X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;fp=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=3702cd08e0bed7a98913f5ba3e826a0bd3db2e50;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=2881e8150261b33d066158fd6399ed0c6b270bb2;hpb=d1bb7a31fc091606aedbc255a5766ac79e36fa91;p=jalview.git diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 2881e81..3702cd0 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -77,8 +77,8 @@ 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; @@ -568,8 +568,6 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle.setSeqNameItalics(default1); } - - @Override public AlignmentI getAlignment() { @@ -666,8 +664,8 @@ public abstract class AlignmentViewport implements AlignViewportI, sg.setColourScheme(cs); if (cs != null) { - sg.getGroupColourScheme() - .alignmentChanged(sg, hiddenRepSequences); + sg.getGroupColourScheme().alignmentChanged(sg, + hiddenRepSequences); } } } @@ -676,8 +674,7 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public ColourSchemeI getGlobalColourScheme() { - return residueShading == null ? null : residueShading - .getColourScheme(); + return residueShading == null ? null : residueShading.getColourScheme(); } @Override @@ -825,11 +822,11 @@ 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)); } } @@ -843,7 +840,8 @@ 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)); } @@ -874,8 +872,8 @@ 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)); @@ -899,7 +897,8 @@ 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)); } @@ -1188,8 +1187,8 @@ 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); } @@ -1406,8 +1405,8 @@ 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); @@ -1430,8 +1429,8 @@ public abstract class AlignmentViewport implements AlignViewportI, int startSeq = ranges.getStartSeq(); int endSeq = ranges.getEndSeq(); - List tmp = alignment.getHiddenSequences().showSequence( - index, hiddenRepSequences); + List tmp = alignment.getHiddenSequences().showSequence(index, + hiddenRepSequences); if (tmp.size() > 0) { if (selectionGroup == null) @@ -1511,8 +1510,8 @@ 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); @@ -1602,8 +1601,8 @@ public abstract class AlignmentViewport implements AlignViewportI, */ public boolean isHiddenRepSequence(SequenceI seq) { - return (hiddenRepSequences != null && hiddenRepSequences - .containsKey(seq)); + return (hiddenRepSequences != null + && hiddenRepSequences.containsKey(seq)); } /** @@ -1621,8 +1620,8 @@ public abstract class AlignmentViewport implements AlignViewportI, @Override public int adjustForHiddenSeqs(int alignmentIndex) { - return alignment.getHiddenSequences().adjustForHiddenSeqs( - alignmentIndex); + return alignment.getHiddenSequences() + .adjustForHiddenSeqs(alignmentIndex); } @Override @@ -1692,10 +1691,10 @@ 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 @@ -1741,8 +1740,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (alignment.getHiddenColumns() != null && alignment.getHiddenColumns().hasHiddenColumns()) { - selection = alignment.getHiddenColumns().getVisibleSequenceStrings( - start, end, seqs); + selection = alignment.getHiddenColumns() + .getVisibleSequenceStrings(start, end, seqs); } else { @@ -1811,8 +1810,8 @@ public abstract class AlignmentViewport implements AlignViewportI, if (selectedOnly && selectionGroup != null) { alignment.getHiddenColumns().makeVisibleAnnotation( - selectionGroup.getStartRes(), - selectionGroup.getEndRes(), clone); + selectionGroup.getStartRes(), selectionGroup.getEndRes(), + clone); } else { @@ -2001,8 +2000,8 @@ 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; @@ -2020,8 +2019,8 @@ 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); @@ -2501,8 +2500,8 @@ public abstract class AlignmentViewport implements AlignViewportI, viewStyle = new ViewStyle(settingsForView); if (residueShading != null) { - residueShading.setConservationApplied(settingsForView - .isConservationColourSelected()); + residueShading.setConservationApplied( + settingsForView.isConservationColourSelected()); } } @@ -2670,7 +2669,8 @@ public abstract class AlignmentViewport implements AlignViewportI, return sortAnnotationsBy; } - public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy) + public void setSortAnnotationsBy( + SequenceAnnotationOrder sortAnnotationsBy) { this.sortAnnotationsBy = sortAnnotationsBy; } @@ -2748,8 +2748,8 @@ 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; @@ -2780,7 +2780,8 @@ 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)) @@ -2791,9 +2792,9 @@ 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; @@ -2928,7 +2929,7 @@ public abstract class AlignmentViewport implements AlignViewportI, } } } - + SequenceI sq = new Sequence("Consensus", seqs.toString()); sq.setDescription("Percentage Identity Consensus " + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));