X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=23c1d003cdcb2a327b363b39496a7c56ddc19057;hb=6c7cac79652fa6c7050311f73f36b9a9d05e6a6b;hp=dfd120b6363c8ec86e8df74c4249b1e21ec927d8;hpb=96356075a122b745936738f478a8ee33ac7e0f0a;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index dfd120b..23c1d00 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -22,6 +22,7 @@ package jalview.viewmodel; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.Conservation; +import jalview.analysis.TreeModel; import jalview.api.AlignCalcManagerI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -33,7 +34,6 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentView; import jalview.datamodel.Annotation; -import jalview.datamodel.CigarArray; import jalview.datamodel.ColumnSelection; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; @@ -57,6 +57,7 @@ import jalview.viewmodel.styles.ViewStyle; import jalview.workers.AlignCalcManager; import jalview.workers.ComplementConsensusThread; import jalview.workers.ConsensusThread; +import jalview.workers.InformationThread; import jalview.workers.StrucConsensusThread; import java.awt.Color; @@ -67,6 +68,7 @@ import java.util.BitSet; import java.util.Deque; import java.util.HashMap; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Map; @@ -77,10 +79,10 @@ import java.util.Map; * @author jimp * */ -public abstract class AlignmentViewport implements AlignViewportI, - CommandListener, VamsasSource +public abstract class AlignmentViewport + implements AlignViewportI, CommandListener, VamsasSource { - final protected ViewportRanges ranges; + protected ViewportRanges ranges; protected ViewStyleI viewStyle = new ViewStyle(); @@ -95,12 +97,32 @@ public abstract class AlignmentViewport implements AlignViewportI, protected Deque historyList = new ArrayDeque<>(); protected Deque redoList = new ArrayDeque<>(); - /** * alignment displayed in the viewport. Please use get/setter */ protected AlignmentI alignment; + + /* + * probably unused indicator that view is of a dataset rather than an + * alignment + */ + + protected boolean ignoreBelowBackGroundFrequencyCalculation = false; + + protected boolean infoLetterHeight = false; + + protected AlignmentAnnotation occupancy; + + /** + * results of alignment consensus analysis for visible portion of view + */ + protected ProfilesI consensusProfiles; + + /** + * HMM profile for the alignment + */ + protected ProfilesI hmmProfiles; public AlignmentViewport(AlignmentI al) { @@ -406,6 +428,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setWrapAlignment(boolean state) { viewStyle.setWrapAlignment(state); + ranges.setWrappedMode(state); } /** @@ -568,8 +591,6 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setSeqNameItalics(default1); } - - @Override public AlignmentI getAlignment() { @@ -589,7 +610,7 @@ public abstract class AlignmentViewport implements AlignViewportI, * alignment */ protected boolean isDataset = false; - + public void setDataset(boolean b) { isDataset = b; @@ -610,10 +631,8 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected boolean ignoreBelowBackGroundFrequencyCalculation = false; - protected ResidueShaderI residueShading = new ResidueShader(); - + @Override public void setGlobalColourScheme(ColourSchemeI cs) { @@ -645,6 +664,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { residueShading.setConservation(hconservation); } + /* + * reset conservation flag in case just set to false if + * Conservation was null (calculation still in progress) + */ + residueShading.setConservationApplied(getConservationSelected()); residueShading.alignmentChanged(alignment, hiddenRepSequences); } @@ -660,11 +684,12 @@ public abstract class AlignmentViewport implements AlignViewportI, * retain any colour thresholds per group while * changing choice of colour scheme (JAL-2386) */ - sg.setColourScheme(cs); + sg.setColourScheme( + cs == null ? null : cs.getInstance(this, sg)); if (cs != null) { - sg.getGroupColourScheme() - .alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme().alignmentChanged(sg, + hiddenRepSequences); } } } @@ -673,8 +698,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return residueShading == null ? null : residueShading - .getColourScheme(); + return residueShading == null ? null : residueShading.getColourScheme(); } @Override @@ -682,7 +706,7 @@ public abstract class AlignmentViewport implements AlignViewportI, { return residueShading; } - + protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; @@ -699,8 +723,6 @@ public abstract class AlignmentViewport implements AlignViewportI, protected AlignmentAnnotation[] groupConservation; - protected AlignmentAnnotation hmmConsensus; - /** * results of alignment consensus analysis for visible portion of view */ @@ -718,7 +740,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected Hashtable[] hStrucConsensus = null; protected Conservation hconservation = null; - + @Override public void setConservation(Conservation cons) { @@ -756,6 +778,18 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override + public void setHmmProfiles(ProfilesI info) + { + hmmProfiles = info; + } + + @Override + public ProfilesI getHmmProfiles() + { + return hmmProfiles; + } + + @Override public Hashtable[] getComplementConsensusHash() { return hcomplementConsensus; @@ -824,11 +858,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator - .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + jalview.workers.ConservationThread.class) == null) { - calculator.registerWorker(new jalview.workers.ConservationThread( - this, ap)); + calculator.registerWorker( + new jalview.workers.ConservationThread(this, ap)); } } @@ -842,7 +876,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null) + if (calculator + .getRegisteredWorkersOfClass(ConsensusThread.class) == null) { calculator.registerWorker(new ConsensusThread(this, ap)); } @@ -873,8 +908,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } if (doConsensus) { - if (calculator - .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + ComplementConsensusThread.class) == null) { calculator .registerWorker(new ComplementConsensusThread(this, ap)); @@ -883,6 +918,16 @@ public abstract class AlignmentViewport implements AlignViewportI, } } + @Override + public void initInformationWorker(final AlignmentViewPanel ap) + { + if (calculator + .getRegisteredWorkersOfClass(InformationThread.class) == null) + { + calculator.registerWorker(new InformationThread(this, ap)); + } + } + // --------START Structure Conservation public void updateStrucConsensus(final AlignmentViewPanel ap) { @@ -898,7 +943,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { return; } - if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + StrucConsensusThread.class) == null) { calculator.registerWorker(new StrucConsensusThread(this, ap)); } @@ -945,14 +991,19 @@ public abstract class AlignmentViewport implements AlignViewportI, strucConsensus = null; conservation = null; quality = null; + consensusProfiles = null; groupConsensus = null; groupConservation = null; hconsensus = null; + hconservation = null; hcomplementConsensus = null; - // colour scheme may hold reference to consensus - residueShading = null; - // TODO remove listeners from changeSupport? + gapcounts = null; + calculator = null; + residueShading = null; // may hold a reference to Consensus changeSupport = null; + ranges = null; + currentTree = null; + selectionGroup = null; setAlignment(null); } @@ -996,6 +1047,21 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean showConsensusHistogram = true; /** + * should hmm profile be rendered by default + */ + protected boolean hmmShowSequenceLogo = false; + + /** + * should hmm profile be rendered normalised to row height + */ + protected boolean hmmNormaliseSequenceLogo = false; + + /** + * should information histograms be rendered by default + */ + protected boolean hmmShowHistogram = true; + + /** * @return the showConsensusProfile */ @Override @@ -1005,6 +1071,15 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** + * @return the showInformationProfile + */ + @Override + public boolean isShowHMMSequenceLogo() + { + return hmmShowSequenceLogo; + } + + /** * @param showSequenceLogo * the new value */ @@ -1022,6 +1097,18 @@ public abstract class AlignmentViewport implements AlignViewportI, this.showSequenceLogo = showSequenceLogo; } + public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo) + { + if (showHMMSequenceLogo != this.hmmShowSequenceLogo) + { + this.hmmShowSequenceLogo = showHMMSequenceLogo; + // TODO: updateAnnotation if description (tooltip) will show + // profile in place of information content? + // calculator.updateAnnotationFor(InformationThread.class); + } + this.hmmShowSequenceLogo = showHMMSequenceLogo; + } + /** * @param showConsensusHistogram * the showConsensusHistogram to set @@ -1032,6 +1119,14 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** + * @param showInformationHistogram + */ + public void setShowInformationHistogram(boolean showInformationHistogram) + { + this.hmmShowHistogram = showInformationHistogram; + } + + /** * @return the showGroupConservation */ public boolean isShowGroupConservation() @@ -1077,6 +1172,17 @@ public abstract class AlignmentViewport implements AlignViewportI, } /** + * + * @return flag to indicate if the information content histogram should be + * rendered by default + */ + @Override + public boolean isShowInformationHistogram() + { + return this.hmmShowHistogram; + } + + /** * when set, updateAlignment will always ensure sequences are of equal length */ private boolean padGaps = false; @@ -1164,7 +1270,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean hasHiddenColumns() { - return colSel != null + return alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(); } @@ -1187,8 +1293,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (sequenceSetID != null) { - System.err - .println("Warning - overwriting a sequenceSetId for a viewport!"); + System.err.println( + "Warning - overwriting a sequenceSetId for a viewport!"); } sequenceSetID = new String(newid); } @@ -1232,22 +1338,16 @@ public abstract class AlignmentViewport implements AlignViewportI, ignoreGapsInConsensusCalculation); } } - } public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap) { ignoreBelowBackGroundFrequencyCalculation = b; - if (ap != null) - { - // updateConsensus(ap); - if (residueShading != null) - { - residueShading.setThreshold(residueShading.getThreshold(), - ignoreBelowBackGroundFrequencyCalculation); - } - } + } + public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap) + { + infoLetterHeight = b; } private long sgrouphash = -1, colselhash = -1; @@ -1304,11 +1404,18 @@ public abstract class AlignmentViewport implements AlignViewportI, return ignoreGapsInConsensusCalculation; } + @Override public boolean isIgnoreBelowBackground() { return ignoreBelowBackGroundFrequencyCalculation; } + @Override + public boolean isInfoLetterHeight() + { + return infoLetterHeight; + } + // property change stuff // JBPNote Prolly only need this in the applet version. private PropertyChangeSupport changeSupport = new PropertyChangeSupport( @@ -1354,7 +1461,10 @@ public abstract class AlignmentViewport implements AlignViewportI, public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) { - changeSupport.removePropertyChangeListener(listener); + if (changeSupport != null) + { + changeSupport.removePropertyChangeListener(listener); + } } /** @@ -1415,6 +1525,9 @@ public abstract class AlignmentViewport implements AlignViewportI, // common hide/show seq stuff public void showAllHiddenSeqs() { + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); + if (alignment.getHiddenSequences().getSize() > 0) { if (selectionGroup == null) @@ -1422,8 +1535,8 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup = new SequenceGroup(); selectionGroup.setEndRes(alignment.getWidth() - 1); } - List tmp = alignment.getHiddenSequences().showAll( - hiddenRepSequences); + List tmp = alignment.getHiddenSequences() + .showAll(hiddenRepSequences); for (SequenceI seq : tmp) { selectionGroup.addSequence(seq, false); @@ -1432,6 +1545,8 @@ public abstract class AlignmentViewport implements AlignViewportI, hiddenRepSequences = null; + ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); + firePropertyChange("alignment", null, alignment.getSequences()); // used to set hasHiddenRows/hiddenRepSequences here, after the property // changed event @@ -1441,8 +1556,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void showSequence(int index) { - List tmp = alignment.getHiddenSequences().showSequence( - index, hiddenRepSequences); + int startSeq = ranges.getStartSeq(); + int endSeq = ranges.getEndSeq(); + + List tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1456,6 +1574,9 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionGroup.addSequence(seq, false); setSequenceAnnotationsVisible(seq, true); } + + ranges.setStartEndSeq(startSeq, endSeq + tmp.size()); + firePropertyChange("alignment", null, alignment.getSequences()); sendSelection(); } @@ -1477,6 +1598,11 @@ public abstract class AlignmentViewport implements AlignViewportI, public void hideSequence(SequenceI[] seq) { + /* + * cache offset to first visible sequence + */ + int startSeq = ranges.getStartSeq(); + if (seq != null) { for (int i = 0; i < seq.length; i++) @@ -1484,6 +1610,7 @@ public abstract class AlignmentViewport implements AlignViewportI, alignment.getHiddenSequences().hideSequence(seq[i]); setSequenceAnnotationsVisible(seq[i], false); } + ranges.setStartSeq(startSeq); firePropertyChange("alignment", null, alignment.getSequences()); } } @@ -1513,8 +1640,8 @@ public abstract class AlignmentViewport implements AlignViewportI, } int gsize = selectionGroup.getSize(); - SequenceI[] hseqs = selectionGroup.getSequences().toArray( - new SequenceI[gsize]); + SequenceI[] hseqs = selectionGroup.getSequences() + .toArray(new SequenceI[gsize]); hideSequence(hseqs); setSelectionGroup(null); @@ -1604,8 +1731,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean isHiddenRepSequence(SequenceI seq) { - return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + return (hiddenRepSequences != null + && hiddenRepSequences.containsKey(seq)); } /** @@ -1623,14 +1750,15 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); + return alignment.getHiddenSequences() + .adjustForHiddenSeqs(alignmentIndex); } @Override public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1676,13 +1804,6 @@ public abstract class AlignmentViewport implements AlignViewportI, } @Override - public CigarArray getViewAsCigars(boolean selectedRegionOnly) - { - return new CigarArray(alignment, alignment.getHiddenColumns(), - (selectedRegionOnly ? selectionGroup : null)); - } - - @Override public jalview.datamodel.AlignmentView getAlignmentView( boolean selectedOnly) { @@ -1694,10 +1815,10 @@ public abstract class AlignmentViewport implements AlignViewportI, boolean selectedOnly, boolean markGroups) { return new AlignmentView(alignment, alignment.getHiddenColumns(), - selectionGroup, alignment.getHiddenColumns() != null + selectionGroup, + alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(), - selectedOnly, - markGroups); + selectedOnly, markGroups); } @Override @@ -1743,8 +1864,12 @@ public abstract class AlignmentViewport implements AlignViewportI, if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns().getVisibleSequenceStrings( - start, end, seqs); + for (i = 0; i < iSize; i++) + { + Iterator blocks = alignment.getHiddenColumns() + .getVisContigsIterator(start, end + 1, false); + selection[i] = seqs[i].getSequenceStringFromIterator(blocks); + } } else { @@ -1771,10 +1896,10 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (start == 0) { - start = hidden.adjustForHiddenColumns(start); + start = hidden.visibleToAbsoluteColumn(start); } - end = hidden.getHiddenBoundaryRight(start); + end = hidden.getNextHiddenBoundary(false, start); if (start == end) { end = max; @@ -1789,8 +1914,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (hidden != null && hidden.hasHiddenColumns()) { - start = hidden.adjustForHiddenColumns(end); - start = hidden.getHiddenBoundaryLeft(start) + 1; + start = hidden.visibleToAbsoluteColumn(end); + start = hidden.getNextHiddenBoundary(true, start) + 1; } } while (end < max); @@ -1812,13 +1937,13 @@ public abstract class AlignmentViewport implements AlignViewportI, AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( - selectionGroup.getStartRes(), - selectionGroup.getEndRes(), clone); + clone.makeVisibleAnnotation( + selectionGroup.getStartRes(), selectionGroup.getEndRes(), + alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@ -1885,7 +2010,6 @@ public abstract class AlignmentViewport implements AlignViewportI, updateAllColourSchemes(); calculator.restartWorkers(); - // alignment.adjustSequenceAnnotations(); } /** @@ -2004,8 +2128,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { gapcounts = new AlignmentAnnotation("Occupancy", MessageManager.getString("label.occupancy_descr"), - new Annotation[1], 0f, - alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, alignment.getHeight(), + AlignmentAnnotation.BAR_GRAPH); gapcounts.hasText = true; gapcounts.autoCalculated = true; gapcounts.scaleColLabel = true; @@ -2023,8 +2147,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { conservation = new AlignmentAnnotation("Conservation", MessageManager.formatMessage("label.conservation_descr", - getConsPercGaps()), new Annotation[1], - 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + getConsPercGaps()), + new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; alignment.addAnnotation(conservation); @@ -2145,6 +2269,9 @@ public abstract class AlignmentViewport implements AlignViewportI, boolean showprf = isShowSequenceLogo(); boolean showConsHist = isShowConsensusHistogram(); boolean normLogo = isNormaliseSequenceLogo(); + boolean showHMMPrf = isShowHMMSequenceLogo(); + boolean showInfoHist = isShowInformationHistogram(); + boolean normHMMLogo = isNormaliseHMMSequenceLogo(); /** * TODO reorder the annotation rows according to group/sequence ordering on @@ -2182,6 +2309,9 @@ public abstract class AlignmentViewport implements AlignViewportI, sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); sg.setNormaliseSequenceLogo(normLogo); + sg.setShowHMMSequenceLogo(showHMMPrf); + sg.setShowInformationHistogram(showInfoHist); + sg.setNormaliseHMMSequenceLogo(normHMMLogo); } if (conv) { @@ -2504,8 +2634,8 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle = new ViewStyle(settingsForView); if (residueShading != null) { - residueShading.setConservationApplied(settingsForView - .isConservationColourSelected()); + residueShading.setConservationApplied( + settingsForView.isConservationColourSelected()); } } @@ -2673,7 +2803,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return sortAnnotationsBy; } - public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + public void setSortAnnotationsBy( + SequenceAnnotationOrder sortAnnotationsBy) { this.sortAnnotationsBy = sortAnnotationsBy; } @@ -2751,8 +2882,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return 0; } boolean iAmProtein = !getAlignment().isNucleotide(); - AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement - .getAlignment(); + AlignmentI proteinAlignment = iAmProtein ? getAlignment() + : complement.getAlignment(); if (proteinAlignment == null) { return 0; @@ -2783,7 +2914,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ int lastSeq = alignment.getHeight() - 1; List seqMappings = null; - for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + for (int seqNo = ranges + .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2794,9 +2926,9 @@ public abstract class AlignmentViewport implements AlignViewportI, { continue; } - seqMappings = MappingUtils - .findMappingsForSequenceAndOthers(sequence, mappings, - getCodingComplement().getAlignment().getSequences()); + seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence, + mappings, + getCodingComplement().getAlignment().getSequences()); if (!seqMappings.isEmpty()) { break; @@ -2879,6 +3011,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ private SearchResultsI searchResults = null; + protected TreeModel currentTree = null; + @Override public boolean hasSearchResults() { @@ -2896,6 +3030,156 @@ public abstract class AlignmentViewport implements AlignViewportI, { return searchResults; } - + /** + * get the consensus sequence as displayed under the PID consensus annotation + * row. + * + * @return consensus sequence as a new sequence object + */ + public SequenceI getConsensusSeq() + { + if (consensus == null) + { + updateConsensus(null); + } + if (consensus == null) + { + return null; + } + StringBuffer seqs = new StringBuffer(); + for (int i = 0; i < consensus.annotations.length; i++) + { + Annotation annotation = consensus.annotations[i]; + if (annotation != null) + { + String description = annotation.description; + if (description != null && description.startsWith("[")) + { + // consensus is a tie - just pick the first one + seqs.append(description.charAt(1)); + } + else + { + seqs.append(annotation.displayCharacter); + } + } + } + + SequenceI sq = new Sequence("Consensus", seqs.toString()); + sq.setDescription("Percentage Identity Consensus " + + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); + return sq; + } + + public boolean hasReferenceAnnotation() + { + AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation(); + for (AlignmentAnnotation annot : annots) + { + if ("RF".equals(annot.label) || annot.label.contains("Reference")) + { + return true; + } + } + return false; + } + + @Override + public void setCurrentTree(TreeModel tree) + { + currentTree = tree; + } + + @Override + public TreeModel getCurrentTree() + { + return currentTree; + } + + @Override + public boolean isNormaliseSequenceLogo() + { + return normaliseSequenceLogo; + } + + public void setNormaliseSequenceLogo(boolean state) + { + normaliseSequenceLogo = state; + } + + @Override + public boolean isNormaliseHMMSequenceLogo() + { + return hmmNormaliseSequenceLogo; + } + + public void setNormaliseHMMSequenceLogo(boolean state) + { + hmmNormaliseSequenceLogo = state; + } + + /** + * flag set to indicate if structure views might be out of sync with sequences + * in the alignment + */ + + private boolean needToUpdateStructureViews = false; + + @Override + public boolean isUpdateStructures() + { + return needToUpdateStructureViews; + } + + @Override + public void setUpdateStructures(boolean update) + { + needToUpdateStructureViews = update; + } + + @Override + public boolean needToUpdateStructureViews() + { + boolean update = needToUpdateStructureViews; + needToUpdateStructureViews = false; + return update; + } + + @Override + public void addSequenceGroup(SequenceGroup sequenceGroup) + { + alignment.addGroup(sequenceGroup); + + Color col = sequenceGroup.idColour; + if (col != null) + { + col = col.brighter(); + + for (SequenceI sq : sequenceGroup.getSequences()) + { + setSequenceColour(sq, col); + } + } + + if (codingComplement != null) + { + SequenceGroup mappedGroup = MappingUtils + .mapSequenceGroup(sequenceGroup, this, codingComplement); + if (mappedGroup.getSequences().size() > 0) + { + codingComplement.getAlignment().addGroup(mappedGroup); + + if (col != null) + { + for (SequenceI seq : mappedGroup.getSequences()) + { + codingComplement.setSequenceColour(seq, col); + } + } + } + // propagate the structure view update flag according to our own setting + codingComplement.setUpdateStructures(needToUpdateStructureViews); + } + } }