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.libralign.alignmentarea.AlignmentArea;
  14 import info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea;
  15 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
  16 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
  17 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
  18 import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;
  19 import info.bioinfweb.libralign.editsettings.EditSettingsListener;
  20 import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
  21 import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
  22 import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider;
  23 import info.bioinfweb.libralign.pherogram.provider.PherogramProvider;
  24 import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;
  25 import info.bioinfweb.libralign.sequenceprovider.implementations.PackedSequenceDataProvider;
  26 import info.bioinfweb.libralign.sequenceprovider.tokenset.BioJavaTokenSet;
  27 import info.bioinfweb.libralign.sequenceprovider.tokenset.TokenSet;
  28
  29 import java.io.File;
  30 import java.io.IOException;
  31 import java.io.InputStream;
  32 import java.net.URI;
  33 import java.util.ArrayList;
  34 import java.util.Collection;
  35 import java.util.Collections;
  36 import java.util.Map;
  37 import java.util.TreeMap;
  38
  39 import org.biojava.bio.chromatogram.ChromatogramFactory;
  40 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
  41 import org.biojava3.core.sequence.compound.DNACompoundSet;
  42 import org.biojava3.core.sequence.compound.NucleotideCompound;
  43 import org.eclipse.core.runtime.IProgressMonitor;
  44 import org.eclipse.swt.SWT;
  45 import org.eclipse.swt.widgets.Composite;
  46 import org.eclipse.ui.IActionBars;
  47 import org.eclipse.ui.IEditorInput;
  48 import org.eclipse.ui.IEditorSite;
  49 import org.eclipse.ui.PartInitException;
  50 import org.eclipse.ui.PlatformUI;
  51 import org.eclipse.ui.commands.ICommandService;
  52 import org.eclipse.ui.part.EditorPart;
  53
  54 import eu.etaxonomy.taxeditor.editor.handler.ToggleInsertOverwriteHandler;
  55 import eu.etaxonomy.taxeditor.editor.handler.ToggleLeftRightInsertionHandler;
  56
  57
  58
  59 /**
  60  * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
  61  * a consensus sequence.
  62  * <p>
  63  * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
  64  *
  65  * @author Ben Stöver
  66  * @author pplitzner
  67  * @date 04.08.2014
  68  */
  69 public class AlignmentEditor extends EditorPart {
  70     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
  71         public static final int READS_AREA_INDEX = 1;
  72         public static final int CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
  73         public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
  74
  75
  76     private MultipleAlignmentsContainer alignmentsContainer = null;
  77     private Map<Integer, URI> uriMap = new TreeMap<Integer, URI>();  //TODO Move this to ContigSequenceDataProvider
  78
  79
  80     private void refreshToolbarElement(String id) {
  81                 ICommandService commandService =
  82                                 (ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);
  83                 if (commandService != null) {
  84                         commandService.refreshElements(id, Collections.EMPTY_MAP);
  85                 }
  86     }
  87
  88
  89     private void registerEditSettingListener(MultipleAlignmentsContainer container) {
  90         container.getEditSettings().addListener(new EditSettingsListener() {
  91                                         @Override
  92                                         public void workingModeChanged(EditSettingsChangeEvent e) {}  // Currently nothing to do
  93
  94                                         @Override
  95                                         public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
  96                                                 updateStatusBar();
  97                                         refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
  98                                         }
  99
 100                                         @Override
 101                                         public void insertChanged(EditSettingsChangeEvent e) {
 102                                                 updateStatusBar();
 103                                         refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
 104                                         }
 105                                 });
 106     }
 107
 108
 109     private AlignmentArea createIndexArea(MultipleAlignmentsContainer container) {
 110                 AlignmentArea result = new AlignmentArea(container);
 111                 result.setAllowVerticalScrolling(false);
 112                 result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));
 113                 return result;
 114     }
 115
 116
 117     private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
 118                 AlignmentArea result = new AlignmentArea(container);
 119                 result.setAllowVerticalScrolling(allowVerticalScrolling);
 120
 121                 TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);
 122                 SequenceDataProvider<NucleotideCompound> provider = new PackedSequenceDataProvider<NucleotideCompound>(tokenSet);
 123                 result.setSequenceProvider(provider, false);
 124
 125                 return result;
 126         }
 127
 128
 129     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
 130                 SequenceDataProvider<?> sequenceProvider) {
 131
 132                 AlignmentArea result = new AlignmentArea(container);
 133                 result.setAllowVerticalScrolling(false);
 134                 result.getDataAreas().getBottomAreas().add(
 135                                 new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));
 136                 return result;
 137     }
 138
 139
 140     private MultipleAlignmentsContainer getAlignmentsContainer() {
 141         if (alignmentsContainer == null) {
 142                 alignmentsContainer = new MultipleAlignmentsContainer();
 143
 144                 AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
 145                 list.add(createIndexArea(alignmentsContainer));
 146                 AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
 147                 list.add(readsArea);  // Make sure READS_AREA_INDEX is correct.
 148                 list.add(createEditableAlignmentArea(alignmentsContainer, false));  // Make sure COMSENSUS_AREA_INDEX is correct.
 149                 list.add(createConsensusHintArea(alignmentsContainer,
 150                                 readsArea.getSequenceProvider()));
 151
 152                 registerEditSettingListener(alignmentsContainer);
 153         }
 154                 return alignmentsContainer;
 155         }
 156
 157
 158     private AlignmentArea getReadsArea() {
 159         return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
 160     }
 161
 162
 163     private AlignmentArea getConsensusArea() {
 164         return getAlignmentsContainer().getAlignmentAreas().get(CONSENSUS_AREA_INDEX);
 165     }
 166
 167
 168         /* (non-Javadoc)
 169      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
 170      */
 171     @Override
 172     public void createPartControl(Composite parent) {
 173                 getAlignmentsContainer().createSWTWidget(parent, SWT.NONE);
 174                 updateStatusBar();
 175
 176                 // Just for testing:
 177                 try {
 178                         addRead(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").toURI());
 179                         addRead(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").toURI());
 180
 181                         // Add test consensus sequence:
 182                         SequenceDataProvider consensusProvider = getConsensusArea().getSequenceProvider();
 183                         int id = consensusProvider.addSequence("Consensus");
 184                         Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.
 185                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('A'));
 186                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('C'));
 187                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('G'));
 188                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('T'));
 189                         consensusProvider.insertTokensAt(id, 0, tokens);
 190                 }
 191                 catch (Exception e) {
 192                         throw new RuntimeException(e);
 193                 }
 194     }
 195
 196
 197     private void updateStatusBar() {
 198         IActionBars bars = getEditorSite().getActionBars();
 199         bars.getStatusLineManager().setMessage("Edit mode: " +
 200                         (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +
 201                         "Insertion in pherogram: " +
 202                         (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
 203     }
 204
 205
 206     /* (non-Javadoc)
 207      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
 208      */
 209     @Override
 210     public void doSave(IProgressMonitor monitor) {
 211         // TODO Auto-generated method stub
 212
 213     }
 214
 215
 216     /* (non-Javadoc)
 217      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
 218      */
 219     @Override
 220     public void doSaveAs() {
 221         // TODO Auto-generated method stub
 222
 223     }
 224
 225
 226     /* (non-Javadoc)
 227      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
 228      */
 229     @Override
 230     public void init(IEditorSite site, IEditorInput input) throws PartInitException {
 231         setSite(site);
 232         setInput(input);
 233     }
 234
 235
 236     /* (non-Javadoc)
 237      * @see org.eclipse.ui.part.EditorPart#isDirty()
 238      */
 239     @Override
 240     public boolean isDirty() {
 241         // TODO Auto-generated method stub
 242         return false;
 243     }
 244
 245
 246     /* (non-Javadoc)
 247      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
 248      */
 249     @Override
 250     public boolean isSaveAsAllowed() {
 251         // TODO Auto-generated method stub
 252         return false;
 253     }
 254
 255
 256     @Override
 257     public void setFocus() {}
 258
 259
 260     public boolean isInsertMode() {
 261         return getAlignmentsContainer().getEditSettings().isInsert();
 262     }
 263
 264
 265     public boolean isInsertLeftInPherogram() {
 266         return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
 267     }
 268
 269
 270     public void toggleLeftRightInsertionInPherogram() {
 271         getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
 272     }
 273
 274
 275     public void toggleInsertOverwrite() {
 276         getAlignmentsContainer().getEditSettings().toggleInsert();
 277     }
 278
 279
 280         public static PherogramProvider readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
 281                 PherogramProvider result;
 282                 InputStream stream = uri.toURL().openStream();
 283                 try {
 284                         result = new BioJavaPherogramProvider(ChromatogramFactory.create(stream));
 285                 }
 286                 finally {
 287                         stream.close();
 288                 }
 289                 return result;
 290         }
 291
 292
 293         private String newReadName() {
 294                 int index = 1;
 295                 while (getReadsArea().getSequenceProvider().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
 296                                 != SequenceDataProvider.NO_SEQUENCE_FOUND) {
 297
 298                         index++;
 299                 }
 300                 return DEFAULT_READ_NAME_PREFIX + index;
 301         }
 302
 303
 304     public void addRead(URI pherogramURI) throws IOException, UnsupportedChromatogramFormatException {
 305         addRead(newReadName(), pherogramURI);
 306     }
 307
 308
 309     public void addRead(String name, URI pherogramURI) throws IOException, UnsupportedChromatogramFormatException {
 310                 SequenceDataProvider provider = getReadsArea().getSequenceProvider();
 311                 PherogramProvider pherogramProvider = readPherogram(pherogramURI);  // Must happen before a sequence is added, because it might throw an exception.
 312
 313         // Create sequence:
 314                 provider.addSequence(name);
 315                 int id = provider.sequenceIDByName(name);
 316
 317                 // Copy base call sequence into alignment:
 318                 Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.
 319                 for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
 320                         tokens.add(provider.getTokenSet().tokenByKeyChar(
 321                                 pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
 322                 }
 323                 provider.insertTokensAt(id, 0, tokens);
 324
 325                 // Add data area:
 326                 PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), pherogramProvider);
 327                 pherogramArea.addMouseListener(new PherogramMouseListener(pherogramURI));
 328                 getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
 329
 330                 // Save source URI:
 331                 uriMap.put(id, pherogramURI);
 332         }
 333 }