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