--- /dev/null
- 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.getContentArea(), pherogramProvider);
- pherogramArea.setFirstSeqPos(1);
- pherogramArea.setLeftCutPosition(13);
- pherogramArea.setRightCutPosition(697);
- pherogramArea.getAlignmentModel().setShiftChange(14, 1);
- pherogramArea.getAlignmentModel().setShiftChange(35, 1);
- result.getContentArea().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"))));
+// $Id$
+/**
+* Copyright (C) 2014 EDIT
+* European Distributed Institute of Taxonomy
+* http://www.e-taxonomy.eu
+*
+* The contents of this file are subject to the Mozilla Public License Version 1.1
+* See LICENSE.TXT at the top of this package for the full license terms.
+*/
+package eu.etaxonomy.taxeditor.editor.molecular;
+
+
+import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
+import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
+import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
+import info.bioinfweb.libralign.AlignmentArea;
+import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
+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;
+
+import java.io.File;
+
+import org.biojava.bio.chromatogram.ChromatogramFactory;
+import org.biojava3.core.sequence.DNASequence;
+import org.biojava3.core.sequence.compound.NucleotideCompound;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.ui.IEditorInput;
+import org.eclipse.ui.IEditorSite;
+import org.eclipse.ui.PartInitException;
+import org.eclipse.ui.part.EditorPart;
+
+
+
+/**
+ * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
+ * a consensus sequence.
+ * <p>
+ * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
+ *
+ * @author pplitzner
+ * @author Ben Stöver
+ * @date 04.08.2014
+ */
+public class AlignmentEditor extends EditorPart {
+ public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
+
+ private AlignmentArea alignmentArea;
+
+
+ private AlignmentArea createAlignmentArea() {
+ try {
+ //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")));
+ //TODO Replace this absolute path with a path working with every workspace location.
+
+ Alignment<DNASequence, NucleotideCompound> alignment =
+ new SimpleAlignment<DNASequence, NucleotideCompound>();
+ 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.
+
+ BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
+ new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
+ new BioJavaTokenSet<NucleotideCompound>(
+ AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet(), true),
+ alignment);
+
+ AlignmentArea result = new AlignmentArea();
+ result.getContentArea().setSequenceProvider(sequenceProvider, false);
+ SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea());
+ //sequenceIndexArea.setFirstIndex(5);
+ //sequenceIndexArea.setHeight(25);
+ result.getContentArea().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("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1")));
++ PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
++ pherogramArea.setFirstSeqPos(1);
++ pherogramArea.setLeftCutPosition(13);
++ pherogramArea.setRightCutPosition(697);
++ pherogramArea.getAlignmentModel().setShiftChange(14, 1);
++ pherogramArea.getAlignmentModel().setShiftChange(35, 1);
++ result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);
++
++ pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
++ new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1"))));
+ pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
+ pherogramArea.setFirstSeqPos(1);
+ pherogramArea.setLeftCutPosition(267);
+ pherogramArea.getAlignmentModel().setShiftChange(273, -1);
+ pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());
+ result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);
+
+
+ result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea()));
+ return result;
+ }
+ catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+
+// 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"));
+//
+// BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
+// new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
+// new BioJavaTokenSet<NucleotideCompound>(
+// AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
+// alignment);
+//
+// AlignmentArea result = new AlignmentArea();
+// result.setSequenceProvider(sequenceProvider, false);
+// SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
+// //sequenceIndexArea.setFirstIndex(5);
+// //sequenceIndexArea.setHeight(25);
+// result.getDataAreas().getTopAreas().add(sequenceIndexArea);
+// result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
+// return result;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
+ */
+ @Override
+ public void createPartControl(Composite parent) {
+ alignmentArea = createAlignmentArea();
+ Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
+ //getSite().setSelectionProvider(provider)
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
+ */
+ @Override
+ public void doSave(IProgressMonitor monitor) {
+ // TODO Auto-generated method stub
+
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#doSaveAs()
+ */
+ @Override
+ public void doSaveAs() {
+ // TODO Auto-generated method stub
+
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
+ */
+ @Override
+ public void init(IEditorSite site, IEditorInput input) throws PartInitException {
+ setSite(site);
+ setInput(input);
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#isDirty()
+ */
+ @Override
+ public boolean isDirty() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
+ */
+ @Override
+ public boolean isSaveAsAllowed() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.WorkbenchPart#setFocus()
+ */
+ @Override
+ public void setFocus() {
+ //alignmentArea.getToolkitComponent().redistributeHeight();
+ }
+}
BGBM BDI Projects / taxeditor.git / commitdiff