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