X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7d02e14b0a4604ba9ec56649ad3241707fa2ffff;hb=52c2c3879d5dc5e7b4ba7916f1ea964f83551f95;hp=30113c3a06996923609ce0b1a0b949883cb5e8ef;hpb=aa73ca0718f823e32eb7c864e1861dc3372467d5;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 30113c3..7d02e14 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -84,7 +84,7 @@ public class AlignViewport /** DOCUMENT ME!! */ - public Vector vconsensus; + public Hashtable [] hconsensus; AlignmentAnnotation consensus; AlignmentAnnotation conservation; AlignmentAnnotation quality; @@ -104,6 +104,14 @@ public class AlignViewport boolean padGaps = false; + Rectangle explodedPosition; + + String viewName; + + String sequenceSetID; + + boolean gatherViewsHere = false; + public AlignViewport(AlignmentI al, boolean dataset) { @@ -179,10 +187,46 @@ public class AlignViewport // We must set conservation and consensus before setting colour, // as Blosum and Clustal require this to be done - if(vconsensus==null && !isDataset) + 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 (showConservation) + { + alignment.addAnnotation(conservation); + } + + if (showQuality) + { + quality = new AlignmentAnnotation("Quality", + "Alignment Quality based on Blosum62 scores", + new Annotation[1], + 0f, + 11f, + AlignmentAnnotation.BAR_GRAPH); + + alignment.addAnnotation(quality); + } + } + + consensus = new AlignmentAnnotation("Consensus", "PID", + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); + consensus.hasText = true; + + if (showIdentity) + { + alignment.addAnnotation(consensus); + } + } if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null) @@ -198,7 +242,7 @@ public class AlignViewport if (globalColourScheme != null) { - globalColourScheme.setConsensus(vconsensus); + globalColourScheme.setConsensus(hconsensus); } } } @@ -220,229 +264,273 @@ public class AlignViewport return showSequenceFeatures; } - /** - * DOCUMENT ME! - */ - public void updateConservation() - { - if(alignment.isNucleotide()) - return; - - 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; + long t = System.currentTimeMillis(); + + int alWidth = alignment.getWidth(); + + Conservation cons = new jalview.analysis.Conservation("All", + jalview.schemes.ResidueProperties.propHash, 3, + alignment.getSequences(), 0, alWidth -1); + + cons.calculate(); + cons.verdict(false, ConsPercGaps); + + if (showQuality) + { + cons.findQuality(); + } + + System.out.println("Conservation took " + (System.currentTimeMillis() - t) + + "ms"); + + + 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 - try + float min = 0f; + float max = 11f; + float qmin = 0f; + float qmax = 0f; + + char c; + + conservation.annotations = new Annotation[alWidth]; + + if (showQuality) { - value = Integer.parseInt(sequence.charAt(i) + ""); + quality.annotations = new Annotation[alWidth]; + qmin = cons.qualityRange[0].floatValue(); + qmax = cons.qualityRange[1].floatValue(); } - catch (Exception ex) + + for (int i = 0; i < alWidth; i++) { - if (sequence.charAt(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 (showQuality) { - 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 (quality != null) + { + quality.graphMax = cons.qualityRange[1].floatValue(); + } } - - 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); - } + 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); + } + }); - quality = new AlignmentAnnotation("Quality", - "Alignment Quality based on Blosum62 scores", - qannotations, - cons.qualityRange[0].floatValue(), - cons.qualityRange[1].floatValue(), - AlignmentAnnotation.BAR_GRAPH); + System.out.println("Conservation calculation: " + error); + System.gc(); - if (showQuality) - { - alignment.addAnnotation(quality); - } } - 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(); - } - } + ConservationThread conservationThread; + + ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + boolean updatingConsensus = false; + + boolean updatingConservation = false; /** * DOCUMENT ME! */ - public void updateConsensus() + public void updateConservation(AlignmentPanel ap) { - try{ - Annotation[] annotations = new Annotation[alignment.getWidth()]; + if (alignment.isNucleotide()) + return; - // this routine prevents vconsensus becoming a new object each time - // consenus is calculated. Important for speed of Blosum62 - // and PID colouring of alignment - if (vconsensus == null) - { - vconsensus = alignment.getAAFrequency(); - } - else - { - Vector temp = alignment.getAAFrequency(); - vconsensus.clear(); + updatingConservation = true; - Enumeration e = temp.elements(); + if (conservationThread == null || !conservationThread.isAlive()) + { + conservationThread = new ConservationThread(ap); + conservationThread.start(); + } + else + { + consUpdateNeeded = true; + System.out.println("come back later"); + } + } - while (e.hasMoreElements()) - { - vconsensus.add(e.nextElement()); - } - } + /** + * DOCUMENT ME! + */ + public void updateConsensus(AlignmentPanel ap) + { + updatingConsensus = true; + + if (consensusThread == null || !consensusThread.isAlive()) + { + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } + else + { + consUpdateNeeded = true; + System.out.println("come back later"); + } + } - Hashtable hash = null; - for (int i = 0; i < alignment.getWidth(); i++) + class ConsensusThread extends Thread + { + AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + public void run() + { + try { - hash = (Hashtable) vconsensus.elementAt(i); + int aWidth = alignment.getWidth(); - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hash.get("pid_nogaps")).floatValue(); - else - value = ( (Float) hash.get("pid_gaps")).floatValue(); + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; + + long t = System.currentTimeMillis(); + hconsensus = new Hashtable[aWidth]; + AAFrequency.calculate(alignment.getSequencesArray(), + 0, + alignment.getWidth(), + hconsensus); - String maxRes = hash.get("maxResidue").toString(); - String mouseOver = hash.get("maxResidue") + " "; + System.out.println("Consensus took " + + (System.currentTimeMillis() - t) + "ms"); - if (maxRes.length() > 1) + for (int i = 0; i < aWidth; i++) { - mouseOver = "[" + maxRes + "] "; - maxRes = "+"; + 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); } - mouseOver += ( (int) value + "%"); - annotations[i] = new Annotation(maxRes, mouseOver, ' ', value); - } - if (consensus == null) - { - consensus = new AlignmentAnnotation("Consensus", "PID", - annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH); + if (globalColourScheme != null) + globalColourScheme.setConsensus(hconsensus); - if (showIdentity) - { - alignment.addAnnotation(consensus); - } } - else + catch (OutOfMemoryError error) { - consensus.annotations = annotations; - } + 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(vconsensus); + 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. @@ -450,7 +538,7 @@ public class AlignViewport */ public SequenceI getConsensusSeq() { if (consensus==null) - updateConsensus(); + updateConsensus(null); if (consensus==null) return null; StringBuffer seqs=new StringBuffer(); @@ -1095,10 +1183,10 @@ 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); @@ -1334,9 +1422,9 @@ public class AlignViewport } // Final match if necessary. if (last