eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java -text
+eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateTaxonUseOperation.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.java -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
+eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>eu.etaxonomy.taxeditor.editor</name>
- <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.pde.ManifestBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.pde.SchemaBuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.pde.PluginNature</nature>
- </natures>
- <linkedResources>
- <link>
- <name>lib/LibrAlign</name>
- <type>2</type>
- <location>/home/pplitzner/svn/LibrAlign/LibrAlign/main/bin</location>
- </link>
- <link>
- <name>lib/bioinfweb.commons</name>
- <type>2</type>
- <location>/home/pplitzner/svn/LibrAlign/commons/main/bin</location>
- </link>
- </linkedResources>
-</projectDescription>
+<?xml version="1.0" encoding="UTF-8"?>\r
+<projectDescription>\r
+ <name>eu.etaxonomy.taxeditor.editor</name>\r
+ <comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>\r
+ <projects>\r
+ </projects>\r
+ <buildSpec>\r
+ <buildCommand>\r
+ <name>org.eclipse.jdt.core.javabuilder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>org.eclipse.pde.ManifestBuilder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ <buildCommand>\r
+ <name>org.eclipse.pde.SchemaBuilder</name>\r
+ <arguments>\r
+ </arguments>\r
+ </buildCommand>\r
+ </buildSpec>\r
+ <natures>\r
+ <nature>org.eclipse.jdt.core.javanature</nature>\r
+ <nature>org.eclipse.pde.PluginNature</nature>\r
+ </natures>\r
+ <linkedResources>\r
+ <link>\r
+ <name>lib/LibrAlign</name>\r
+ <type>2</type>\r
+ <locationURI>WORKSPACE_LOC/LibrAlign/bin</locationURI>\r
+ </link>\r
+ <link>\r
+ <name>lib/bioinfweb.commons</name>\r
+ <type>2</type>\r
+ <locationURI>WORKSPACE_LOC/_Lib/bin</locationURI>\r
+ </link>\r
+ </linkedResources>\r
+</projectDescription>\r
import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
+import info.bioinfweb.libralign.pherogram.PherogramProvider;
+import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider;
import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
//ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf");
//System.out.println(AlignmentEditor.class.getResource("/"));
//System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf"));
- BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
- new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
+// BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
+// new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
//TODO Replace this absolute path with a path working with every workspace location.
Alignment<DNASequence, NucleotideCompound> alignment =
new SimpleAlignment<DNASequence, NucleotideCompound>();
- alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
- alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
- alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
+ alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
+ alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
+ //alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
- StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
- for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
- seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
- }
- alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +
- seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below.
+// StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
+// for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
+// seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
+// }
+// alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +
+// seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below.
BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
//sequenceIndexArea.setHeight(25);
result.getDataAreas().getTopAreas().add(sequenceIndexArea);
+// PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
+// pherogramArea.setFirstSeqPos(34 + 5);
+// pherogramArea.setLeftCutPosition(34);
+// pherogramArea.setRightCutPosition(820);
+// pherogramArea.getAlignmentModel().setShiftChange(38, -1);
+// pherogramArea.getAlignmentModel().setShiftChange(49, 2);
+// result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);
+
+ PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
+ new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR430_JR-P01.ab1")));
PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
- pherogramArea.setFirstSeqPos(34 + 5);
- pherogramArea.setLeftCutPosition(34);
- pherogramArea.setRightCutPosition(820);
- pherogramArea.getAlignmentModel().setShiftChange(38, -1);
- pherogramArea.getAlignmentModel().setShiftChange(49, 2);
- result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);
-
- result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
+ pherogramArea.setFirstSeqPos(1);
+ pherogramArea.setLeftCutPosition(13);
+ pherogramArea.setRightCutPosition(697);
+ pherogramArea.getAlignmentModel().setShiftChange(14, 1);
+ pherogramArea.getAlignmentModel().setShiftChange(35, 1);
+ result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);
+
+ pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
+ new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\AlignmentTestData\\JR444_JR-P05.ab1"))));
+ pherogramArea = new PherogramArea(result, pherogramProvider);
+ pherogramArea.setFirstSeqPos(1);
+ pherogramArea.setLeftCutPosition(267);
+ pherogramArea.getAlignmentModel().setShiftChange(273, -1);
+ pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());
+ result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);
+
+
+ result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
return result;
}
catch (Exception e) {
--- /dev/null
+// $Id$\r
+/**\r
+* Copyright (C) 2014 EDIT\r
+* European Distributed Institute of Taxonomy\r
+* http://www.e-taxonomy.eu\r
+*\r
+* The contents of this file are subject to the Mozilla Public License Version 1.1\r
+* See LICENSE.TXT at the top of this package for the full license terms.\r
+*/\r
+package eu.etaxonomy.taxeditor.editor.molecular;\r
+\r
+\r
+import org.biojava3.core.sequence.compound.NucleotideCompound;\r
+\r
+import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet;\r
+import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;\r
+import info.bioinfweb.libralign.sequenceprovider.implementations.PackedSequenceDataProvider;\r
+import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;\r
+\r
+\r
+\r
+/**\r
+ * The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}.\r
+ * \r
+ * @author Ben Stöver\r
+ * @date 04.08.2014\r
+ */\r
+public class ContigSequenceDataProvider extends PackedSequenceDataProvider<NucleotideCompound> \r
+ implements SequenceDataProvider<NucleotideCompound> {\r
+\r
+ \r
+ public ContigSequenceDataProvider() {\r
+ super(new BioJavaTokenSet<NucleotideCompound>(AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet()));\r
+ }\r
+ \r
+ \r
+ public void saveToCMD() { //TODO Add cmd node as parameter \r
+ //TODO impl.\r
+ }\r
+ \r
+ \r
+ public void loadFromCMD() { //TODO Add cmd node as parameter\r
+ //TODO impl.\r
+ }\r
+}\r