eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2014 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.editor.molecular;
  11
  12
  13 import info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment;
  14 import info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment;
  15 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityNucleotideCompoundSet;
  16 import info.bioinfweb.libralign.AlignmentArea;
  17 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
  18 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
  19 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
  20 import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
  21 import info.bioinfweb.libralign.pherogram.PherogramProvider;
  22 import info.bioinfweb.libralign.pherogram.ReverseComplementPherogramProvider;
  23 import info.bioinfweb.libralign.sequenceprovider.implementations.BioJavaSequenceDataProvider;
  24 import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
  25
  26 import java.io.File;
  27
  28 import org.biojava.bio.chromatogram.ChromatogramFactory;
  29 import org.biojava3.core.sequence.DNASequence;
  30 import org.biojava3.core.sequence.compound.NucleotideCompound;
  31 import org.eclipse.core.runtime.IProgressMonitor;
  32 import org.eclipse.swt.SWT;
  33 import org.eclipse.swt.widgets.Composite;
  34 import org.eclipse.ui.IEditorInput;
  35 import org.eclipse.ui.IEditorSite;
  36 import org.eclipse.ui.PartInitException;
  37 import org.eclipse.ui.part.EditorPart;
  38
  39
  40
  41 /**
  42  * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
  43  * a consensus sequence.
  44  * <p>
  45  * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
  46  *
  47  * @author pplitzner
  48  * @author Ben Stöver
  49  * @date 04.08.2014
  50  */
  51 public class AlignmentEditor extends EditorPart {
  52     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
  53
  54     private AlignmentArea alignmentArea;
  55
  56
  57         private AlignmentArea createAlignmentArea() {
  58                 try {
  59                         //ResourcesPlugin.getWorkspace().getRoot().getFile("/eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf");
  60                         //System.out.println(AlignmentEditor.class.getResource("/"));
  61                         //System.out.println(AlignmentEditor.class.getResource("/../resources/TestPherogram_qualityScore.scf"));
  62 //                      BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
  63 //                                      new File("D:\\Users\\BenStoever\\Documents\\Studium\\Projekte\\Promotion\\EDITor\\Quelltexte\\LibrAlign branch\\Repository\\eu.etaxonomy.taxeditor.editor\\src\\main\\resources\\TestPherogram_qualityScore.scf")));
  64                     //TODO Replace this absolute path with a path working with every workspace location.
  65
  66                         Alignment<DNASequence, NucleotideCompound> alignment =
  67                                         new SimpleAlignment<DNASequence, NucleotideCompound>();
  68                         alignment.add("Read 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCA-CCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
  69                         alignment.add("Read 2", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
  70                         //alignment.add("Consensus edit 1", new DNASequence("TAAGATACAACAAGGTTTCGGGCAACCTTATCCACGCAGTAAGGGGATCAGAGGTTTTTCTCTCATTCATGTATCGTGGATCAGTAAGGCAATTTTGCTACCCTGTCTGCTCTTTCTAGCATTTTACTAATGCCCCAGAAATTAGGAATAAAGATTTTATATGAAAGAAAGGGCGAATTAATTCATAAGGGACTGGTATCCATTCTTATTTGATTTGATACATTGTATCCATTAACATTACATTGGCGAATTGGGCGAAGGTGCGGAAAGAGAGGGATTCGAACCCTCGGTAAACAAAAGTCTACATAGCAGTTCCAATGCTACGCCTTGAACCACTCGGCCACCTCTCCTACATAAGGATTTTGGTCCCAAACCAAAAAGAGGGAGTTGTTCAAATTAGATTCTTAGGTAGGTCCGGACAACGAATTCAAATGAATAAGGTAAGGGGACATCCCCCCTCCCTCCCCTTTGTTTTTTTCTTTATTTGGTTAGGGCGGGGGACTCGACTCTTATTGAATTTTCATATGTATCACAGCTCGAAACGAAAGAACTCGTGGGGGGGTCGTTTCCTTTTTGGATCTTGAACGACTAGGTTCAAGAGATGAGAGAATTCAGGATACCCACAAGAAAGACTAATCCAATCCATAACGATGTACCAGAAAAGACAATATTTTTATTACCTGACCA"));
  71
  72 //                      StringBuffer seqBuffer = new StringBuffer(pherogramProvider.getSequenceLength());
  73 //                      for (int i = 1; i <= pherogramProvider.getSequenceLength(); i++) {
  74 //                              seqBuffer.append(pherogramProvider.getBaseCall(i).getUpperedBase());
  75 //                      }
  76 //                      alignment.add("Sequence 4", new DNASequence("-----" + seqBuffer.substring(0, 38) +
  77 //                                      seqBuffer.substring(39, 49) + "--" + seqBuffer.substring(49)));  // One A is deleted for shift change specified below.
  78
  79                         BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
  80                                         new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
  81                                                         new BioJavaTokenSet<NucleotideCompound>(
  82                                                                         AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
  83                                                         alignment);
  84
  85                         AlignmentArea result = new AlignmentArea();
  86                         result.getContentArea().setSequenceProvider(sequenceProvider, false);
  87                         SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result.getContentArea());
  88                         //sequenceIndexArea.setFirstIndex(5);
  89                         //sequenceIndexArea.setHeight(25);
  90                         result.getContentArea().getDataAreas().getTopAreas().add(sequenceIndexArea);
  91
  92 //                      PherogramArea pherogramArea = new PherogramArea(result, pherogramProvider);
  93 //                      pherogramArea.setFirstSeqPos(34 + 5);
  94 //                      pherogramArea.setLeftCutPosition(34);
  95 //                      pherogramArea.setRightCutPosition(820);
  96 //                      pherogramArea.getAlignmentModel().setShiftChange(38, -1);
  97 //                      pherogramArea.getAlignmentModel().setShiftChange(49, 2);
  98 //                      result.getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Sequence 4")).add(pherogramArea);
  99
 100                         PherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(
 101                                     new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1")));
 102                         PherogramArea pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
 103                         pherogramArea.setFirstSeqPos(1);
 104                         pherogramArea.setLeftCutPosition(13);
 105                         pherogramArea.setRightCutPosition(697);
 106                         pherogramArea.getAlignmentModel().setShiftChange(14, 1);
 107                         pherogramArea.getAlignmentModel().setShiftChange(35, 1);
 108                         result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 1")).add(pherogramArea);
 109
 110                         pherogramProvider = new ReverseComplementPherogramProvider(new BioJavaPherogramProvider(ChromatogramFactory.create(
 111                                 new File("/home/pplitzner/svn/LibrAlign/taxeditor/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1"))));
 112                         pherogramArea = new PherogramArea(result.getContentArea(), pherogramProvider);
 113                         pherogramArea.setFirstSeqPos(1);
 114                         pherogramArea.setLeftCutPosition(267);
 115                         pherogramArea.getAlignmentModel().setShiftChange(273, -1);
 116                         pherogramArea.setVerticalScale(20 * pherogramArea.getVerticalScale());
 117                         result.getContentArea().getDataAreas().getSequenceAreas(sequenceProvider.sequenceIDByName("Read 2")).add(pherogramArea);
 118
 119
 120                     result.getContentArea().getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result.getContentArea()));
 121                         return result;
 122                 }
 123                 catch (Exception e) {
 124                         throw new RuntimeException(e);
 125                 }
 126
 127 //              Alignment<DNASequence, NucleotideCompound> alignment =
 128 //                              new SimpleAlignment<DNASequence, NucleotideCompound>();
 129 //              alignment.add("Sequence 1", new DNASequence("ATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAGATCGTAG"));
 130 //              alignment.add("Sequence 2", new DNASequence("AT-GTTG"));
 131 //              alignment.add("Sequence 3", new DNASequence("AT-GTAG"));
 132 //
 133 //              BioJavaSequenceDataProvider<DNASequence, NucleotideCompound> sequenceProvider =
 134 //                              new BioJavaSequenceDataProvider<DNASequence, NucleotideCompound>(
 135 //                                              new BioJavaTokenSet<NucleotideCompound>(
 136 //                                                              AlignmentAmbiguityNucleotideCompoundSet.getAlignmentAmbiguityNucleotideCompoundSet()),
 137 //                                              alignment);
 138 //
 139 //              AlignmentArea result = new AlignmentArea();
 140 //              result.setSequenceProvider(sequenceProvider, false);
 141 //              SequenceIndexArea sequenceIndexArea = new SequenceIndexArea(result);
 142 //              //sequenceIndexArea.setFirstIndex(5);
 143 //              //sequenceIndexArea.setHeight(25);
 144 //              result.getDataAreas().getTopAreas().add(sequenceIndexArea);
 145 //              result.getDataAreas().getBottomAreas().add(new ConsensusSequenceArea(result));
 146 //              return result;
 147         }
 148
 149
 150     /* (non-Javadoc)
 151      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
 152      */
 153     @Override
 154     public void createPartControl(Composite parent) {
 155         alignmentArea = createAlignmentArea();
 156                 Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
 157                 //getSite().setSelectionProvider(provider)
 158     }
 159
 160
 161     /* (non-Javadoc)
 162      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
 163      */
 164     @Override
 165     public void doSave(IProgressMonitor monitor) {
 166         // TODO Auto-generated method stub
 167
 168     }
 169
 170
 171     /* (non-Javadoc)
 172      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
 173      */
 174     @Override
 175     public void doSaveAs() {
 176         // TODO Auto-generated method stub
 177
 178     }
 179
 180
 181     /* (non-Javadoc)
 182      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
 183      */
 184     @Override
 185     public void init(IEditorSite site, IEditorInput input) throws PartInitException {
 186         setSite(site);
 187         setInput(input);
 188     }
 189
 190
 191     /* (non-Javadoc)
 192      * @see org.eclipse.ui.part.EditorPart#isDirty()
 193      */
 194     @Override
 195     public boolean isDirty() {
 196         // TODO Auto-generated method stub
 197         return false;
 198     }
 199
 200
 201     /* (non-Javadoc)
 202      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
 203      */
 204     @Override
 205     public boolean isSaveAsAllowed() {
 206         // TODO Auto-generated method stub
 207         return false;
 208     }
 209
 210
 211     /* (non-Javadoc)
 212      * @see org.eclipse.ui.part.WorkbenchPart#setFocus()
 213      */
 214     @Override
 215     public void setFocus() {
 216         //alignmentArea.getToolkitComponent().redistributeHeight();
 217     }
 218 }