X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=23c1d003cdcb2a327b363b39496a7c56ddc19057;hb=6c7cac79652fa6c7050311f73f36b9a9d05e6a6b;hp=b260cabf12784ba6c5c62304b57c66ea4ff412d1;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index b260cab..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; @@ -56,6 +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; @@ -66,6 +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; @@ -79,7 +82,7 @@ import java.util.Map; public abstract class AlignmentViewport implements AlignViewportI, CommandListener, VamsasSource { - final protected ViewportRanges ranges; + protected ViewportRanges ranges; protected ViewStyleI viewStyle = new ViewStyle(); @@ -99,6 +102,27 @@ public abstract class AlignmentViewport * 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) { @@ -586,7 +610,7 @@ public abstract class AlignmentViewport * alignment */ protected boolean isDataset = false; - + public void setDataset(boolean b) { isDataset = b; @@ -608,7 +632,7 @@ public abstract class AlignmentViewport protected boolean ignoreGapsInConsensusCalculation = false; protected ResidueShaderI residueShading = new ResidueShader(); - + @Override public void setGlobalColourScheme(ColourSchemeI cs) { @@ -660,7 +684,8 @@ public abstract class AlignmentViewport * 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, @@ -681,7 +706,7 @@ public abstract class AlignmentViewport { return residueShading; } - + protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; @@ -715,7 +740,7 @@ public abstract class AlignmentViewport protected Hashtable[] hStrucConsensus = null; protected Conservation hconservation = null; - + @Override public void setConservation(Conservation cons) { @@ -753,6 +778,18 @@ public abstract class AlignmentViewport } @Override + public void setHmmProfiles(ProfilesI info) + { + hmmProfiles = info; + } + + @Override + public ProfilesI getHmmProfiles() + { + return hmmProfiles; + } + + @Override public Hashtable[] getComplementConsensusHash() { return hcomplementConsensus; @@ -881,6 +918,16 @@ public abstract class AlignmentViewport } } + @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) { @@ -944,14 +991,19 @@ public abstract class AlignmentViewport 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); } @@ -995,6 +1047,21 @@ public abstract class AlignmentViewport 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 @@ -1004,6 +1071,15 @@ public abstract class AlignmentViewport } /** + * @return the showInformationProfile + */ + @Override + public boolean isShowHMMSequenceLogo() + { + return hmmShowSequenceLogo; + } + + /** * @param showSequenceLogo * the new value */ @@ -1021,6 +1097,18 @@ public abstract class AlignmentViewport 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 @@ -1031,6 +1119,14 @@ public abstract class AlignmentViewport } /** + * @param showInformationHistogram + */ + public void setShowInformationHistogram(boolean showInformationHistogram) + { + this.hmmShowHistogram = showInformationHistogram; + } + + /** * @return the showGroupConservation */ public boolean isShowGroupConservation() @@ -1076,6 +1172,17 @@ public abstract class AlignmentViewport } /** + * + * @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; @@ -1231,7 +1338,16 @@ public abstract class AlignmentViewport ignoreGapsInConsensusCalculation); } } + } + public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap) + { + ignoreBelowBackGroundFrequencyCalculation = b; + } + + public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap) + { + infoLetterHeight = b; } private long sgrouphash = -1, colselhash = -1; @@ -1288,6 +1404,18 @@ public abstract class AlignmentViewport 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( @@ -1333,7 +1461,10 @@ public abstract class AlignmentViewport public void removePropertyChangeListener( java.beans.PropertyChangeListener listener) { - changeSupport.removePropertyChangeListener(listener); + if (changeSupport != null) + { + changeSupport.removePropertyChangeListener(listener); + } } /** @@ -1627,6 +1758,7 @@ public abstract class AlignmentViewport public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1732,8 +1864,12 @@ public abstract class AlignmentViewport 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 { @@ -1760,10 +1896,10 @@ public abstract class AlignmentViewport { 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; @@ -1778,8 +1914,8 @@ public abstract class AlignmentViewport 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); @@ -1801,13 +1937,13 @@ public abstract class AlignmentViewport AlignmentAnnotation clone = new AlignmentAnnotation(annot); if (selectedOnly && selectionGroup != null) { - alignment.getHiddenColumns().makeVisibleAnnotation( + clone.makeVisibleAnnotation( selectionGroup.getStartRes(), selectionGroup.getEndRes(), - clone); + alignment.getHiddenColumns()); } else { - alignment.getHiddenColumns().makeVisibleAnnotation(clone); + clone.makeVisibleAnnotation(alignment.getHiddenColumns()); } ala.add(clone); } @@ -1874,7 +2010,6 @@ public abstract class AlignmentViewport updateAllColourSchemes(); calculator.restartWorkers(); - // alignment.adjustSequenceAnnotations(); } /** @@ -1927,6 +2062,7 @@ public abstract class AlignmentViewport MessageManager.getString("label.consensus_descr"), new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); + initGapCounts(); initComplementConsensus(); @@ -2133,6 +2269,9 @@ public abstract class AlignmentViewport 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 @@ -2170,6 +2309,9 @@ public abstract class AlignmentViewport sg.setshowSequenceLogo(showprf); sg.setShowConsensusHistogram(showConsHist); sg.setNormaliseSequenceLogo(normLogo); + sg.setShowHMMSequenceLogo(showHMMPrf); + sg.setShowInformationHistogram(showInfoHist); + sg.setNormaliseHMMSequenceLogo(normHMMLogo); } if (conv) { @@ -2773,7 +2915,7 @@ public abstract class AlignmentViewport int lastSeq = alignment.getHeight() - 1; List seqMappings = null; for (int seqNo = ranges - .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++) + .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++) { sequence = getAlignment().getSequenceAt(seqNo); if (hiddenSequences != null && hiddenSequences.isHidden(sequence)) @@ -2869,6 +3011,8 @@ public abstract class AlignmentViewport */ private SearchResultsI searchResults = null; + protected TreeModel currentTree = null; + @Override public boolean hasSearchResults() { @@ -2927,4 +3071,115 @@ public abstract class AlignmentViewport + ((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); + } + } }