X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=a9334ff46e15ac0c93d85b0ba4ca33ad5c0936b8;hb=b3eead416d4a16141910b7dae1eda4eaf2272b6a;hp=ca32ee759b06087939e9eac5ef8ea61a8957b6b9;hpb=0356abc2cb7040672bc8fde68cafb77a2d623b5d;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index ca32ee7..a9334ff 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -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; @@ -101,6 +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) { @@ -588,7 +610,7 @@ public abstract class AlignmentViewport * alignment */ protected boolean isDataset = false; - + public void setDataset(boolean b) { isDataset = b; @@ -610,7 +632,7 @@ public abstract class AlignmentViewport protected boolean ignoreGapsInConsensusCalculation = false; protected ResidueShaderI residueShading = new ResidueShader(); - + @Override public void setGlobalColourScheme(ColourSchemeI cs) { @@ -662,7 +684,8 @@ public abstract class AlignmentViewport * retain any colour thresholds per group while * changing choice of colour scheme (JAL-2386) */ - sg.setColourScheme(cs.getInstance(sg, hiddenRepSequences)); + sg.setColourScheme( + cs == null ? null : cs.getInstance(this, sg)); if (cs != null) { sg.getGroupColourScheme().alignmentChanged(sg, @@ -683,7 +706,7 @@ public abstract class AlignmentViewport { return residueShading; } - + protected AlignmentAnnotation consensus; protected AlignmentAnnotation complementConsensus; @@ -717,7 +740,7 @@ public abstract class AlignmentViewport protected Hashtable[] hStrucConsensus = null; protected Conservation hconservation = null; - + @Override public void setConservation(Conservation cons) { @@ -755,6 +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; @@ -883,6 +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) { @@ -946,6 +991,7 @@ public abstract class AlignmentViewport strucConsensus = null; conservation = null; quality = null; + consensusProfiles = null; groupConsensus = null; groupConservation = null; hconsensus = null; @@ -1001,6 +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 @@ -1010,6 +1071,15 @@ public abstract class AlignmentViewport } /** + * @return the showInformationProfile + */ + @Override + public boolean isShowHMMSequenceLogo() + { + return hmmShowSequenceLogo; + } + + /** * @param showSequenceLogo * the new value */ @@ -1027,6 +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 @@ -1037,6 +1119,14 @@ public abstract class AlignmentViewport } /** + * @param showInformationHistogram + */ + public void setShowInformationHistogram(boolean showInformationHistogram) + { + this.hmmShowHistogram = showInformationHistogram; + } + + /** * @return the showGroupConservation */ public boolean isShowGroupConservation() @@ -1082,6 +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; @@ -1237,7 +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; @@ -1294,6 +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( @@ -1636,6 +1758,7 @@ public abstract class AlignmentViewport public void invertColumnSelection() { colSel.invertColumnSelection(0, alignment.getWidth(), alignment); + isColSelChanged(true); } @Override @@ -1887,7 +2010,6 @@ public abstract class AlignmentViewport updateAllColourSchemes(); calculator.restartWorkers(); - // alignment.adjustSequenceAnnotations(); } /** @@ -1940,6 +2062,7 @@ public abstract class AlignmentViewport MessageManager.getString("label.consensus_descr"), new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); + initGapCounts(); initComplementConsensus(); @@ -2146,6 +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 @@ -2183,6 +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) { @@ -2714,6 +2843,30 @@ public abstract class AlignmentViewport viewStyle.setProteinFontAsCdna(b); } + @Override + public void setShowComplementFeatures(boolean b) + { + viewStyle.setShowComplementFeatures(b); + } + + @Override + public boolean isShowComplementFeatures() + { + return viewStyle.isShowComplementFeatures(); + } + + @Override + public void setShowComplementFeaturesOnTop(boolean b) + { + viewStyle.setShowComplementFeaturesOnTop(b); + } + + @Override + public boolean isShowComplementFeaturesOnTop() + { + return viewStyle.isShowComplementFeaturesOnTop(); + } + /** * @return true if view should scroll to show the highlighted region of a * sequence @@ -2943,6 +3096,19 @@ public abstract class AlignmentViewport 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) { @@ -2954,4 +3120,132 @@ public abstract class AlignmentViewport { 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); + } + } + + /** + * Filters out sequences with an eValue higher than the specified value. The + * filtered sequences are hidden or deleted. Sequences with no eValues are also + * filtered out. + * + * @param eValue + * @param delete + */ + public void filterByEvalue(double eValue) + { + for (SequenceI seq : alignment.getSequencesArray()) + { + if ((seq.getAnnotation("Search Scores") == null + || seq.getAnnotation("Search Scores")[0].getEValue() > eValue) + && seq.getHMM() == null) + { + hideSequence(new SequenceI[] { seq }); + } + } + } + + /** + * Filters out sequences with an score lower than the specified value. The + * filtered sequences are hidden or deleted. + * + * @param score + * @param delete + */ + public void filterByScore(double score) + { + for (SequenceI seq : alignment.getSequencesArray()) + { + if ((seq.getAnnotation("Search Scores") == null + || seq.getAnnotation("Search Scores")[0] + .getBitScore() < score) + && seq.getHMM() == null) + { + hideSequence(new SequenceI[] { seq }); + } + } + } }