ------
.../src/org/rki/rambok/indexer/Indexer.java | 189 -------------------
.../src/org/rki/rambok/indexer/IndexerPlugin.java | 92 ---------
.../rki/rambok/indexer/RAMBOKProgressListener.java | 43 -----
.../src/org/rki/rambok/indexer/RAMBOKresult.java | 206 ---------------------
.../rambok/indexer/RAMBOKresultDocumentViewer.java | 79 --------
ReadClassifier_eclipse/.classpath | 1 -
.../src/org/rki/readclassifier/AbstractWriter.java | 7 -
.../src/org/rki/readclassifier/Classifier.java | 2 +-
.../readclassifier/ClassifierProgressListener.java | 5 -
.../org/rki/readclassifier/ClassifierThread.java | 41 ++--
.../src/org/rki/readclassifier/MMClassifier.java | 38 ----
.../src/org/rki/readclassifier/Read.java | 19 +-
.../src/org/rki/readclassifier/Reader.java | 6 +-
.../src/org/rki/readclassifier/Writer.java | 2 +-
.../src/org/rki/readtrainer/AbstractReader.java | 9 -
.../src/org/rki/readtrainer/Trainer.java | 2 +-
.../rki/readtrainer/TrainerProgressListener.java | 5 -
.../src/org/rki/readtrainer/TrainerThread.java | 9 +-
28 files changed, 30 insertions(+), 1093 deletions(-)
diff --git a/RAMBO-K-plugin_eclipse/.classpath b/RAMBO-K-plugin_eclipse/.classpath
deleted file mode 100644
index 20c0f69..0000000
--- a/RAMBO-K-plugin_eclipse/.classpath
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="src"/>
- <classpathentry combineaccessrules="false" kind="src" path="/GeneiousFiles"/>
- <classpathentry combineaccessrules="false" kind="src" path="/ReadTrainer"/>
- <classpathentry combineaccessrules="false" kind="src" path="/ReadClassifier"/>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="output" path="bin"/>
-</classpath>
diff --git a/RAMBO-K-plugin_eclipse/.project b/RAMBO-K-plugin_eclipse/.project
deleted file mode 100644
index 629e25b..0000000
--- a/RAMBO-K-plugin_eclipse/.project
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>RAMBO-K-plugin_eclipse</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- </natures>
-</projectDescription>
diff --git a/RAMBO-K-plugin_eclipse/RAMBO-K Indexer (32 bit).launch b/RAMBO-K-plugin_eclipse/RAMBO-K Indexer (32 bit).launch
deleted file mode 100644
index 36e92e1..0000000
--- a/RAMBO-K-plugin_eclipse/RAMBO-K Indexer (32 bit).launch
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/RAMBO-K-Indexer"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="./activation/macos:./native_libs/macos"/>
-<mapEntry key="LD_LIBRARY_PATH" value="./activation/linux32:./native_libs/linux32"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
-</listAttribute>
-<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER" javaProject="RAMBO-K-Indexer" path="1" type="4"/>
"/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry id="org.eclipse.jdt.launching.classpathentry.defaultClasspath">
<memento exportedEntriesOnly="false" project="RAMBO-K-Indexer"/>
</runtimeClasspathEntry>
"/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry internalArchive="/GeneiousFiles/resources" path="3" type="2"/>
"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.biomatters.iseek.application.ISeekMain"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="extraPlugins="org.rki.rambok.indexer.IndexerPlugin""/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="RAMBO-K-Indexer"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-ea -Xss512K -Xms256M -Xmx768M -XX:MaxPermSize=96M -Djava.util.logging.config.file=no_logging.properties"/>
-<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:GeneiousFiles}"/>
-</launchConfiguration>
diff --git a/RAMBO-K-plugin_eclipse/RAMBO-K indexer (64 bit).launch b/RAMBO-K-plugin_eclipse/RAMBO-K indexer (64 bit).launch
deleted file mode 100644
index 87532e4..0000000
--- a/RAMBO-K-plugin_eclipse/RAMBO-K indexer (64 bit).launch
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
-<listEntry value="/RAMBO-K-Indexer"/>
-</listAttribute>
-<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
-<listEntry value="4"/>
-</listAttribute>
-<mapAttribute key="org.eclipse.debug.core.environmentVariables">
-<mapEntry key="DYLD_LIBRARY_PATH" value="./activation/macos:./native_libs/macos"/>
-<mapEntry key="LD_LIBRARY_PATH" value="./activation/linux64:./native_libs/linux64"/>
-</mapAttribute>
-<listAttribute key="org.eclipse.debug.ui.favoriteGroups">
-<listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
-</listAttribute>
-<listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry containerPath="org.eclipse.jdt.launching.JRE_CONTAINER" javaProject="RAMBO-K-Indexer" path="1" type="4"/>
"/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry id="org.eclipse.jdt.launching.classpathentry.defaultClasspath">
<memento exportedEntriesOnly="false" project="RAMBO-K-Indexer"/>
</runtimeClasspathEntry>
"/>
-<listEntry value="<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<runtimeClasspathEntry internalArchive="/GeneiousFiles/resources" path="3" type="2"/>
"/>
-</listAttribute>
-<booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.biomatters.iseek.application.ISeekMain"/>
-<stringAttribute key="org.eclipse.jdt.launching.PROGRAM_ARGUMENTS" value="extraPlugins="org.rki.rambok.indexer.IndexerPlugin""/>
-<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="RAMBO-K-Indexer"/>
-<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-XX:+UseConcMarkSweepGC -ea -Xss512K -Xms256M -Xmx768M -XX:MaxPermSize=256M -Djava.util.logging.config.file=no_logging.properties"/>
-<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:GeneiousFiles}"/>
-</launchConfiguration>
diff --git a/RAMBO-K-plugin_eclipse/RAMBO-K-Indexer.iml b/RAMBO-K-plugin_eclipse/RAMBO-K-Indexer.iml
deleted file mode 100644
index a8a2107..0000000
--- a/RAMBO-K-plugin_eclipse/RAMBO-K-Indexer.iml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
- <component name="NewModuleRootManager" inherit-compiler-output="true">
- <exclude-output />
- <content url="file://$MODULE_DIR$">
- <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
- </content>
- <orderEntry type="inheritedJdk" />
- <orderEntry type="sourceFolder" forTests="false" />
- <orderEntry type="module" module-name="GeneiousFiles" />
- </component>
-</module>
-
diff --git a/RAMBO-K-plugin_eclipse/plugin.properties b/RAMBO-K-plugin_eclipse/plugin.properties
deleted file mode 100644
index a69ba44..0000000
--- a/RAMBO-K-plugin_eclipse/plugin.properties
+++ /dev/null
@@ -1,11 +0,0 @@
-# This file contains important information about the plugin
-# and must be included in the plugin jar file.
-
-# This is the fully qualified name of the main class
-# of the plugin you are developing. This is required by
-# Geneious to install a plugin.
-plugin-name=org.rki.rambok.indexer.IndexerPlugin
-
-# This is the short name for your plugin. It is used
-# to name the gplugin file for distribution.
-short-plugin-name=IndexerPlugin
\ No newline at end of file
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataReader.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataReader.java
deleted file mode 100644
index 8af469c..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataReader.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.List;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.rki.readclassifier.Read;
-import org.rki.readclassifier.ReadPair;
-import org.rki.readtrainer.AbstractReader;
-
-import com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraphSequenceDocument;
-import com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument;
-import com.biomatters.geneious.publicapi.documents.sequence.SequenceListDocument;
-
-public class GeneiousDataReader extends AbstractReader {
- private List<NucleotideSequenceDocument> _seqs;
- private int _numThreads;
-
- public GeneiousDataReader(SequenceListDocument doc, int numThreads) {
- _seqs = doc.getNucleotideSequences();
- _numThreads = numThreads;
- try {
- reads = new LinkedBlockingQueue<ReadPair>(50000);
- } catch(Exception e) {
- System.out.println("--------------\n");
- e.printStackTrace();
- System.out.println("--------------\n");
- }
- }
-
- public void run() {
- readReads();
- try {
- for(int i=0; i<_numThreads; i++) {
- reads.put(new ReadPair(null, null));
- }
- } catch(Exception e) {
- e.printStackTrace();
- }
- }
-
- private void readReads() {
- for(NucleotideSequenceDocument seq : _seqs) {
- NucleotideGraphSequenceDocument gseq = (NucleotideGraphSequenceDocument)seq;
- byte[] intQualities = new byte[gseq.getSequenceLength()];
- for(int i=0; i<gseq.getSequenceLength(); i++) {
- intQualities[i] = (byte)gseq.getSequenceQuality(i);
- }
- Read read = new Read(seq.getName(), gseq.getSequenceString(), intQualities, true);
- try {
- reads.put(new ReadPair(read, null));
- } catch(InterruptedException e) {
- e.printStackTrace();
- }
- }
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataWriter.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataWriter.java
deleted file mode 100644
index 4f52b0d..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousDataWriter.java
+++ /dev/null
@@ -1,73 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.Date;
-import java.util.LinkedList;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.rki.readclassifier.AbstractWriter;
-import org.rki.readclassifier.Read;
-import org.rki.readclassifier.ReadPair;
-
-import com.biomatters.geneious.publicapi.documents.sequence.CompactQualityOnlyGraph;
-import com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument;
-import com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideGraphSequence;
-
-public class GeneiousDataWriter extends AbstractWriter {
- private int _numThreads;
- private DefaultSequenceListDocument _out1;
- private int _scoreCutoff;
- private int _numToTrain;
- private int _numTrained;
- private RAMBOKresult _resdoc;
-
- public GeneiousDataWriter(int numThreads, DefaultSequenceListDocument out1, DefaultSequenceListDocument out2, int scoreCutoff, int numToTrain, RAMBOKresult resdoc) {
- outReads = new LinkedBlockingQueue<ReadPair>(50000);
- _numThreads = numThreads;
- _out1 = out1;
- _scoreCutoff = scoreCutoff;
- _numToTrain = numToTrain;
- _numTrained = 0;
- _resdoc = resdoc;
- }
-
- public void run() {
- LinkedList<Double> scores = new LinkedList<Double>();
- int threadsRunning = _numThreads;
- while(true) {
- try {
- ReadPair reads = outReads.take();
- if(reads.read1 == null) {
- threadsRunning --;
- if(threadsRunning == 0)
- break;
- continue;
- }
- if(reads.read1.invalid && (reads.read2 == null || reads.read2.invalid))
- continue;
- if(reads.read1.score > _scoreCutoff) {
- _out1.addNucleotideSequence(makeSeqGraph(reads.read1));
- }
- _numTrained += 1;
- if(_numTrained < _numToTrain) {
- scores.add(reads.read1.score);
- }
- else if(_numTrained == _numToTrain) {
- _resdoc.setRealScores(scores);
- }
-// else {
-// _out2.addNucleotideSequence(makeSeqGraph(reads.read1));
-// }
- } catch(Exception e) {
- e.printStackTrace();
- }
- }
- if(_numTrained < _numToTrain) {
- _resdoc.setRealScores(scores);
- }
- }
-
- private DefaultNucleotideGraphSequence makeSeqGraph(Read read) {
- DefaultNucleotideGraphSequence gdoc = new DefaultNucleotideGraphSequence(read.name, "", read.bases, new Date(), new CompactQualityOnlyGraph(read.intQualities));
- return gdoc;
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousReader.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousReader.java
deleted file mode 100644
index 3d40ee1..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousReader.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.List;
-import java.util.Random;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.rki.readclassifier.Read;
-import org.rki.readclassifier.ReadPair;
-import org.rki.readtrainer.AbstractReader;
-
-import com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument;
-import com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument;
-import com.biomatters.geneious.publicapi.documents.sequence.SequenceCharSequence;
-
-public class GeneiousReader extends AbstractReader {
- private List<NucleotideSequenceDocument> _seqs;
- private int _numReads;
- private int _numThreads;
- private int _readsRead = 0;
-
- public GeneiousReader(DefaultSequenceListDocument doc, int numReads, int numThreads) {
- _seqs = doc.getNucleotideSequences();
- _numReads = numReads;
- _numThreads = numThreads;
- try {
- reads = new LinkedBlockingQueue<ReadPair>(numReads);
- } catch(Exception e) {
- System.out.println("--------------\n");
- e.printStackTrace();
- System.out.println("--------------\n");
- }
- }
-
- public void run() {
- readReads();
- try {
- for(int i=0; i<_numThreads; i++) {
- reads.put(new ReadPair(null, null));
- }
- } catch(Exception e) {
- e.printStackTrace();
- }
- }
-
- private void readReads() {
- int readLength = 100;
- Random rand = new Random();
- int numpos = 0;
- for(NucleotideSequenceDocument seq : _seqs) {
- numpos += seq.getSequenceLength();
- }
- double posOdds = (double)_numReads / (double)numpos;
- readloop: while(_readsRead < _numReads) {
- for(NucleotideSequenceDocument seq : _seqs) {
- int numToDraw = (int)(posOdds*rand.nextDouble()*seq.getSequenceLength());
- int numDrawn = 0;
- SequenceCharSequence seqSeq = seq.getCharSequence();
- while(numDrawn < numToDraw) {
- int seqPos = (int)(rand.nextDouble()*(seq.getSequenceLength()-readLength));
- SequenceCharSequence readSeq = seqSeq.subSequence(seqPos, seqPos+readLength);
- boolean canKeep = true;
- for(int i=0; i<readSeq.length(); i++) {
- if(readSeq.charAt(i) != 'A' &&
- readSeq.charAt(i) != 'G' &&
- readSeq.charAt(i) != 'C' &&
- readSeq.charAt(i) != 'T') {
- canKeep = false;
- break;
- }
- }
- if(canKeep) {
- Read read = new Read("1", readSeq.toString(), null);
- reads.add(new ReadPair(read, null));
- _readsRead += 1;
- if(_readsRead >= _numReads-1)
- break readloop;
- }
- }
- }
- }
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousWriter.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousWriter.java
deleted file mode 100644
index 3638d92..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/GeneiousWriter.java
+++ /dev/null
@@ -1,53 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.LinkedList;
-import java.util.concurrent.LinkedBlockingQueue;
-
-import org.rki.readclassifier.AbstractWriter;
-import org.rki.readclassifier.Classifier;
-import org.rki.readclassifier.ReadPair;
-
-public class GeneiousWriter extends AbstractWriter {
-
- private int _numThreads;
- private LinkedList<Double> _scores;
- private int _currentOrg = 0;
-
- public GeneiousWriter(int numReads, int numThreads) {
- outReads = new LinkedBlockingQueue<ReadPair>(numReads);
- _numThreads = numThreads;
- _scores = new LinkedList<Double>();
- }
-
- public void setCurrentOrg(int currentOrg) {
- _currentOrg = currentOrg;
- }
-
- public void run() {
- int threadsRunning = _numThreads;
- while(true) {
- try {
- ReadPair reads = outReads.take();
- if(reads.read1 == null) {
- threadsRunning --;
- if(threadsRunning == 0)
- break;
- }
- if(reads.read1.invalid && reads.read2.invalid)
- continue;
- _scores.add(reads.read1.score);
-// if(Classifier.useCutoff == Classifier.Cutoff.HIGHER && reads.read1.score < Classifier.cutoffHigher)
-// continue;
-// else if(Classifier.useCutoff == Classifier.Cutoff.LOWER && reads.read1.score > Classifier.cutoffLower)
-// continue;
-// out1w.write(reads.read1.toString(true));
- } catch(Exception e) {
- }
- }
- }
-
- public LinkedList<Double> getScores() {
- return _scores;
- }
-
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/Indexer.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/Indexer.java
deleted file mode 100644
index d705bbd..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/Indexer.java
+++ /dev/null
@@ -1,189 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.Date;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.concurrent.atomic.AtomicInteger;
-
-import org.rki.readclassifier.ClassifierThread;
-import org.rki.readclassifier.MMClassifier;
-import org.rki.readtrainer.Trainer;
-import org.rki.readtrainer.TrainerThread;
-
-import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
-import com.biomatters.geneious.publicapi.documents.DocumentUtilities;
-import com.biomatters.geneious.publicapi.documents.sequence.DefaultSequenceListDocument;
-import com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence;
-import com.biomatters.geneious.publicapi.plugin.DocumentOperation;
-import com.biomatters.geneious.publicapi.plugin.DocumentSelectionOption;
-import com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature;
-import com.biomatters.geneious.publicapi.plugin.DocumentType;
-import com.biomatters.geneious.publicapi.plugin.GeneiousActionOptions;
-import com.biomatters.geneious.publicapi.plugin.Options;
-import com.biomatters.geneious.publicapi.plugin.Options.IntegerOption;
-
-import jebl.util.ProgressListener;
-
-/**
- * This plugin shows how to create a simple AlignmentOperation by providing an implementation that just pads the alignment
- * to make all sequences the same length
- *
- * @author Matt Kearse
- * @version $Id$
- */
-
-public class Indexer extends DocumentOperation {
- public String getHelp() {
- return "This plugin separates foreground reads from background reads using RAMBO-K.";
- }
-
- public String getName() {
- return "RAMBO-K";
- }
-
- public double getTabPosition() {
- return 0.5;
- }
-
- public DocumentSelectionSignature[] getSelectionSignatures() {
- return new DocumentSelectionSignature[] { DocumentSelectionSignature.forNucleotideSequences(1, Integer.MAX_VALUE) };
- }
-
- public boolean isProOnly() {
- return false;
- }
-
- @Override
- public Options getOptions(AnnotatedPluginDocument[] docs) {
- Options opt= new Options(this.getClass());
- opt.addIntegerOption("kMerSize", "Kmer size to use", 8, 2, 10);
- opt.addIntegerOption("scoreCutoff", "Score cutoff (everything with a lower score will be considered background)", 0, -1000, 1000);
- opt.addIntegerOption("numThreads", "Number of threads to use", 4, 1, 64);
- HashSet<DocumentType> allowedDocs = new HashSet<DocumentType>();
- allowedDocs.add(DocumentType.NUCLEOTIDE_SEQUENCE_LIST_TYPE);
- allowedDocs.add(DocumentType.NUCLEOTIDE_SEQUENCE_TYPE);
- opt.addDocumentSelectionOption("foregroundReference", "Foreground reference(s)", DocumentSelectionOption.FolderOrDocuments.EMPTY, allowedDocs, null, "Reference sequence(s)", null, false, new LinkedList<AnnotatedPluginDocument>());
- opt.addDocumentSelectionOption("backgroundReference", "Background reference(s)", DocumentSelectionOption.FolderOrDocuments.EMPTY, allowedDocs, null, "Background sequence(s)", null, false, new LinkedList<AnnotatedPluginDocument>());
- return opt;
- }
-
- @Override
- public GeneiousActionOptions getActionOptions() {
-/* GeneiousActionOptions parent = new GeneiousActionOptions("RAMBO-K").setMainMenuLocation(GeneiousActionOptions.MainMenu.Tools).setInMainToolbar(true);
- GeneiousActionOptions index = new GeneiousActionOptions("Build index", "Builds a RAMBO-K index from reference sequence(s)", null);
- GeneiousActionOptions res = GeneiousActionOptions.createSubmenuActionOptions(index, parent);
- return res;*/
- return new GeneiousActionOptions("Spearate reads through RAMBO-K").setMainMenuLocation(GeneiousActionOptions.MainMenu.Tools).setInMainToolbar(true);
- }
-
- public List performOperation(AnnotatedPluginDocument[] docs, ProgressListener progress, Options options) {
- int numToTrain = 50000;
- int numThreads = ((IntegerOption)(options.getOption("numThreads"))).getValue();
- int kmersize = ((IntegerOption)(options.getOption("kMerSize"))).getValue();
- int scoreCutoff = ((IntegerOption)(options.getOption("scoreCutoff"))).getValue();
- Trainer.kmersize = kmersize;
- int numReal = 0;
- DefaultSequenceListDocument realReads = null;
- try {
- realReads = (DefaultSequenceListDocument)(docs[0].getDocument());
- numReal = realReads.getNucleotideSequences().size();
- } catch(Exception e) {
- e.printStackTrace();
- }
- RAMBOKProgressListener prog = new RAMBOKProgressListener(progress, 2*numToTrain, 2*numToTrain+numReal);
- AtomicInteger[][] matrix1 = new AtomicInteger[(int)Math.pow(4, kmersize)][4];
- AtomicInteger[][] matrix2 = new AtomicInteger[(int)Math.pow(4, kmersize)][4];
- List<AnnotatedPluginDocument> res = new LinkedList<AnnotatedPluginDocument>();
- LinkedList<Double>[] scores = new LinkedList[] {new LinkedList<Double>(), new LinkedList<Double>()};
- try {
- prog.setTitle("Training model...");
- DefaultSequenceListDocument seqDoc1 = (DefaultSequenceListDocument)(((DocumentSelectionOption)(options.getOption("foregroundReference"))).getDocuments().get(0).getDocument());
- trainMatrix(seqDoc1, matrix1, numToTrain, numThreads, prog);
- DefaultSequenceListDocument seqDoc2 = (DefaultSequenceListDocument)(((DocumentSelectionOption)(options.getOption("backgroundReference"))).getDocuments().get(0).getDocument());
- trainMatrix(seqDoc2, matrix2, numToTrain, numThreads, prog);
-
- prog.setTitle("Classifying simulated reads...");
- MMClassifier classifier = new MMClassifier();
- classifier.setMatrices(matrix1, matrix2, seqDoc1.getName(), seqDoc2.getName(), kmersize);
- scores[0] = testReads(seqDoc1, classifier, numToTrain, numThreads, kmersize, prog);
- scores[1] = testReads(seqDoc2, classifier, numToTrain, numThreads, kmersize, prog);
- RAMBOKresult resdoc = new RAMBOKresult("RAMBOK summary: foreground " + seqDoc1.getName() + " vs. background " + seqDoc2.getName(), seqDoc1.getName(), seqDoc2.getName(), scores[0], scores[1]);
- prog.setTitle("Classifying real reads...");
- res = classifyReads(realReads, numThreads, classifier, prog, scoreCutoff, numToTrain, resdoc);
- res.get(0).setName("RAMBO-K foreground reads: " + seqDoc1.getName());
-// res.add(resdoc);
- res.add(DocumentUtilities.createAnnotatedPluginDocument(resdoc));
- res.get(1).setName(resdoc.getName());
- // res.get(1).setName("RAMBO-K reads: " + seqDoc2.getName());
- } catch (Exception e) {
- e.printStackTrace();
- }
- return res;
- }
-
- private LinkedList<AnnotatedPluginDocument> classifyReads(DefaultSequenceListDocument doc, int numThreads, MMClassifier classifier, RAMBOKProgressListener prog, int scoreCutoff, int numToTrain, RAMBOKresult resdoc) throws InterruptedException {
- GeneiousDataReader reader = new GeneiousDataReader(doc, numThreads);
- DefaultSequenceListDocument out1 = new DefaultSequenceListDocument();
- DefaultSequenceListDocument out2 = new DefaultSequenceListDocument();
- GeneiousDataWriter writer = new GeneiousDataWriter(numThreads, out1, out2, scoreCutoff, numToTrain, resdoc);
- System.out.println("\n====" + scoreCutoff + "====");
- writer.start();
- reader.start();
- LinkedList<ClassifierThread> threadList = new LinkedList<ClassifierThread>();
- while(threadList.size() < numThreads) {
- threadList.add(new ClassifierThread(reader, writer, classifier, prog));
- }
- for(ClassifierThread c : threadList) {
- c.start();
- }
- for(ClassifierThread c : threadList) {
- c.join();
- }
- reader.join();
- writer.join();
- out1.addNucleotideSequence(new DefaultNucleotideSequence("test", "AG"));
-// out2.addNucleotideSequence(new DefaultNucleotideSequence("test", "AG"));
- LinkedList<AnnotatedPluginDocument> res = new LinkedList<AnnotatedPluginDocument>();
- res.add(DocumentUtilities.createAnnotatedPluginDocument(out1));
-// res.add(DocumentUtilities.createAnnotatedPluginDocument(out2));
- return res;
- }
-
- private LinkedList<Double> testReads(DefaultSequenceListDocument doc, MMClassifier classifier, int numToTrain, int numThreads, int kmersize, RAMBOKProgressListener prog) throws InterruptedException {
- GeneiousWriter writer = new GeneiousWriter(numToTrain, numThreads);
- writer.start();
- GeneiousReader reader = new GeneiousReader(doc, numToTrain, numThreads);
- reader.start();
- LinkedList<ClassifierThread> threadList = new LinkedList<ClassifierThread>();
- while(threadList.size() < numThreads) {
- threadList.add(new ClassifierThread(reader, writer, classifier, prog));
- }
- for(ClassifierThread c : threadList) {
- c.start();
- }
- for(ClassifierThread c : threadList) {
- c.join();
- }
- reader.join();
- writer.join();
- return writer.getScores();
- }
-
- private void trainMatrix(DefaultSequenceListDocument doc, AtomicInteger[][] matrix, int numToTrain, int numThreads, RAMBOKProgressListener prog) throws InterruptedException {
- Trainer.clearMatrix(matrix);
- GeneiousReader reader = new GeneiousReader(doc, numToTrain, numThreads);
- reader.start();
- LinkedList<TrainerThread> trainers = new LinkedList<TrainerThread>();
- for(int i=0; i<numThreads; i++) {
- trainers.add(new TrainerThread(reader, matrix, prog));
- }
- for(TrainerThread trainer : trainers) {
- trainer.start();
- }
- for(TrainerThread trainer : trainers) {
- trainer.join();
- }
- reader.join();
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/IndexerPlugin.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/IndexerPlugin.java
deleted file mode 100644
index dc3c3ca..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/IndexerPlugin.java
+++ /dev/null
@@ -1,92 +0,0 @@
-package org.rki.rambok.indexer;
-
-import com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument;
-import com.biomatters.geneious.publicapi.plugin.DocumentOperation;
-import com.biomatters.geneious.publicapi.plugin.DocumentSelectionSignature;
-import com.biomatters.geneious.publicapi.plugin.DocumentViewer;
-import com.biomatters.geneious.publicapi.plugin.DocumentViewerFactory;
-import com.biomatters.geneious.publicapi.plugin.GeneiousPlugin;
-
-/**
- * This plugin shows how to create a simple alignment operation plugin. This allows
- * the user to create an alignment document out of sequences.
- * <p/>
- * All the plugin has to do, is given a list of sequences return a list of aligned sequences to be
- * appear in the alignment and the Geneious framework handles the rest (such as:
- * <ul>;
- * <li>The type of documents that have been selected (sequence documents, sequence list documents, or alignment documents)</li>;
- * <li>Reordering and reversing of the sequences</li>;
- * <li>Whether the alignment is local or global</li>;
- * <li>Referenced documents</li>;
- * <li>Bases/residues unsupported by the underlying algorithm</li>;
- * </ul>;
- * <p/>
- * This class just provides the framework to hook the {@link RAMBO-K-Indexer}
- * into Geneious. All of the real work happens in {@link RAMBO-K-Indexer}.
- */
-public class IndexerPlugin extends GeneiousPlugin {
- @Override
- public DocumentOperation[] getDocumentOperations() {
- return new DocumentOperation[] {new Indexer() };
- }
-
- public DocumentViewerFactory[] getDocumentViewerFactories() {
- return new DocumentViewerFactory[] {
- new DocumentViewerFactory() {
-
- @Override
- public DocumentSelectionSignature[] getSelectionSignatures() {
- return new DocumentSelectionSignature[] { new DocumentSelectionSignature(RAMBOKresult.class, 1, 1)};
- }
-
- @Override
- public String getName() {
- return "RAMBO-K results viewer";
- }
-
- @Override
- public String getHelp() {
- return "Shows the metrics associated with a RAMBO-K result.";
- }
-
- @Override
- public String getDescription() {
- return "Shows the metrics associated with a RAMBO-K result.";
- }
-
- @Override
- public DocumentViewer createViewer(AnnotatedPluginDocument[] docs) {
- return new RAMBOKresultDocumentViewer((RAMBOKresult)docs[0].getDocumentOrCrash());
- }
- }
- };
- }
-
- public String getName() {
- return "RAMBO-K";
- }
-
- public String getHelp() {
- return "RAMBO-K";
- }
-
- public String getDescription() {
- return "RAMBO-K";
- }
-
- public String getAuthors() {
- return "Piotr Wojciech Dabrowski & Simon H. Tausch, Robert Koch Insitute";
- }
-
- public String getVersion() {
- return "0.1";
- }
-
- public String getMinimumApiVersion() {
- return "4.11";
- }
-
- public int getMaximumApiVersion() {
- return 4;
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKProgressListener.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKProgressListener.java
deleted file mode 100644
index 6a90f91..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKProgressListener.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.concurrent.atomic.AtomicInteger;
-
-import org.rki.readclassifier.ClassifierProgressListener;
-import org.rki.readtrainer.TrainerProgressListener;
-
-import jebl.util.ProgressListener;
-
-public class RAMBOKProgressListener implements TrainerProgressListener, ClassifierProgressListener {
- private AtomicInteger _numReadsProcessed = new AtomicInteger(0);
- private int _numReadsToTrain;
- private int _numReadsToClassify;
- private int _numSteps;
- private ProgressListener _progress;
-
- public RAMBOKProgressListener(ProgressListener progress, int readsToTrain, int readsToClassify) {
- _numReadsProcessed = new AtomicInteger(0);
- _numReadsToTrain = readsToTrain;
- _numReadsToClassify = readsToClassify;
- _progress = progress;
- _numSteps = _numReadsToTrain + _numReadsToClassify;
- _progress.setProgress(0, _numReadsToTrain);
- }
-
- public void readTrained() {
- int numt = _numReadsProcessed.incrementAndGet();
- if(numt % 1000 == 0) {
- _progress.setProgress(numt, _numSteps);
- }
- }
-
- public void readClassified() {
- int numt = _numReadsProcessed.incrementAndGet();
- if(numt % 1000 == 0) {
- _progress.setProgress(numt, _numSteps);
- }
- }
-
- public void setTitle(String title) {
- _progress.setTitle(title);
- }
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresult.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresult.java
deleted file mode 100644
index 1c859c4..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresult.java
+++ /dev/null
@@ -1,206 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.util.Collections;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-
-import org.jdom.Element;
-
-import com.biomatters.geneious.publicapi.documents.DocumentField;
-import com.biomatters.geneious.publicapi.documents.PluginDocument;
-import com.biomatters.geneious.publicapi.documents.URN;
-import com.biomatters.geneious.publicapi.documents.XMLSerializationException;
-
-public class RAMBOKresult implements PluginDocument {
- private int NUMBINS = 100;
-
- private static int HIST_ORG1 = 0;
- private static int HIST_ORG2 = 1;
- private static int HIST_REAL = 2;
-
- private String _name;
- private String _oname1;
- private String _oname2;
- private LinkedList<Double> _scores1;
- private LinkedList<Double> _scores2;
- private LinkedList<Double> _realScores;
- private Date _creationDate;
- private int[][] _scoreHist;
- private double _histMin;
- private double _histMax;
- private double _histStep;
- private int _highestNum;
-
- public RAMBOKresult(String docname, String oname1, String oname2, LinkedList<Double> scores1, LinkedList<Double> scores2) {
- _name = docname;
- _oname1 = oname1;
- _oname2 = oname2;
- _scores1 = scores1;
- _scores2 = scores2;
- _scoreHist = new int[NUMBINS][3];
- for(int i=0; i<NUMBINS; i++) {
- for(int j=0; j<3; j++) {
- _scoreHist[i][j] = 0;
- }
- }
- }
-
- public RAMBOKresult() {}
-
- public void setRealScores(LinkedList<Double> scores) {
- _realScores = scores;
- calculateHistograms();
- }
-
- private void calculateHistograms() {
- Collections.sort(_scores1);
- Collections.sort(_scores2);
- Collections.sort(_realScores);
- LinkedList<Double> allscores = new LinkedList<Double>();
- allscores.addAll(_scores1);
- allscores.addAll(_scores2);
- allscores.addAll(_realScores);
- Collections.sort(allscores);
- _histMin = allscores.get(5*allscores.size()/100);
- _histMax = allscores.get(allscores.size()-(5*allscores.size()/100));
- _histStep = (_histMax - _histMin)/NUMBINS;
-
- double currVal = _histMin;
- int currpos = 0;
- Iterator<Double> s1it = _scores1.iterator();
- Iterator<Double> s2it = _scores2.iterator();
- Iterator<Double> srit = _realScores.iterator();
- double n1 = s1it.next();
- double n2 = s2it.next();
- double nr = srit.next();
- while(currVal <= _histMax && currpos < _scoreHist.length) {
- while(n1 <= currVal) {
- _scoreHist[currpos][0] += 1;
- if(s1it.hasNext())
- n1 = s1it.next();
- else
- n1 = Double.MAX_VALUE;
- }
- while(n2 <= currVal) {
- _scoreHist[currpos][1] += 1;
- if(s2it.hasNext())
- n2 = s2it.next();
- else
- n2 = Double.MAX_VALUE;
- }
- while(nr <= currVal) {
- _scoreHist[currpos][2] += 1;
- if(srit.hasNext())
- nr = srit.next();
- else
- nr = Double.MAX_VALUE;
- }
- currVal += _histStep;
- currpos += 1;
- }
- _highestNum = 0;
- for(int i=0; i<NUMBINS; i++) {
- _highestNum = Math.max(_highestNum, getLargest(_scoreHist[i]));
- }
- }
-
- private int getLargest(int[] vals) {
- int max = 0;
- for(int i=0; i<vals.length; i++) {
- if(vals[i] > max)
- max = vals[i];
- }
- return max;
- }
-
- public int[][] getHistogram() {
- return _scoreHist;
- }
-
- public int getHighestNum() {
- return _highestNum;
- }
-
- public void fromXML(Element doc) throws XMLSerializationException {
- _name = doc.getChildText("name");
- _oname1 = doc.getChildText("oname1");
- _oname2 = doc.getChildText("oname2");
- _histMin = Double.parseDouble(doc.getChildText("histMin"));
- _histMax = Double.parseDouble(doc.getChildText("histMax"));
- _histStep = Double.parseDouble(doc.getChildText("histStep"));
- NUMBINS = Integer.parseInt(doc.getChildText("histBins"));
- _highestNum = Integer.parseInt(doc.getChildText("highestNum"));
- histFromString(doc.getChildText("scoreHist"));
- }
-
- public Element toXML() {
- Element root = new Element("TextDocument");
- root.addContent(new Element("name").setText(_name));
- root.addContent(new Element("oname1").setText(_oname1));
- root.addContent(new Element("oname2").setText(_oname2));
- root.addContent(new Element("histMin").setText(Double.toString(_histMin)));
- root.addContent(new Element("histMax").setText(Double.toString(_histMax)));
- root.addContent(new Element("histStep").setText(Double.toString(_histStep)));
- root.addContent(new Element("histBins").setText(Integer.toString(NUMBINS)));
- root.addContent(new Element("highestNum").setText(Integer.toString(_highestNum)));
- root.addContent(new Element("scoreHist").setText(histToString()));
- return root;
- }
-
- private String histToString() {
- StringBuilder res = new StringBuilder();
- for(int i=0; i<NUMBINS; i++) {
- for(int j=0; j<3; j++) {
- res.append(Integer.toString(_scoreHist[i][j]));
- res.append(",");
- }
- }
- return res.toString();
- }
-
- private void histFromString(String hist) {
- _scoreHist = new int[NUMBINS][3];
- String[] vals = hist.split(",");
- for(int i=0; i<NUMBINS; i++) {
- for(int j=0; j<3; j++) {
- _scoreHist[i][j] = Integer.parseInt(vals[3*i+j]);
- }
- }
- }
-
- public Date getCreationDate() {
- return _creationDate;
- }
-
- public String getDescription() {
- // TODO Auto-generated method stub
- return null;
- }
-
- public List<DocumentField> getDisplayableFields() {
- // TODO Auto-generated method stub
- return null;
- }
-
- public Object getFieldValue(String arg0) {
- // TODO Auto-generated method stub
- return null;
- }
-
- public String getName() {
- return _name;
- }
-
- public URN getURN() {
- // TODO Auto-generated method stub
- return null;
- }
-
- public String toHTML() {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
diff --git a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresultDocumentViewer.java b/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresultDocumentViewer.java
deleted file mode 100644
index 3b0fc2b..0000000
--- a/RAMBO-K-plugin_eclipse/src/org/rki/rambok/indexer/RAMBOKresultDocumentViewer.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package org.rki.rambok.indexer;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import com.biomatters.geneious.publicapi.plugin.DocumentViewer;
-
-public class RAMBOKresultDocumentViewer extends DocumentViewer {
-
- private int _histHeight=300;
- private int _histWidth = 500;
- private int _offsetX = 10;
- private int _offsetY = 10;
- private int _topSpace = 50;
- private int _fillAlpha = 80;
- private RAMBOKresult _doc;
-
- public RAMBOKresultDocumentViewer(RAMBOKresult doc) {
- _doc = doc;
- }
-
- @Override
- public JComponent getComponent() {
- JPanel res = new JPanel() {
- public void paintComponent(Graphics g) {
- int maxHeight = _histHeight - _topSpace;
- int[][] hist = _doc.getHistogram();
- int stepX = _histWidth / hist.length;
- int highestNum = _doc.getHighestNum();
- int[] scaled = new int[hist.length+2];
- int[] xpoints = new int[hist.length+2];
- xpoints[0] = _offsetX;
- scaled[0] = _offsetY+_histHeight;
- xpoints[xpoints.length-1] = _offsetX+_histWidth;
- scaled[scaled.length - 1] = _offsetY+_histHeight;
- for(int i=0; i<hist.length; i++) {
- scaled[i+1] = maxHeight*hist[i][0];
- scaled[i+1] /= highestNum;
- scaled[i+1] = _offsetY+_topSpace+maxHeight - scaled[i+1];
- xpoints[i+1] = i*stepX+_offsetX;
- }
- g.setColor(new Color(255, 0, 0, _fillAlpha));
- g.fillPolygon(xpoints, scaled, scaled.length);
- g.setColor(new Color(255, 0, 0, 255));
- g.drawPolyline(xpoints, scaled, scaled.length);
- for(int i=0; i<hist.length; i++) {
- scaled[i+1] = maxHeight*hist[i][1];
- scaled[i+1] /= highestNum;
- scaled[i+1] = _offsetY+_topSpace+maxHeight - scaled[i+1];
- }
- g.setColor(new Color(0, 0, 255, _fillAlpha));
- g.fillPolygon(xpoints, scaled, scaled.length);
- g.setColor(new Color(0, 0, 255, 255));
- g.drawPolyline(xpoints, scaled, scaled.length);
- for(int i=0; i<hist.length; i++) {
- scaled[i+1] = maxHeight*hist[i][2];
- scaled[i+1] /= highestNum;
- scaled[i+1] = _offsetY+_topSpace+maxHeight - scaled[i+1];
- }
- g.setColor(new Color(0, 150, 0, _fillAlpha));
- g.fillPolygon(xpoints, scaled, scaled.length);
- g.setColor(new Color(0, 150, 0, 255));
- g.drawPolyline(xpoints, scaled, scaled.length);
- g.setColor(Color.BLACK);
- g.drawRect(_offsetX, _offsetY, _histWidth, _histHeight);
- }
-
- public Dimension getPreferredSize() {
- return new Dimension(800, 800);
- }
- };
- return res;
- }
-
-}
diff --git a/ReadClassifier_eclipse/.classpath b/ReadClassifier_eclipse/.classpath
index 93d6cb1..ecb5636 100644
--- a/ReadClassifier_eclipse/.classpath
+++ b/ReadClassifier_eclipse/.classpath
@@ -4,6 +4,5 @@
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="lib/commons-cli-1.2.jar"/>
<classpathentry kind="lib" path="lib/log4j-1.2.15.jar"/>
- <classpathentry combineaccessrules="false" kind="src" path="/ReadTrainer"/>
<classpathentry kind="output" path="bin"/>
</classpath>
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/AbstractWriter.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/AbstractWriter.java
deleted file mode 100644
index 470dd32..0000000
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/AbstractWriter.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package org.rki.readclassifier;
-
-import java.util.concurrent.BlockingQueue;
-
-public abstract class AbstractWriter extends Thread {
- public BlockingQueue<ReadPair> outReads;
-}
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/Classifier.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/Classifier.java
index 6b68a1a..e5bc477 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/Classifier.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/Classifier.java
@@ -77,7 +77,7 @@ public class Classifier {
reader.start();
writer.start();
while(threadList.size() < threads) {
- threadList.add(new ClassifierThread(reader, writer, selectedClassifier, null));
+ threadList.add(new ClassifierThread(reader, writer, selectedClassifier));
}
for(ClassifierThread c : threadList) {
c.start();
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierProgressListener.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierProgressListener.java
deleted file mode 100644
index 8fb5c62..0000000
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierProgressListener.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package org.rki.readclassifier;
-
-public interface ClassifierProgressListener {
- public void readClassified();
-}
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierThread.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierThread.java
index ed0a44d..e9b7250 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierThread.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/ClassifierThread.java
@@ -1,42 +1,35 @@
package org.rki.readclassifier;
-import org.rki.readtrainer.AbstractReader;
public class ClassifierThread extends Thread {
- private AbstractReader reader;
- private AbstractWriter writer;
+ private Reader reader;
+ private Writer writer;
private ReadClassifier readClassifier;
- private ClassifierProgressListener prog;
-
- public ClassifierThread(AbstractReader reader, AbstractWriter writer, ReadClassifier readClassifier,
- ClassifierProgressListener prog) {
+
+ public ClassifierThread(Reader reader, Writer writer, ReadClassifier readClassifier) {
super();
this.reader = reader;
this.writer = writer;
this.readClassifier = readClassifier;
- this.prog = prog;
}
-
+
public void run() {
try {
- while (true) {
+ while(true) {
ReadPair reads = reader.reads.take();
- if (reads.read1 == null) {
- writer.outReads.put(new ReadPair(null, null));
- return;
- }
- reads.read1.bases = reads.read1.bases.toUpperCase();
- if (reads.read2 != null)
- reads.read2.bases = reads.read2.bases.toUpperCase();
+ if(reads.read1 == null) {
+ writer.outReads.put(new ReadPair(null, null));
+ return;
+ }
+ reads.read1.bases = reads.read1.bases.toUpperCase();
+ if(reads.read2 != null)
+ reads.read2.bases = reads.read2.bases.toUpperCase();
readClassifier.getScore(reads);
- reads.read1.toString();
- if (reads.read2 != null)
- reads.read2.toString();
- writer.outReads.put(reads);
- if (prog != null) {
- prog.readClassified();
- }
+ reads.read1.toString();
+ if(reads.read2 != null)
+ reads.read2.toString();
+ writer.outReads.put(reads);
}
} catch (Exception e) {
e.printStackTrace();
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/MMClassifier.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/MMClassifier.java
index 024dd6b..425217f 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/MMClassifier.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/MMClassifier.java
@@ -3,9 +3,6 @@ package org.rki.readclassifier;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
-import java.util.concurrent.atomic.AtomicInteger;
-
-import org.rki.readtrainer.Trainer;
public class MMClassifier implements ReadClassifier {
private double tmorg1[][];
@@ -26,41 +23,6 @@ public class MMClassifier implements ReadClassifier {
return("Classifies reads based on Markov Model of Kmer transitions.");
}
- public void setMatrices(AtomicInteger[][] matrix1, AtomicInteger[][] matrix2, String o1name, String o2name, int kmersize) {
- this.kmersize = kmersize;
- kmermask = (int)Math.pow(4, kmersize) - 1;
- tmorg1 = new double[(int)Math.pow(4, kmersize)][4];
- tmorg2 = new double[(int)Math.pow(4, kmersize)][4];
- setMatrix(matrix1, tmorg1);
- setMatrix(matrix2, tmorg2);
- org1name = o1name;
- org2name = o2name;
- }
-
- private void setMatrix(AtomicInteger[][] matrix, double[][] tm) {
- for(int i=0; i<matrix.length; i++) {
- int rowsum = 0;
- for(int j=0; j<4; j++) {
- rowsum += matrix[i][j].get();
- }
- if(rowsum == 0) {
- for(int j=0; j<4; j++) {
- tm[i][j] = Double.NaN;
- }
- continue;
- }
- for(int j=0; j<4; j++) {
- double val = (double)matrix[i][j].get();
- if(val == 0)
- val = Trainer.absentval;
- val = val/(double)rowsum*4.0d;
- val = Math.log(val);
- tm[i][j] = val;
- }
- }
-
- }
-
@Override
public void readData(InputStream in) throws Exception {
BufferedReader reader = new BufferedReader(new InputStreamReader(in));
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/Read.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/Read.java
index 9ce25b7..3a4fe6e 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/Read.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/Read.java
@@ -1,13 +1,10 @@
package org.rki.readclassifier;
-import java.util.LinkedList;
-
public class Read {
public boolean invalid = false;
public String name;
public String bases;
public String qualities;
- public byte[] intQualities = null;
public double score = 0;
public double score1 = 0;
public double score2 = 0;
@@ -22,20 +19,12 @@ public class Read {
this.score2 = 0;
}
- public Read(String name, String bases, byte[] qualities, boolean intQuals) {
- this.name = name;
- this.bases = bases;
- this.intQualities = qualities;
- this.score1 = 0;
- this.score2 = 0;
- }
-
public String toString(boolean showQuals) {
- if(intQualities == null)
- return "";
- if(qualities != null)
+ if(qualities != null) {
return toFastq(showQuals);
- return toFasta(showQuals);
+ }
+ else
+ return toFasta(showQuals);
}
public void normalizeTo(int length) {
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/Reader.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/Reader.java
index 7e4c489..e9378f7 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/Reader.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/Reader.java
@@ -4,9 +4,10 @@ import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
-public class Reader extends AbstractReader {
+public class Reader extends Thread {
private InputStream in1;
private InputStream in2;
private int numReads;
@@ -19,8 +20,9 @@ public class Reader extends AbstractReader {
private boolean firstRead2 = true;
private int numThreads;
+ public BlockingQueue<ReadPair> reads;
public Boolean fileDone = false;
- public boolean stop = false;
+ public boolean stop = false;
public Reader(InputStream infile1, InputStream infile2, int numReads, int bufferSize, int numThreads) {
super();
diff --git a/ReadClassifier_eclipse/src/org/rki/readclassifier/Writer.java b/ReadClassifier_eclipse/src/org/rki/readclassifier/Writer.java
index 794c70b..0bb7aea 100644
--- a/ReadClassifier_eclipse/src/org/rki/readclassifier/Writer.java
+++ b/ReadClassifier_eclipse/src/org/rki/readclassifier/Writer.java
@@ -7,7 +7,7 @@ import java.io.OutputStreamWriter;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
-public class Writer extends AbstractWriter {
+public class Writer extends Thread {
private BufferedWriter out1w;
private BufferedWriter out2w;
public BlockingQueue<ReadPair> outReads;
diff --git a/ReadTrainer_eclipse/src/org/rki/readtrainer/AbstractReader.java b/ReadTrainer_eclipse/src/org/rki/readtrainer/AbstractReader.java
deleted file mode 100644
index 7c98462..0000000
--- a/ReadTrainer_eclipse/src/org/rki/readtrainer/AbstractReader.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package org.rki.readtrainer;
-
-import java.util.concurrent.BlockingQueue;
-
-import org.rki.readclassifier.ReadPair;
-
-public abstract class AbstractReader extends Thread {
- public BlockingQueue<ReadPair> reads;
-}
diff --git a/ReadTrainer_eclipse/src/org/rki/readtrainer/Trainer.java b/ReadTrainer_eclipse/src/org/rki/readtrainer/Trainer.java
index 175768c..ba90ffb 100644
--- a/ReadTrainer_eclipse/src/org/rki/readtrainer/Trainer.java
+++ b/ReadTrainer_eclipse/src/org/rki/readtrainer/Trainer.java
@@ -132,7 +132,7 @@ public class Trainer {
reader.start();
LinkedList<TrainerThread> trainers = new LinkedList<TrainerThread>();
for(int i=0; i<threads; i++) {
- trainers.add(new TrainerThread(reader, matrix, null));
+ trainers.add(new TrainerThread(reader, matrix));
}
for(TrainerThread trainer : trainers) {
trainer.start();
diff --git a/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerProgressListener.java b/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerProgressListener.java
deleted file mode 100644
index 6598d3a..0000000
--- a/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerProgressListener.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package org.rki.readtrainer;
-
-public interface TrainerProgressListener {
- public void readTrained();
-}
diff --git a/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerThread.java b/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerThread.java
index 82368e0..36d5c72 100644
--- a/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerThread.java
+++ b/ReadTrainer_eclipse/src/org/rki/readtrainer/TrainerThread.java
@@ -8,16 +8,14 @@ import org.rki.readclassifier.ReadPair;
import org.rki.readclassifier.Reader;
public class TrainerThread extends Thread {
- private AbstractReader reader;
+ private Reader reader;
private int kmermask;
private AtomicInteger[][] matrix;
- private TrainerProgressListener listener;
- public TrainerThread(AbstractReader reader, AtomicInteger[][] matrix, TrainerProgressListener listener) {
+ public TrainerThread(Reader reader, AtomicInteger[][] matrix) {
super();
this.reader = reader;
this.matrix = matrix;
- this.listener = listener;
}
public void run() {
@@ -33,9 +31,6 @@ public class TrainerThread extends Thread {
pair.read2.bases = pair.read2.bases.toUpperCase();
trainRead(pair.read2);
}
- if(listener != null) {
- listener.readTrained();
- }
}
} catch(Exception e) {
e.printStackTrace();
--
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