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.selection.SelectionModel;
  15 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
  16 import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
  17 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramAlignmentModel;
  18 import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
  19 import info.bioinfweb.libralign.dataarea.implementations.pherogram.ShiftChange;
  20 import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;
  21 import info.bioinfweb.libralign.editsettings.EditSettingsListener;
  22 import info.bioinfweb.libralign.model.AlignmentModel;
  23 import info.bioinfweb.libralign.model.AlignmentModelChangeListener;
  24 import info.bioinfweb.libralign.model.SequenceUtils;
  25 import info.bioinfweb.libralign.model.adapters.StringAdapter;
  26 import info.bioinfweb.libralign.model.events.SequenceChangeEvent;
  27 import info.bioinfweb.libralign.model.events.SequenceRenamedEvent;
  28 import info.bioinfweb.libralign.model.events.TokenChangeEvent;
  29 import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
  30 import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;
  31 import info.bioinfweb.libralign.model.tokenset.TokenSet;
  32 import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
  33 import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
  34 import info.bioinfweb.libralign.pherogram.model.BioJavaPherogramModel;
  35 import info.bioinfweb.libralign.pherogram.model.PherogramModel;
  36 import info.bioinfweb.libralign.pherogram.model.ReverseComplementPherogramModel;
  37
  38 import java.io.File;
  39 import java.io.IOException;
  40 import java.io.InputStream;
  41 import java.net.URI;
  42 import java.util.ArrayList;
  43 import java.util.Collection;
  44 import java.util.Collections;
  45 import java.util.Iterator;
  46 import java.util.Map;
  47 import java.util.TreeMap;
  48
  49 import org.biojava.bio.chromatogram.ChromatogramFactory;
  50 import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
  51 import org.biojava3.core.sequence.compound.DNACompoundSet;
  52 import org.biojava3.core.sequence.compound.NucleotideCompound;
  53 import org.eclipse.core.runtime.IProgressMonitor;
  54 import org.eclipse.swt.SWT;
  55 import org.eclipse.swt.widgets.Composite;
  56 import org.eclipse.ui.IActionBars;
  57 import org.eclipse.ui.IEditorInput;
  58 import org.eclipse.ui.IEditorPart;
  59 import org.eclipse.ui.IEditorSite;
  60 import org.eclipse.ui.PartInitException;
  61 import org.eclipse.ui.PlatformUI;
  62 import org.eclipse.ui.commands.ICommandService;
  63 import org.eclipse.ui.part.EditorPart;
  64
  65 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  66 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  67 import eu.etaxonomy.cdm.model.media.MediaUtils;
  68 import eu.etaxonomy.cdm.model.molecular.Sequence;
  69 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  70 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  71 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
  72 import eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleInsertOverwriteHandler;
  73 import eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleLeftRightInsertionHandler;
  74 import eu.etaxonomy.taxeditor.store.CdmStore;
  75
  76
  77
  78 /**
  79  * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
  80  * a consensus sequence.
  81  * <p>
  82  * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
  83  *
  84  * @author Ben Stöver
  85  * @author pplitzner
  86  * @date 04.08.2014
  87  */
  88 public class AlignmentEditor extends EditorPart {
  89     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
  90
  91         public static final int READS_AREA_INDEX = 1;
  92         public static final int CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
  93         public static final int PHEROGRAM_AREA_INDEX = 0;
  94         public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
  95         public static final String CONSENSUS_NAME = "Consensus";
  96
  97
  98     private final ConversationHolder conversationHolder;
  99
 100         private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {
 101                                 @Override
 102                                 public <T> void afterTokenChange(TokenChangeEvent<T> e) {
 103                                         setDirty();
 104                                 }
 105
 106                                 @Override
 107                                 public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {
 108                                         setDirty();
 109                                 }
 110
 111                                 @Override
 112                                 public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {
 113                                         setDirty();
 114                                 }
 115
 116                                 @Override
 117                                 public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider,
 118                                                 AlignmentModel<U> newProvider) {  // Not expected.
 119
 120                                         setDirty();
 121                                 }
 122                         };
 123
 124     private MultipleAlignmentsContainer alignmentsContainer = null;
 125     private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>();  //TODO Move this to ContigSequenceDataProvider
 126     private boolean dirty = false;
 127
 128
 129     public AlignmentEditor() {
 130         super();
 131         //conversationHolder = CdmStore.createConversation();
 132         conversationHolder = null;
 133     }
 134
 135
 136     private void refreshToolbarElement(String id) {
 137                 ICommandService commandService =
 138                                 (ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);
 139                 if (commandService != null) {
 140                         commandService.refreshElements(id, Collections.EMPTY_MAP);
 141                 }
 142     }
 143
 144
 145     private void registerEditSettingListener(MultipleAlignmentsContainer container) {
 146         container.getEditSettings().addListener(new EditSettingsListener() {
 147                                         @Override
 148                                         public void workingModeChanged(EditSettingsChangeEvent e) {}  // Currently nothing to do
 149
 150                                         @Override
 151                                         public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
 152                                                 updateStatusBar();
 153                                         refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
 154                                         }
 155
 156                                         @Override
 157                                         public void insertChanged(EditSettingsChangeEvent e) {
 158                                                 updateStatusBar();
 159                                         refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
 160                                         }
 161                                 });
 162     }
 163
 164
 165     private AlignmentArea createIndexArea(MultipleAlignmentsContainer container) {
 166                 AlignmentArea result = new AlignmentArea(container);
 167                 result.setAllowVerticalScrolling(false);
 168                 result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));
 169                 return result;
 170     }
 171
 172
 173     private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
 174                 AlignmentArea result = new AlignmentArea(container);
 175                 result.setAllowVerticalScrolling(allowVerticalScrolling);
 176
 177                 TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);
 178                 AlignmentModel<NucleotideCompound> provider = new PackedAlignmentModel<NucleotideCompound>(tokenSet);
 179                 result.setAlignmentModel(provider, false);
 180                 provider.getChangeListeners().add(DIRTY_LISTENER);
 181
 182                 return result;
 183         }
 184
 185
 186     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
 187                 AlignmentModel<?> sequenceProvider) {
 188
 189                 AlignmentArea result = new AlignmentArea(container);
 190                 result.setAllowVerticalScrolling(false);
 191                 result.getDataAreas().getBottomAreas().add(
 192                                 new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));
 193                 return result;
 194     }
 195
 196
 197     private MultipleAlignmentsContainer getAlignmentsContainer() {
 198         if (alignmentsContainer == null) {
 199                 alignmentsContainer = new MultipleAlignmentsContainer();
 200
 201                 AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
 202                 list.add(createIndexArea(alignmentsContainer));
 203                 AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
 204                 list.add(readsArea);  // Make sure READS_AREA_INDEX is correct.
 205                 list.add(createEditableAlignmentArea(alignmentsContainer, false));  // Make sure COMSENSUS_AREA_INDEX is correct.
 206                 list.add(createConsensusHintArea(alignmentsContainer,
 207                                 readsArea.getAlignmentModel()));
 208
 209                 registerEditSettingListener(alignmentsContainer);
 210         }
 211                 return alignmentsContainer;
 212         }
 213
 214
 215     private AlignmentArea getReadsArea() {
 216         return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
 217     }
 218
 219
 220     private AlignmentArea getConsensusArea() {
 221         return getAlignmentsContainer().getAlignmentAreas().get(CONSENSUS_AREA_INDEX);
 222     }
 223
 224
 225     private PherogramArea getPherogramArea(int sequenceID) {
 226         return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
 227     }
 228
 229
 230     private void createTestContents() {
 231                 // Just for testing:
 232                 try {
 233                         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(), false);
 234                         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(), false);
 235
 236                         // Add test consensus sequence:
 237                         AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();
 238                         int id = consensusProvider.addSequence(CONSENSUS_NAME);
 239                         Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.
 240                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('A'));
 241                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('C'));
 242                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('G'));
 243                         tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('T'));
 244                         consensusProvider.insertTokensAt(id, 0, tokens);
 245                 }
 246                 catch (Exception e) {
 247                         throw new RuntimeException(e);
 248                 }
 249     }
 250
 251
 252     private void readCDMData(Sequence sequenceNode) {
 253         //TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).
 254
 255                 // Add reads:
 256                 for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {
 257                         try {
 258                                 SingleRead pherogramInfo = singleReadAlignment.getSingleRead();
 259                                 int id = addRead(pherogramInfo.getPrimer().getLabel(),  //TODO Should the sequence name contain other/additional/alternative data? Can the same string as in the derivative tree be used here?
 260                                                 MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri(),
 261                                                 singleReadAlignment.isReverseComplement(),
 262                                                 singleReadAlignment.getEditedSequence(),
 263                                                 singleReadAlignment.getShifts());
 264                                 cdmMap.put(id, singleReadAlignment);
 265                         }
 266                         catch (IOException e) {
 267                                 e.printStackTrace();  //TODO Output to user (Possibly collect for all pherograms and display in the end.)
 268                         }
 269                         catch (UnsupportedChromatogramFormatException e) {
 270                                 e.printStackTrace();  //TODO Output to user (Possibly collect for all pherograms and display in the end.)
 271                         }
 272                 }
 273
 274                 // Set consensus sequence:
 275                 AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();
 276                 int id = consensusProvider.addSequence(CONSENSUS_NAME);
 277                 consensusProvider.insertTokensAt(id, 0, SequenceUtils.stringToTokenList(
 278                                 sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
 279                 //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
 280     }
 281
 282
 283         /* (non-Javadoc)
 284      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
 285      */
 286     @Override
 287     public void createPartControl(Composite parent) {
 288                 getAlignmentsContainer().createSWTWidget(parent, SWT.NONE);
 289                 updateStatusBar();
 290
 291                 if (getEditorInput() instanceof AlignmentEditorInput) {
 292                         if (((AlignmentEditorInput)getEditorInput()).getSequenceNode() != null) {
 293                             Sequence sequenceNode = ((AlignmentEditorInput)getEditorInput()).getSequenceNode();
 294                         //re-load into the current session if it is already persisted in the DB
 295                         if(sequenceNode!=null && sequenceNode.getId()!=0){
 296                             sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());
 297                         }
 298                                 readCDMData(sequenceNode);
 299                         }
 300                         else {
 301                                 createTestContents();  // This case will removed after the test phase and an exception should probably be thrown.
 302                         }
 303                 }
 304                 else {
 305                         throw new IllegalArgumentException("The editor input must have the type " +
 306                                         AlignmentEditorInput.class.getCanonicalName());  //TODO What should be done here?
 307                 }
 308     }
 309
 310
 311     private void updateStatusBar() {
 312         IActionBars bars = getEditorSite().getActionBars();
 313         bars.getStatusLineManager().setMessage("Edit mode: " +
 314                         (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +
 315                         "Insertion in pherogram: " +
 316                         (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
 317     }
 318
 319
 320     private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAlignmentModel alignmentModel) {
 321         SingleReadAlignment.Shift[] result = new SingleReadAlignment.Shift[alignmentModel.getShiftChangeCount()];
 322         Iterator<ShiftChange> iterator = alignmentModel.shiftChangeIterator();
 323         int pos = 0;
 324         while (iterator.hasNext()) {
 325                 ShiftChange shiftChange = iterator.next();
 326                 result[pos] = new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange());
 327         }
 328         return result;
 329     }
 330
 331
 332     /* (non-Javadoc)
 333      * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
 334      */
 335     @Override
 336     public void doSave(IProgressMonitor monitor) {
 337         if (getEditorInput() instanceof AlignmentEditorInput) {
 338                 String taskName = "Saving alignment";
 339             monitor.beginTask(taskName, 3);
 340
 341                 Sequence sequenceNode = ((AlignmentEditorInput)getEditorInput()).getSequenceNode();
 342                 StringAdapter stringProvider = new StringAdapter(getConsensusArea().getAlignmentModel(), false);  // Throws an exception if a token has more than one character.
 343
 344                 // Write consensus sequence:
 345                 SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence();
 346                 String newConsensusSequence = stringProvider.getSequence(
 347                                 getConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
 348                 if (consensusSequenceObj == null) {
 349                         sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence));
 350                 }
 351                 else {
 352                         consensusSequenceObj.setString(newConsensusSequence);
 353                 }
 354
 355                 // Write single reads:
 356                 stringProvider.setUnderlyingProvider(getReadsArea().getAlignmentModel());
 357                 sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values());  // Remove all reads that are not in the alignment anymore.
 358                 Iterator<Integer> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
 359                 while (iterator.hasNext()) {
 360                         int id = iterator.next();
 361                         SingleReadAlignment singleRead = cdmMap.get(id);
 362                         if (singleRead == null) {
 363                                 //TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?
 364                                 //singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);
 365                         }
 366
 367                         singleRead.setEditedSequence(stringProvider.getSequence(id));
 368                         singleRead.setReverseComplement(getPherogramArea(id).getProvider() instanceof ReverseComplementPherogramModel);  // Works only if ReverseComplementPherogramProvider instances are not nested.
 369                         singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getAlignmentModel()));
 370                 }
 371
 372                 if (!conversationHolder.isBound()) {
 373                 conversationHolder.bind();
 374             }
 375             monitor.worked(1);
 376
 377             // Commit the conversation and start a new transaction immediately:
 378             conversationHolder.commit(true);
 379             monitor.worked(1);
 380
 381             dirty = false;
 382             monitor.worked(1);
 383             monitor.done();
 384             firePropertyChange(PROP_DIRTY);
 385         }
 386         else {
 387                 //TODO Throw exception as soon as testing period which allows unlinked AlignmentEditor is over.
 388         }
 389     }
 390
 391
 392     /* (non-Javadoc)
 393      * @see org.eclipse.ui.part.EditorPart#doSaveAs()
 394      */
 395     @Override
 396     public void doSaveAs() {}
 397
 398
 399     /* (non-Javadoc)
 400      * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
 401      */
 402     @Override
 403     public void init(IEditorSite site, IEditorInput input) throws PartInitException {
 404         setSite(site);
 405         setInput(input);
 406     }
 407
 408
 409     /* (non-Javadoc)
 410      * @see org.eclipse.ui.part.EditorPart#isDirty()
 411      */
 412     @Override
 413     public boolean isDirty() {
 414         return dirty;
 415     }
 416
 417
 418     private void setDirty() {
 419         dirty = true;
 420         firePropertyChange(IEditorPart.PROP_DIRTY);
 421     }
 422
 423
 424     /* (non-Javadoc)
 425      * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
 426      */
 427     @Override
 428     public boolean isSaveAsAllowed() {
 429         return false;  // "Save as" not allowed.
 430     }
 431
 432
 433     @Override
 434     public void setFocus() {
 435         if(conversationHolder!=null){
 436             conversationHolder.bind();
 437         }
 438     }
 439
 440
 441     public boolean isInsertMode() {
 442         return getAlignmentsContainer().getEditSettings().isInsert();
 443     }
 444
 445
 446     public boolean isInsertLeftInPherogram() {
 447         return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
 448     }
 449
 450
 451     public void toggleLeftRightInsertionInPherogram() {
 452         getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
 453     }
 454
 455
 456     public void toggleInsertOverwrite() {
 457         getAlignmentsContainer().getEditSettings().toggleInsert();
 458     }
 459
 460
 461     public void reverseComplementSelection() {
 462         SelectionModel selection = getReadsArea().getSelection();
 463         AlignmentModel<?> provider = getReadsArea().getAlignmentModel();
 464         for (int row = selection.getStartRow(); row < selection.getStartRow() + selection.getCursorHeight(); row++) {
 465                         int sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
 466                         //TODO rc edited sequence
 467
 468                         if (getPherogramArea(sequenceID).getProvider() instanceof ReverseComplementPherogramModel) {
 469                                 //getPherogramArea(sequenceID).
 470                                 //TODO Allow to set new provider in PherogramArea or create new PherogramArea
 471                                 //TODO Reposition pherogram according to previous position in edited sequence and length
 472                         }
 473                 }
 474     }
 475
 476
 477         public static PherogramModel readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
 478                 PherogramModel result;
 479                 InputStream stream = uri.toURL().openStream();
 480                 try {
 481                         result = new BioJavaPherogramModel(ChromatogramFactory.create(stream));
 482                 }
 483                 finally {
 484                         stream.close();
 485                 }
 486                 return result;
 487         }
 488
 489
 490         private String newReadName() {
 491                 int index = 1;
 492                 while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
 493                                 != AlignmentModel.NO_SEQUENCE_FOUND) {
 494
 495                         index++;
 496                 }
 497                 return DEFAULT_READ_NAME_PREFIX + index;
 498         }
 499
 500
 501     public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException {
 502         addRead(newReadName(), pherogramURI, reverseComplemented, null, null);
 503     }
 504
 505
 506     /**
 507      * Adds a new sequence with attached phergram data area to the reads alignment.
 508      * <p>
 509      * If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will
 510      * be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited
 511      * and the base calls sequence are assumed.
 512      *
 513      * @param name the name of the new sequence
 514      * @param pherogramURI the URI where the associated pherogram file is located
 515      * @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should
 516      *        be added, {@code false} otherwise.
 517      * @param editedSequence the edited version of the base call sequence (May be {@code null}.)
 518      * @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.)
 519      * @return the sequence ID of the added read
 520      * @throws IOException if an error occurred when trying to read the pherogram file
 521      * @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
 522      */
 523     public int addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
 524                 SingleReadAlignment.Shift[] shifts) throws IOException, UnsupportedChromatogramFormatException {
 525
 526                 AlignmentModel provider = getReadsArea().getAlignmentModel();
 527                 PherogramModel pherogramProvider = readPherogram(pherogramURI);  // Must happen before a sequence is added, because it might throw an exception.
 528                 if (reverseComplemented) {
 529                         pherogramProvider = new ReverseComplementPherogramModel(pherogramProvider);
 530                 }
 531
 532         // Create sequence:
 533                 provider.addSequence(name);
 534                 int id = provider.sequenceIDByName(name);
 535
 536                 // Set edited sequence:
 537                 Collection<Object> tokens;  // First save tokens in a collection to avoid GUI updated for each token.
 538                 if (editedSequence != null) {
 539                         tokens = SequenceUtils.stringToTokenList(editedSequence, provider.getTokenSet());
 540                 }
 541                 else {  // Copy base call sequence into alignment:
 542                         tokens = new ArrayList<Object>();
 543                         for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
 544                                 tokens.add(provider.getTokenSet().tokenByKeyChar(
 545                                         pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
 546                         }
 547                         setDirty();
 548                 }
 549                 provider.insertTokensAt(id, 0, tokens);
 550
 551                 // Create pherogram area:
 552                 PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), pherogramProvider);
 553
 554                 // Set shifts:
 555                 if ((shifts != null) && (shifts.length > 0)) {
 556                         PherogramAlignmentModel alignmentModel = pherogramArea.getAlignmentModel();
 557                         for (int i = 0; i < shifts.length; i++) {
 558                                 alignmentModel.addShiftChange(shifts[i].position, shifts[i].shift);
 559                         }
 560                         setDirty();
 561                 }
 562
 563                 // Add pherogram area to GUI:
 564                 pherogramArea.addMouseListener(new PherogramMouseListener(pherogramURI));
 565                 getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
 566
 567                 // Save source URI:
 568                 return id;
 569         }
 570 }