Revision c3a66f55
Added by Ben Stöver over 9 years ago
.gitattributes | ||
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429 | 429 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text |
430 | 430 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text |
431 | 431 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CMDAlignmentObjectPlaceholder.java -text |
432 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text |
|
432 | 433 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text |
433 | 434 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text |
434 | 435 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text |
... | ... | |
598 | 599 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateTaxonUseOperation.java -text |
599 | 600 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseRecordOperation.java -text |
600 | 601 |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/uses/operation/CreateUseSummaryOperation.java -text |
602 |
eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text |
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603 |
eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text |
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601 | 604 |
eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text |
602 | 605 |
eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text |
603 | 606 |
eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text |
eu.etaxonomy.taxeditor.editor/.project | ||
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<?xml version="1.0" encoding="UTF-8"?> |
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<projectDescription> |
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<name>eu.etaxonomy.taxeditor.editor</name> |
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<comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment> |
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<projects> |
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</projects> |
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<buildSpec> |
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<buildCommand> |
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<name>org.eclipse.jdt.core.javabuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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<buildCommand> |
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<name>org.eclipse.pde.ManifestBuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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<buildCommand> |
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<name>org.eclipse.pde.SchemaBuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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</buildSpec> |
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<natures> |
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<nature>org.eclipse.jdt.core.javanature</nature> |
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<nature>org.eclipse.pde.PluginNature</nature> |
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</natures> |
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<linkedResources> |
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<link> |
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<name>lib/LibrAlign</name> |
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<type>2</type> |
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<location>/home/pplitzner/svn/LibrAlign/LibrAlign/main/bin</location> |
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</link> |
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<link> |
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<name>lib/bioinfweb.commons</name> |
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<type>2</type> |
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<location>/home/pplitzner/svn/LibrAlign/commons/main/bin</location> |
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</link> |
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</linkedResources> |
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</projectDescription> |
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<?xml version="1.0" encoding="UTF-8"?> |
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<projectDescription> |
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<name>eu.etaxonomy.taxeditor.editor</name> |
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<comment>NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment> |
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<projects> |
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</projects> |
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<buildSpec> |
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<buildCommand> |
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<name>org.eclipse.jdt.core.javabuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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<buildCommand> |
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<name>org.eclipse.pde.ManifestBuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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<buildCommand> |
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<name>org.eclipse.pde.SchemaBuilder</name> |
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<arguments> |
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</arguments> |
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</buildCommand> |
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</buildSpec> |
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<natures> |
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<nature>org.eclipse.jdt.core.javanature</nature> |
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<nature>org.eclipse.pde.PluginNature</nature> |
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</natures> |
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<linkedResources> |
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<link> |
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<name>lib/LibrAlign</name> |
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<type>2</type> |
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<locationURI>WORKSPACE_LOC/LibrAlign/bin</locationURI> |
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</link> |
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<link> |
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<name>lib/bioinfweb.commons</name> |
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<type>2</type> |
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<locationURI>WORKSPACE_LOC/_Lib/bin</locationURI> |
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</link> |
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</linkedResources> |
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</projectDescription> |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java | ||
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20 | 20 |
import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea; |
21 | 21 |
import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea; |
22 | 22 |
import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider; |
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import info.bioinfweb.libralign.pherogram.PherogramProvider; |
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import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider; |
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23 | 25 |
import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider; |
24 | 26 |
import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet; |
25 | 27 |
|
... | ... | |
59 | 61 |
//ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf"); |
60 | 62 |
//System.out.println(AlignmentEditor.class.getResource("/")); |
61 | 63 |
//System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf")); |
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BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create( |
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new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf"))); |
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// BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
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// new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
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64 | 66 |
//TODO Replace this absolute path with a path working with every workspace location. |
65 | 67 |
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66 | 68 |
Alignment<DNASequence, NucleotideCompound> alignment = |
67 | 69 |
new SimpleAlignment<DNASequence, NucleotideCompound>(); |
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alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
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alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
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alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
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alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
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alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
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//alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
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71 | 73 |
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StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength()); |
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for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) { |
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seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase()); |
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} |
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alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) + |
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seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below. |
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// StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
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// for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
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// seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
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// }
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// alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +
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// seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49))); // One A is deleted for shift change specified below.
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78 | 80 |
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BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider = |
80 | 82 |
new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>( |
... | ... | |
89 | 91 |
//sequenceIndexArea.setHeight(25); |
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result.getDataAreas().getTopAreas().add(sequenceIndexArea); |
91 | 93 |
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// PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider); |
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// pherogramArea.setFirstSeqPos(34 + 5); |
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// pherogramArea.setLeftCutPosition(34); |
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// pherogramArea.setRightCutPosition(820); |
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// pherogramArea.getAlignmentModel().setShiftChange(38, -1); |
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// pherogramArea.getAlignmentModel().setShiftChange(49, 2); |
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// result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea); |
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PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create( |
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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"))); |
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92 | 104 |
PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider); |
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pherogramArea.setFirstSeqPos(34 + 5); |
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pherogramArea.setLeftCutPosition(34); |
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pherogramArea.setRightCutPosition(820); |
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pherogramArea.getAlignmentModel().setShiftChange(38, -1); |
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pherogramArea.getAlignmentModel().setShiftChange(49, 2); |
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result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea); |
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result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result)); |
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pherogramArea.setFirstSeqPos(1); |
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pherogramArea.setLeftCutPosition(13); |
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pherogramArea.setRightCutPosition(697); |
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pherogramArea.getAlignmentModel().setShiftChange(14, 1); |
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pherogramArea.getAlignmentModel().setShiftChange(35, 1); |
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result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea); |
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pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create( |
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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")))); |
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pherogramArea = new PherogramArea(result, pherogramProvider); |
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pherogramArea.setFirstSeqPos(1); |
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pherogramArea.setLeftCutPosition(267); |
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pherogramArea.getAlignmentModel().setShiftChange(273, -1); |
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pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale()); |
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result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea); |
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result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result)); |
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101 | 123 |
return result; |
102 | 124 |
} |
103 | 125 |
catch (Exception e) { |
eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2014 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.taxeditor.editor.molecular; |
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import org.biojava3.core.sequence.compound.NucleotideCompound; |
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import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet; |
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import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider; |
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import info.bioinfweb.libralign.sequenceprovider.implementations.PackedSequenceDataProvider; |
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import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet; |
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/** |
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* The LibrAlign sequence data provider used to edit contig alignments with the {@link AlignmentEditor}. |
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* |
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* @author Ben Stöver |
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* @date 04.08.2014 |
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*/ |
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public class ContigSequenceDataProvider extends PackedSequenceDataProvider<NucleotideCompound> |
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implements SequenceDataProvider<NucleotideCompound> { |
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public ContigSequenceDataProvider() { |
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super(new BioJavaTokenSet<NucleotideCompound>(AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet())); |
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} |
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public void saveToCMD() { //TODO Add cmd node as parameter |
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//TODO impl. |
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} |
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public void loadFromCMD() { //TODO Add cmd node as parameter |
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//TODO impl. |
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} |
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} |
Also available in: Unified diff
Example in AlignmentEditor changed to a more realistic case.