X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=efce038fde607092cbcf8ff3c05ff1d5ec9b02e0;hb=36244a2f01fed95c198b8f8c84b6f0020f679b66;hp=743c8dd5f8baa122df4d80400e563256af0c3a7d;hpb=b45345a4ee49f07b6f66e80535ca5f140a954e41;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 743c8dd..efce038 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -51,9 +51,6 @@ public class AlignViewport boolean renderGaps = true; boolean showSequenceFeatures = false; boolean showAnnotation = true; - boolean showConservation = true; - boolean showQuality = true; - boolean showIdentity = true; boolean colourAppliesToAllGroups = true; ColourSchemeI globalColourScheme = null; boolean conservationColourSelected = false; @@ -112,13 +109,6 @@ public class AlignViewport boolean gatherViewsHere = false; - - public AlignViewport(AlignmentI al, boolean dataset) - { - isDataset = dataset; - setAlignment(al); - init(); - } /** * Creates a new AlignViewport object. * @@ -155,14 +145,10 @@ public class AlignViewport showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true); showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true); - showConservation = Cache.getDefault("SHOW_CONSERVATION", true); - - showQuality = Cache.getDefault("SHOW_QUALITY", true); - showIdentity = Cache.getDefault("SHOW_IDENTITY", true); autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true); - padGaps = Cache.getDefault("PAD_GAPS", false); + padGaps = Cache.getDefault("PAD_GAPS", true); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ; @@ -181,7 +167,6 @@ public class AlignViewport setFont(new Font(fontName, style, Integer.parseInt(fontSize))); - alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) ); @@ -199,12 +184,13 @@ public class AlignViewport AlignmentAnnotation.BAR_GRAPH); conservation.hasText = true; - if (showConservation) + + if (Cache.getDefault("SHOW_CONSERVATION", true)) { alignment.addAnnotation(conservation); } - if (showQuality) + if (Cache.getDefault("SHOW_QUALITY", true)) { quality = new AlignmentAnnotation("Quality", "Alignment Quality based on Blosum62 scores", @@ -212,6 +198,7 @@ public class AlignViewport 0f, 11f, AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; alignment.addAnnotation(quality); } @@ -222,11 +209,10 @@ public class AlignViewport AlignmentAnnotation.BAR_GRAPH); consensus.hasText = true; - if (showIdentity) + if (Cache.getDefault("SHOW_IDENTITY", true)) { alignment.addAnnotation(consensus); } - } if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -278,24 +264,22 @@ public class AlignViewport { try { - long t = System.currentTimeMillis(); + int alWidth = alignment.getWidth(); + if(alWidth<0) + return; Conservation cons = new jalview.analysis.Conservation("All", jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); + alignment.getSequences(), 0, alWidth -1); cons.calculate(); cons.verdict(false, ConsPercGaps); - if (showQuality) + if (quality!=null) { cons.findQuality(); } - System.out.println("Conservation took " + (System.currentTimeMillis() - t) + - "ms"); - - int alWidth = alignment.getWidth(); String sequence = cons.getConsSequence().getSequence(); float minR; float minG; @@ -319,8 +303,9 @@ public class AlignViewport conservation.annotations = new Annotation[alWidth]; - if (showQuality) + if (quality!=null) { + quality.graphMax = cons.qualityRange[1].floatValue(); quality.annotations = new Annotation[alWidth]; qmin = cons.qualityRange[0].floatValue(); qmax = cons.qualityRange[1].floatValue(); @@ -349,7 +334,7 @@ public class AlignViewport minB + (maxB * vprop))); // Quality calc - if (showQuality) + if (quality!=null) { value = ( (Double) cons.quality.get(i)).floatValue(); vprop = value - qmin; @@ -361,16 +346,13 @@ public class AlignViewport minB + (maxB * vprop))); } } - - if (quality != null) - { - quality.graphMax = cons.qualityRange[1].floatValue(); - } } catch (OutOfMemoryError error) { javax.swing.SwingUtilities.invokeLater(new Runnable() { + + public void run() { javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -382,6 +364,9 @@ public class AlignViewport } }); + conservation = null; + quality = null; + System.out.println("Conservation calculation: " + error); System.gc(); @@ -396,9 +381,9 @@ public class AlignViewport } - ConservationThread conservationThread; + static ConservationThread conservationThread; - ConsensusThread consensusThread; + static ConsensusThread consensusThread; boolean consUpdateNeeded = false; @@ -409,42 +394,49 @@ public class AlignViewport /** * DOCUMENT ME! */ - public void updateConservation(AlignmentPanel ap) + public void updateConservation(final AlignmentPanel ap) { - if (alignment.isNucleotide()) + if (alignment.isNucleotide() || conservation==null) return; updatingConservation = true; - - if (conservationThread == null || !conservationThread.isAlive()) - { - conservationThread = new ConservationThread(ap); - conservationThread.start(); - } - else - { - consUpdateNeeded = true; - System.out.println("come back later"); - } + // javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { + while (conservationThread != null && conservationThread.isAlive()) + { + try + { + // Thread.sleep(100); + ap.repaint(); + } + catch (Exception ex) + {} + } + conservationThread = new ConservationThread(ap); + conservationThread.start(); + // } }); } /** * DOCUMENT ME! */ - public void updateConsensus(AlignmentPanel ap) + public void updateConsensus(final AlignmentPanel ap) { updatingConsensus = true; - if (consensusThread == null || !consensusThread.isAlive()) - { - consensusThread = new ConsensusThread(ap); - consensusThread.start(); - } - else - { - consUpdateNeeded = true; - System.out.println("come back later"); - } + // javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { + while (consensusThread != null && consensusThread.isAlive()) + { + try + { + // Thread.sleep(100); + ap.repaint(); + } + catch (Exception ex) + {} + } + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + // } }); } @@ -460,20 +452,19 @@ public class AlignViewport try { int aWidth = alignment.getWidth(); + if(aWidth<0) + return; consensus.annotations = null; consensus.annotations = new Annotation[aWidth]; - long t = System.currentTimeMillis(); + hconsensus = new Hashtable[aWidth]; AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment.getWidth(), hconsensus); - System.out.println("Consensus took " + - (System.currentTimeMillis() - t) + "ms"); - for (int i = 0; i < aWidth; i++) { float value = 0; @@ -504,6 +495,8 @@ public class AlignViewport } catch (OutOfMemoryError error) { + consensus = null; + hconsensus = null; javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() @@ -1503,4 +1496,63 @@ public class AlignViewport return sequenceSetID; } + public void alignmentChanged(AlignmentPanel ap) + { + if (padGaps) + alignment.padGaps(); + + if (hconsensus != null && autoCalculateConsensus) + { + updateConsensus(ap); + updateConservation(ap); + } + + resetAllColourSchemes(); + + alignment.adjustSequenceAnnotations(); + } + + + void resetAllColourSchemes() + { + ColourSchemeI cs = globalColourScheme; + if(cs!=null) + { + if (cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) cs). + resetClustalX(alignment.getSequences(), + alignment.getWidth()); + } + + cs.setConsensus(hconsensus); + if (cs.conservationApplied()) + { + Alignment al = (Alignment) alignment; + Conservation c = new Conservation("All", + ResidueProperties.propHash, 3, + al.getSequences(), 0, + al.getWidth() - 1); + c.calculate(); + c.verdict(false, ConsPercGaps); + + cs.setConservation(c); + } + } + + int s, sSize = alignment.getGroups().size(); + for(s=0; s