X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=9a08a2b7671a0559f93e7f756ba155fda9168e5d;hb=30f552046feaba47955d5ffdcec6d0fc67a7e13b;hp=eefad4a2b6ff5a990bbdf457ec829ae80c27b236;hpb=536a4a9c407a4c07b71e86e75135eaa2ba5e8850;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index eefad4a..9a08a2b 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -52,6 +52,7 @@ import jalview.structure.VamsasSource; import jalview.util.Comparison; import jalview.util.MapList; import jalview.util.MappingUtils; +import jalview.util.MessageManager; import jalview.viewmodel.styles.ViewStyle; import jalview.workers.AlignCalcManager; import jalview.workers.ComplementConsensusThread; @@ -91,9 +92,9 @@ public abstract class AlignmentViewport implements AlignViewportI, FeaturesDisplayedI featuresDisplayed = null; - protected Deque historyList = new ArrayDeque(); + protected Deque historyList = new ArrayDeque<>(); - protected Deque redoList = new ArrayDeque(); + protected Deque redoList = new ArrayDeque<>(); /** * alignment displayed in the viewport. Please use get/setter @@ -608,7 +609,7 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean ignoreGapsInConsensusCalculation = false; - protected ResidueShaderI residueShading; + protected ResidueShaderI residueShading = new ResidueShader(); @Override public void setGlobalColourScheme(ColourSchemeI cs) @@ -832,7 +833,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public void updateConsensus(final AlignmentViewPanel ap) { // see note in mantis : issue number 8585 - if ((consensus == null || gapcounts == null) || !autoCalculateConsensus) + if (consensus == null || !autoCalculateConsensus) { return; } @@ -1112,7 +1113,6 @@ public abstract class AlignmentViewport implements AlignViewportI, public void setHiddenColumns(HiddenColumns hidden) { this.alignment.setHiddenColumns(hidden); - // this.colSel = colsel; } @Override @@ -1159,7 +1159,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public boolean hasHiddenColumns() { - return colSel != null + return alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns(); } @@ -1295,7 +1295,9 @@ public abstract class AlignmentViewport implements AlignViewportI, protected boolean showConsensus = true; - private Map sequenceColours = new HashMap(); + protected boolean showOccupancy = true; + + private Map sequenceColours = new HashMap<>(); protected SequenceAnnotationOrder sortAnnotationsBy = null; @@ -1525,7 +1527,7 @@ public abstract class AlignmentViewport implements AlignViewportI, if (hiddenRepSequences == null) { - hiddenRepSequences = new Hashtable(); + hiddenRepSequences = new Hashtable<>(); } hiddenRepSequences.put(repSequence, sg); @@ -1733,7 +1735,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public List getVisibleRegionBoundaries(int min, int max) { - ArrayList regions = new ArrayList(); + ArrayList regions = new ArrayList<>(); int start = min; int end = max; @@ -1776,7 +1778,7 @@ public abstract class AlignmentViewport implements AlignViewportI, public List getVisibleAlignmentAnnotation( boolean selectedOnly) { - ArrayList ala = new ArrayList(); + ArrayList ala = new ArrayList<>(); AlignmentAnnotation[] aa; if ((aa = alignment.getAlignmentAnnotation()) != null) { @@ -1907,14 +1909,11 @@ public abstract class AlignmentViewport implements AlignViewportI, { initRNAStructure(); } - consensus = new AlignmentAnnotation("Consensus", "PID", + consensus = new AlignmentAnnotation("Consensus", + MessageManager.getString("label.consensus_descr"), new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(consensus); - gapcounts = new AlignmentAnnotation("Occupancy", - "Number of aligned positions", - new Annotation[1], 0f, alignment.getHeight(), - AlignmentAnnotation.BAR_GRAPH); - initGapCounts(gapcounts); + initGapCounts(); initComplementConsensus(); } @@ -1948,7 +1947,9 @@ public abstract class AlignmentViewport implements AlignViewportI, if (doConsensus) { complementConsensus = new AlignmentAnnotation("cDNA Consensus", - "PID for cDNA", new Annotation[1], 0f, 100f, + MessageManager + .getString("label.complement_consensus_descr"), + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); initConsensus(complementConsensus); return true; @@ -1971,15 +1972,20 @@ public abstract class AlignmentViewport implements AlignViewportI, // these should be extracted from the view model - style and settings for // derived annotation - private void initGapCounts(AlignmentAnnotation counts) + private void initGapCounts() { - counts.hasText = false; - counts.autoCalculated = true; - counts.graph = AlignmentAnnotation.BAR_GRAPH; - - if (showConsensus) + if (showOccupancy) { - alignment.addAnnotation(counts); + gapcounts = new AlignmentAnnotation("Occupancy", + MessageManager.getString("label.occupancy_descr"), + new Annotation[1], 0f, + alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH); + gapcounts.hasText = true; + gapcounts.autoCalculated = true; + gapcounts.scaleColLabel = true; + gapcounts.graph = AlignmentAnnotation.BAR_GRAPH; + + alignment.addAnnotation(gapcounts); } } @@ -1990,8 +1996,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (conservation == null) { conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " - + getConsPercGaps() + "% gaps", new Annotation[1], + MessageManager.formatMessage("label.conservation_descr", + getConsPercGaps()), new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; conservation.autoCalculated = true; @@ -2007,7 +2013,7 @@ public abstract class AlignmentViewport implements AlignViewportI, if (quality == null) { quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", + MessageManager.getString("label.quality_descr"), new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); quality.hasText = true; quality.autoCalculated = true; @@ -2020,7 +2026,8 @@ public abstract class AlignmentViewport implements AlignViewportI, { if (alignment.hasRNAStructure() && strucConsensus == null) { - strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", + strucConsensus = new AlignmentAnnotation("StrucConsensus", + MessageManager.getString("label.strucconsensus_descr"), new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); strucConsensus.hasText = true; strucConsensus.autoCalculated = true; @@ -2125,7 +2132,7 @@ public abstract class AlignmentViewport implements AlignViewportI, // intersect alignment annotation with alignment groups AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation(); - List oldrfs = new ArrayList(); + List oldrfs = new ArrayList<>(); if (aan != null) { for (int an = 0; an < aan.length; an++) @@ -2667,6 +2674,18 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setScaleProteinAsCdna(b); } + @Override + public boolean isProteinFontAsCdna() + { + return viewStyle.isProteinFontAsCdna(); + } + + @Override + public void setProteinFontAsCdna(boolean b) + { + viewStyle.setProteinFontAsCdna(b); + } + /** * @return true if view should scroll to show the highlighted region of a * sequence @@ -2826,8 +2845,7 @@ public abstract class AlignmentViewport implements AlignViewportI, selectionIsDefinedGroup = gps.contains(selectionGroup); } } - return selectionGroup.getContext() == alignment - || selectionIsDefinedGroup; + return selectionGroup.isDefined() || selectionIsDefinedGroup; } /** @@ -2852,4 +2870,45 @@ 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; + } }