From f2b6ee8c1feb4f6a7e229ee94741ef93f0bd453d Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 30 May 2012 09:02:19 +0100 Subject: [PATCH] formatting --- src/jalview/viewmodel/AlignmentViewport.java | 198 +++++++++++++++----------- 1 file changed, 118 insertions(+), 80 deletions(-) diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index ae1a4fd..fc96f62 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -41,9 +41,11 @@ import java.util.Hashtable; import java.util.Vector; /** - * base class holding visualization and analysis attributes and common logic for an active alignment view displayed in the GUI + * base class holding visualization and analysis attributes and common logic for + * an active alignment view displayed in the GUI + * * @author jimp - * + * */ public abstract class AlignmentViewport implements AlignViewportI { @@ -55,7 +57,8 @@ public abstract class AlignmentViewport implements AlignViewportI protected String sequenceSetID; /** - * probably unused indicator that view is of a dataset rather than an alignment + * probably unused indicator that view is of a dataset rather than an + * alignment */ protected boolean isDataset = false; @@ -63,13 +66,11 @@ public abstract class AlignmentViewport implements AlignViewportI protected ColumnSelection colSel = new ColumnSelection(); - public boolean autoCalculateConsensus = true; protected boolean autoCalculateStrucConsensus = true; protected boolean ignoreGapsInConsensusCalculation = false; - protected ColourSchemeI globalColourScheme = null; @@ -84,7 +85,6 @@ public abstract class AlignmentViewport implements AlignViewportI return globalColourScheme; } - protected AlignmentAnnotation consensus; protected AlignmentAnnotation strucConsensus; @@ -97,22 +97,23 @@ public abstract class AlignmentViewport implements AlignViewportI protected AlignmentAnnotation[] groupConservation; - /** - * results of alignment consensus analysis for visible portion of view + /** + * results of alignment consensus analysis for visible portion of view */ - protected Hashtable[] hconsensus=null; + protected Hashtable[] hconsensus = null; /** - * results of secondary structure base pair consensus for visible portion of view + * results of secondary structure base pair consensus for visible portion of + * view */ - protected Hashtable[] hStrucConsensus=null; + protected Hashtable[] hStrucConsensus = null; /** - * percentage gaps allowed in a column before all amino acid properties should be considered unconserved + * percentage gaps allowed in a column before all amino acid properties should + * be considered unconserved */ int ConsPercGaps = 25; // JBPNote : This should be a scalable property! - public int getConsPercGaps() { return ConsPercGaps; @@ -120,8 +121,8 @@ public abstract class AlignmentViewport implements AlignViewportI @Override public void setSequenceConsensusHash(Hashtable[] hconsensus) { - this.hconsensus=hconsensus; - + this.hconsensus = hconsensus; + } @Override @@ -135,12 +136,14 @@ public abstract class AlignmentViewport implements AlignViewportI { return hStrucConsensus; } + @Override public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus) { - this.hStrucConsensus=hStrucConsensus; - + this.hStrucConsensus = hStrucConsensus; + } + @Override public AlignmentAnnotation getAlignmentQualityAnnot() { @@ -152,18 +155,20 @@ public abstract class AlignmentViewport implements AlignViewportI { return conservation; } + @Override public AlignmentAnnotation getAlignmentConsensusAnnotation() { return consensus; } + @Override public AlignmentAnnotation getAlignmentStrucConsensusAnnotation() { return strucConsensus; } - - protected AlignCalcManagerI calculator=new AlignCalcManager(); + + protected AlignCalcManagerI calculator = new AlignCalcManager(); /** * trigger update of conservation annotation @@ -176,9 +181,11 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - if (!calculator.startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)) + if (!calculator + .startRegisteredWorkersOfClass(jalview.workers.ConservationThread.class)) { - calculator.registerWorker(new jalview.workers.ConservationThread(this, ap)); + calculator.registerWorker(new jalview.workers.ConservationThread( + this, ap)); } } @@ -201,9 +208,10 @@ public abstract class AlignmentViewport implements AlignViewportI // --------START Structure Conservation public void updateStrucConsensus(final AlignmentViewPanel ap) { - if (autoCalculateStrucConsensus && strucConsensus==null && alignment.isNucleotide() && alignment.hasRNAStructure()) + if (autoCalculateStrucConsensus && strucConsensus == null + && alignment.isNucleotide() && alignment.hasRNAStructure()) { - + } // see note in mantis : issue number 8585 @@ -211,9 +219,10 @@ public abstract class AlignmentViewport implements AlignViewportI { return; } - if (!calculator.startRegisteredWorkersOfClass(StrucConsensusThread.class)) + if (!calculator + .startRegisteredWorkersOfClass(StrucConsensusThread.class)) { - calculator.registerWorker(new StrucConsensusThread(this,ap)); + calculator.registerWorker(new StrucConsensusThread(this, ap)); } } @@ -229,16 +238,18 @@ public abstract class AlignmentViewport implements AlignViewportI return false; if (calculator.workingInvolvedWith(alignmentAnnotation)) { -// System.err.println("grey out ("+alignmentAnnotation.label+")"); + // System.err.println("grey out ("+alignmentAnnotation.label+")"); return true; } return false; } + @Override public boolean isClosed() { - // TODO: check that this isClosed is only true after panel is closed, not before it is fully constructed. - return alignment==null; + // TODO: check that this isClosed is only true after panel is closed, not + // before it is fully constructed. + return alignment == null; } @Override @@ -418,9 +429,10 @@ public abstract class AlignmentViewport implements AlignViewportI { return colSel; } + public void setColumnSelection(ColumnSelection colSel) { - this.colSel=colSel; + this.colSel = colSel; } public Hashtable getHiddenRepSequences() { @@ -434,12 +446,13 @@ public abstract class AlignmentViewport implements AlignViewportI public void updateHiddenColumns() { - hasHiddenColumns = colSel.getHiddenColumns() != null; + hasHiddenColumns = colSel.getHiddenColumns() != null; } - + protected boolean hasHiddenRows = false; - - public boolean hasHiddenRows() { + + public boolean hasHiddenRows() + { return hasHiddenRows; } @@ -447,12 +460,14 @@ public abstract class AlignmentViewport implements AlignViewportI public void setSequenceSetId(String newid) { - if (sequenceSetID!=null) + 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); + sequenceSetID = new String(newid); } + public String getSequenceSetId() { if (sequenceSetID == null) @@ -462,6 +477,7 @@ public abstract class AlignmentViewport implements AlignViewportI return sequenceSetID; } + /** * unique viewId for synchronizing state (e.g. with stored Jalview Project) * @@ -476,17 +492,22 @@ public abstract class AlignmentViewport implements AlignViewportI } return viewId; } + public void setIgnoreGapsConsensus(boolean b, AlignmentViewPanel ap) { ignoreGapsInConsensusCalculation = b; - if (ap!=null) {updateConsensus(ap); - if (globalColourScheme != null) + if (ap != null) { - globalColourScheme.setThreshold(globalColourScheme.getThreshold(), - ignoreGapsInConsensusCalculation); - }} - + updateConsensus(ap); + if (globalColourScheme != null) + { + globalColourScheme.setThreshold(globalColourScheme.getThreshold(), + ignoreGapsInConsensusCalculation); + } + } + } + private long sgrouphash = -1, colselhash = -1; /** @@ -541,7 +562,7 @@ public abstract class AlignmentViewport implements AlignViewportI return ignoreGapsInConsensusCalculation; } - /// property change stuff + // / property change stuff // JBPNote Prolly only need this in the applet version. private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( @@ -661,7 +682,8 @@ public abstract class AlignmentViewport implements AlignViewportI hiddenRepSequences = null; firePropertyChange("alignment", null, alignment.getSequences()); - // used to set hasHiddenRows/hiddenRepSequences here, after the property changed event + // used to set hasHiddenRows/hiddenRepSequences here, after the property + // changed event sendSelection(); } } @@ -682,7 +704,8 @@ public abstract class AlignmentViewport implements AlignViewportI { selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false); } - // JBPNote: refactor: only update flag if we modified visiblity (used to do this regardless) + // JBPNote: refactor: only update flag if we modified visiblity (used to + // do this regardless) if (alignment.getHiddenSequences().getSize() < 1) { hasHiddenRows = false; @@ -752,7 +775,7 @@ public abstract class AlignmentViewport implements AlignViewportI seqs[index++] = sg.getSequenceAt(i); } } - sg.setSeqrep(repSequence); // note: not done in 2.7applet + sg.setSeqrep(repSequence); // note: not done in 2.7applet sg.setHidereps(true); // note: not done in 2.7applet hideSequence(seqs); @@ -761,11 +784,13 @@ public abstract class AlignmentViewport implements AlignViewportI public boolean isHiddenRepSequence(SequenceI seq) { return hiddenRepSequences != null - && hiddenRepSequences.containsKey(seq); + && hiddenRepSequences.containsKey(seq); } + public SequenceGroup getRepresentedSequences(SequenceI seq) { - return (SequenceGroup) (hiddenRepSequences == null ? null : hiddenRepSequences.get(seq)); + return (SequenceGroup) (hiddenRepSequences == null ? null + : hiddenRepSequences.get(seq)); } public int adjustForHiddenSeqs(int alignmentIndex) @@ -786,7 +811,6 @@ public abstract class AlignmentViewport implements AlignViewportI colSel.invertColumnSelection(0, alignment.getWidth()); } - /** * This method returns an array of new SequenceI objects derived from the * whole alignment or just the current selection with start and end points @@ -799,8 +823,11 @@ public abstract class AlignmentViewport implements AlignViewportI public SequenceI[] getSelectionAsNewSequence() { SequenceI[] sequences; - // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - this was the only caller in the applet for this method - // JBPNote: in applet, this method returned references to the alignment sequences, and it did not honour the presence/absence of annotation attached to the alignment (probably!) + // JBPNote: Need to test jalviewLite.getSelectedSequencesAsAlignmentFrom - + // this was the only caller in the applet for this method + // JBPNote: in applet, this method returned references to the alignment + // sequences, and it did not honour the presence/absence of annotation + // attached to the alignment (probably!) if (selectionGroup == null) { sequences = alignment.getSequencesArray(); @@ -821,7 +848,6 @@ public abstract class AlignmentViewport implements AlignViewportI return sequences; } - /** * get the currently selected sequence objects or all the sequences in the * alignment. @@ -937,11 +963,13 @@ public abstract class AlignmentViewport implements AlignViewportI return selection; } - /** * return visible region boundaries within given column range - * @param min first column (inclusive, from 0) - * @param max last column (exclusive) + * + * @param min + * first column (inclusive, from 0) + * @param max + * last column (exclusive) * @return int[][] range of {start,end} visible positions */ public int[][] getVisibleRegionBoundaries(int min, int max) @@ -994,15 +1022,20 @@ public abstract class AlignmentViewport implements AlignViewportI { return padGaps; } + /** - * @param padGaps the padGaps to set + * @param padGaps + * the padGaps to set */ public void setPadGaps(boolean padGaps) { this.padGaps = padGaps; } + /** - * apply any post-edit constraints and trigger any calculations needed after an edit has been performed on the alignment + * apply any post-edit constraints and trigger any calculations needed after + * an edit has been performed on the alignment + * * @param ap */ public void alignmentChanged(AlignmentViewPanel ap) @@ -1100,48 +1133,53 @@ public abstract class AlignmentViewport implements AlignViewportI { if (showConservation) { - if (conservation==null) - { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + getConsPercGaps() - + "% gaps", new Annotation[1], 0f, 11f, - AlignmentAnnotation.BAR_GRAPH); - conservation.hasText = true; - conservation.autoCalculated = true; - alignment.addAnnotation(conservation); - } + if (conservation == null) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + + getConsPercGaps() + "% gaps", + new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + conservation.autoCalculated = true; + alignment.addAnnotation(conservation); + } } if (showQuality) { - if (quality==null) + if (quality == null) { - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH); - quality.hasText = true; - quality.autoCalculated = true; - alignment.addAnnotation(quality); + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], 0f, 11f, + AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + quality.autoCalculated = true; + alignment.addAnnotation(quality); + } } - } - } else { + } + else + { if (alignment.hasRNAStructure()) { strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID", - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); strucConsensus.hasText = true; strucConsensus.autoCalculated = true; } } - + consensus = new AlignmentAnnotation("Consensus", "PID", new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; consensus.autoCalculated = true; - + if (showConsensus) { alignment.addAnnotation(consensus); - if (strucConsensus!=null) + if (strucConsensus != null) { alignment.addAnnotation(strucConsensus); } -- 1.7.10.2