public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
public static final int READS_AREA_INDEX = 1;
- public static final int CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
+ public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
+ public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1;
public static final int PHEROGRAM_AREA_INDEX = 0;
+ public static final int CONSENSUS_DATA_AREA_INDEX = 0;
public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
public static final String CONSENSUS_NAME = "Consensus";
AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
- list.add(createIndexArea(alignmentsContainer, readsArea));
+ list.add(createIndexArea(alignmentsContainer, readsArea));
list.add(readsArea); // Make sure READS_AREA_INDEX is correct.
list.add(createEditableAlignmentArea(alignmentsContainer, false)); // Make sure COMSENSUS_AREA_INDEX is correct.
list.add(createConsensusHintArea(alignmentsContainer, readsArea));
}
- private AlignmentArea getConsensusArea() {
- return getAlignmentsContainer().getAlignmentAreas().get(CONSENSUS_AREA_INDEX);
+ private AlignmentArea getEditableConsensusArea() {
+ return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX);
}
private PherogramArea getPherogramArea(int sequenceID) {
- return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
+ return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(
+ PHEROGRAM_AREA_INDEX);
+ }
+
+
+ private ConsensusSequenceArea getConsensusHintDataArea() {
+ return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas().
+ get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas().
+ get(CONSENSUS_DATA_AREA_INDEX);
}
addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);
// Add test consensus sequence:
- AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();
- int id = consensusProvider.addSequence(CONSENSUS_NAME);
+ AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
+ int id = consensusModel.addSequence(CONSENSUS_NAME);
Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token.
- tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('A'));
- tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('C'));
- tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('G'));
- tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('T'));
- consensusProvider.insertTokensAt(id, 0, tokens);
+ tokens.add(consensusModel.getTokenSet().tokenByKeyChar('A'));
+ tokens.add(consensusModel.getTokenSet().tokenByKeyChar('C'));
+ tokens.add(consensusModel.getTokenSet().tokenByKeyChar('G'));
+ tokens.add(consensusModel.getTokenSet().tokenByKeyChar('T'));
+ consensusModel.insertTokensAt(id, 0, tokens);
}
catch (Exception e) {
throw new RuntimeException(e);
}
// Set consensus sequence:
- AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();
+ AlignmentModel consensusProvider = getEditableConsensusArea().getAlignmentModel();
int id = consensusProvider.addSequence(CONSENSUS_NAME);
consensusProvider.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
}
- private void updateStatusBar() {
+ private void updateStatusBar() {
IActionBars bars = getEditorSite().getActionBars();
bars.getStatusLineManager().setMessage("Edit mode: " +
(getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + " " +
monitor.beginTask(taskName, 3);
Sequence sequenceNode = ((AlignmentEditorInput)getEditorInput()).getSequenceNode();
- StringAdapter stringProvider = new StringAdapter(getConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character.
+ StringAdapter stringProvider = new StringAdapter(getEditableConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character.
// Write consensus sequence:
SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence();
String newConsensusSequence = stringProvider.getSequence(
- getConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
+ getEditableConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
if (consensusSequenceObj == null) {
sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence));
}
}
+ /**
+ * Recreates the whole consensus sequence from all single read sequences. The previous consensus
+ * sequence is overwritte.
+ */
+ @SuppressWarnings("unchecked")
+ public <T> void createConsensusSequence() {
+ ConsensusSequenceArea area = getConsensusHintDataArea();
+ AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
+ int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
+ int length = getReadsArea().getAlignmentModel().getMaxSequenceLength();
+
+ Collection<T> tokens = new ArrayList<T>(length);
+ for (int column = 0; column < length; column++) {
+ tokens.add(model.getTokenSet().tokenByRepresentation(area.getConsensusToken(column)));
+ }
+
+ model.removeTokensAt(sequenceID, 0, model.getSequenceLength(sequenceID));
+ model.insertTokensAt(sequenceID, 0, tokens);
+ }
+
+
+ /**
+ * Updates the current consensus sequence by replacing gaps by the according consensus tokens
+ * calculated from the single read sequences and extends the consensus sequence if necessary.
+ */
+ @SuppressWarnings("unchecked")
+ public <T> void updateConsensusSequence() {
+ ConsensusSequenceArea area = getConsensusHintDataArea();
+ AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
+ TokenSet<T> tokenSet = model.getTokenSet();
+ int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
+ int currentConsensusLength = model.getSequenceLength(sequenceID);
+ int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength();
+
+ // Replace gaps by new information:
+ for (int column = 0; column < currentConsensusLength; column++) {
+ if (tokenSet.isGapToken(model.getTokenAt(sequenceID, column))) {
+ T newToken = tokenSet.tokenByRepresentation(area.getConsensusToken(column));
+ if (!tokenSet.isGapToken(newToken)) {
+ model.setTokenAt(sequenceID, column, newToken);
+ }
+ }
+ }
+
+ // Append additional tokens:
+ if (overallLength > currentConsensusLength) {
+ Collection<T> tokens = new ArrayList<T>(overallLength);
+ for (int column = currentConsensusLength; column < overallLength; column++) {
+ tokens.add(tokenSet.tokenByRepresentation(area.getConsensusToken(column)));
+ }
+ model.appendTokens(sequenceID, tokens);
+ }
+ }
+
+
public static PherogramModel readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
PherogramModel result;
InputStream stream = uri.toURL().openStream();
BGBM BDI Projects / taxeditor.git / commitdiff