X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=efce038fde607092cbcf8ff3c05ff1d5ec9b02e0;hb=36244a2f01fed95c198b8f8c84b6f0020f679b66;hp=07a745336b2b9c14e3404e494847151655d96f2d;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 07a7453..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) ); @@ -189,8 +174,45 @@ public class AlignViewport // as Blosum and Clustal require this to be done if(hconsensus==null && !isDataset) { - updateConservation(); - updateConsensus(); + if(!alignment.isNucleotide()) + { + conservation = new AlignmentAnnotation("Conservation", + "Conservation of total alignment less than " + + ConsPercGaps + "% gaps", + new Annotation[1], 0f, + 11f, + AlignmentAnnotation.BAR_GRAPH); + conservation.hasText = true; + + + if (Cache.getDefault("SHOW_CONSERVATION", true)) + { + alignment.addAnnotation(conservation); + } + + if (Cache.getDefault("SHOW_QUALITY", true)) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], + 0f, + 11f, + AlignmentAnnotation.BAR_GRAPH); + quality.hasText = true; + + alignment.addAnnotation(quality); + } + } + + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + + if (Cache.getDefault("SHOW_IDENTITY", true)) + { + alignment.addAnnotation(consensus); + } } if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -228,216 +250,278 @@ public class AlignViewport return showSequenceFeatures; } - /** - * DOCUMENT ME! - */ - public void updateConservation() - { - if(alignment.isNucleotide()) - return; - - // System.out.println("UPDATING CONSERVATION"); - - try{ - Conservation cons = new jalview.analysis.Conservation("All", - jalview.schemes.ResidueProperties.propHash, 3, - alignment.getSequences(), 0, alignment.getWidth() - 1); - cons.calculate(); - cons.verdict(false, ConsPercGaps); - cons.findQuality(); - - int alWidth = alignment.getWidth(); - Annotation[] annotations = new Annotation[alWidth]; - Annotation[] qannotations = new Annotation[alWidth]; - String sequence = cons.getConsSequence().getSequence(); - float minR; - float minG; - float minB; - float maxR; - float maxG; - float maxB; - minR = 0.3f; - minG = 0.0f; - minB = 0f; - maxR = 1.0f - minR; - maxG = 0.9f - minG; - maxB = 0f - minB; // scalable range for colouring both Conservation and Quality - - float min = 0f; - float max = 11f; - float qmin = cons.qualityRange[0].floatValue(); - float qmax = cons.qualityRange[1].floatValue(); - - for (int i = 0; i < alWidth; i++) + + + class ConservationThread extends Thread + { + AlignmentPanel ap; + public ConservationThread(AlignmentPanel ap) + { + this.ap = ap; + } + + public void run() + { + try { - float value = 0; + int alWidth = alignment.getWidth(); + if(alWidth<0) + return; + + Conservation cons = new jalview.analysis.Conservation("All", + jalview.schemes.ResidueProperties.propHash, 3, + alignment.getSequences(), 0, alWidth -1); - try + cons.calculate(); + cons.verdict(false, ConsPercGaps); + + if (quality!=null) { - value = Integer.parseInt(sequence.charAt(i) + ""); + cons.findQuality(); } - catch (Exception ex) + + String sequence = cons.getConsSequence().getSequence(); + float minR; + float minG; + float minB; + float maxR; + float maxG; + float maxB; + minR = 0.3f; + minG = 0.0f; + minB = 0f; + maxR = 1.0f - minR; + maxG = 0.9f - minG; + maxB = 0f - minB; // scalable range for colouring both Conservation and Quality + + float min = 0f; + float max = 11f; + float qmin = 0f; + float qmax = 0f; + + char c; + + conservation.annotations = new Annotation[alWidth]; + + if (quality!=null) { - if (sequence.charAt(i) == '*') - { + quality.graphMax = cons.qualityRange[1].floatValue(); + quality.annotations = new Annotation[alWidth]; + qmin = cons.qualityRange[0].floatValue(); + qmax = cons.qualityRange[1].floatValue(); + } + + for (int i = 0; i < alWidth; i++) + { + float value = 0; + + c = sequence.charAt(i); + + if (Character.isDigit(c)) + value = (int) (c - '0'); + else if (c == '*') value = 11; - } + else if (c == '+') + value = 10; - if (sequence.charAt(i) == '+') + float vprop = value - min; + vprop /= max; + conservation.annotations[i] = + new Annotation(String.valueOf(c), + String.valueOf(value), ' ', value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); + + // Quality calc + if (quality!=null) { - value = 10; + value = ( (Double) cons.quality.get(i)).floatValue(); + vprop = value - qmin; + vprop /= qmax; + quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ', + value, + new Color(minR + (maxR * vprop), + minG + (maxG * vprop), + minB + (maxB * vprop))); } } - - float vprop = value - min; - vprop /= max; - annotations[i] = new Annotation(sequence.charAt(i) + "", - String.valueOf(value), ' ', value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); - - // Quality calc - value = ( (Double) cons.quality.get(i)).floatValue(); - vprop = value - qmin; - vprop /= qmax; - qannotations[i] = new Annotation(" ", String.valueOf(value), ' ', - value, - new Color(minR + (maxR * vprop), - minG + (maxG * vprop), - minB + (maxB * vprop))); } - - if (conservation == null) + catch (OutOfMemoryError error) { - conservation = new AlignmentAnnotation("Conservation", - "Conservation of total alignment less than " + - ConsPercGaps + "% gaps", - annotations, 0f, // cons.qualityRange[0].floatValue(), - 11f, // cons.qualityRange[1].floatValue() - AlignmentAnnotation.BAR_GRAPH); - - if (showConservation) + javax.swing.SwingUtilities.invokeLater(new Runnable() { - alignment.addAnnotation(conservation); - } - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - AlignmentAnnotation.BAR_GRAPH); - if (showQuality) - { - alignment.addAnnotation(quality); - } + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory calculating conservation!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); + + conservation = null; + quality = null; + + System.out.println("Conservation calculation: " + error); + System.gc(); + } - else + + if(ap!=null) { - conservation.annotations = annotations; - quality.annotations = qannotations; - quality.graphMax = cons.qualityRange[1].floatValue(); + ap.repaint(); } + updatingConservation = false; } - catch (OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating conservation!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); + } - System.out.println("Conservation calculation: " + error); - System.gc(); - } - } + static ConservationThread conservationThread; + + static ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + boolean updatingConsensus = false; + boolean updatingConservation = false; /** * DOCUMENT ME! */ - public void updateConsensus() + public void updateConservation(final AlignmentPanel ap) { - try{ - int aWidth = alignment.getWidth(); - - Annotation[] annotations = new Annotation[aWidth]; - - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); + if (alignment.isNucleotide() || conservation==null) + return; - for (int i = 0; i < aWidth; i++) - { - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hconsensus[i].get("pid_nogaps")).floatValue(); - else - value = ( (Float) hconsensus[i].get("pid_gaps")).floatValue(); + updatingConservation = true; + // 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(); + // } }); + } - String maxRes = hconsensus[i].get("maxResidue").toString(); - String mouseOver = hconsensus[i].get("maxResidue") + " "; + /** + * DOCUMENT ME! + */ + public void updateConsensus(final AlignmentPanel ap) + { + updatingConsensus = true; - if (maxRes.length() > 1) + // javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { + while (consensusThread != null && consensusThread.isAlive()) { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; + try + { + // Thread.sleep(100); + ap.repaint(); + } + catch (Exception ex) + {} } + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + // } }); + } - mouseOver += ( (int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } - if (consensus == null) + class ConsensusThread extends Thread + { + AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + public void run() + { + try { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH); + int aWidth = alignment.getWidth(); + if(aWidth<0) + return; + + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + - if (showIdentity) + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), + 0, + alignment.getWidth(), + hconsensus); + + for (int i = 0; i < aWidth; i++) { - alignment.addAnnotation(consensus); + float value = 0; + if (ignoreGapsInConsensusCalculation) + value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)). + floatValue(); + else + value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)). + floatValue(); + + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } + + mouseOver += ( (int) value + "%"); + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); } + + + if (globalColourScheme != null) + globalColourScheme.setConsensus(hconsensus); + } - else + catch (OutOfMemoryError error) { - consensus.annotations = annotations; - } + consensus = null; + hconsensus = null; + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory calculating consensus!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); - if (globalColourScheme != null) - globalColourScheme.setConsensus(hconsensus); + System.out.println("Consensus calculation: " + error); + System.gc(); + } - }catch(OutOfMemoryError error) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() + if (ap != null) { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory calculating consensus!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); + ap.repaint(); + } - System.out.println("Consensus calculation: " + error); - System.gc(); + updatingConsensus = false; } - } /** * get the consensus sequence as displayed under the PID consensus annotation row. @@ -445,7 +529,7 @@ public class AlignViewport */ public SequenceI getConsensusSeq() { if (consensus==null) - updateConsensus(); + updateConsensus(null); if (consensus==null) return null; StringBuffer seqs=new StringBuffer(); @@ -1090,10 +1174,10 @@ public class AlignViewport changeSupport.firePropertyChange(prop, oldvalue, newvalue); } - public void setIgnoreGapsConsensus(boolean b) + public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap) { ignoreGapsInConsensusCalculation = b; - updateConsensus(); + updateConsensus(ap); if(globalColourScheme!=null) { globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation); @@ -1347,8 +1431,10 @@ public class AlignViewport // object. Refactoring of Cigar and alignment view representation should // be done to remove redundancy. CigarArray aligview = getViewAsCigars(selectedOnly); - if (aligview!=null) - return new AlignmentView(aligview); + if (aligview!=null) { + return new AlignmentView(aligview, + (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0); + } return null; } /** @@ -1410,4 +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