From 82cbe684b0afeb8a6a8c6014b9266cb90439dfe7 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 10 Oct 2006 10:26:58 +0000 Subject: [PATCH] Consensus and conservation updated in threads --- src/jalview/gui/AlignFrame.java | 8 +- src/jalview/gui/AlignViewport.java | 425 ++++++++++++++++++++------------- src/jalview/gui/AnnotationLabels.java | 7 +- src/jalview/gui/AnnotationPanel.java | 24 ++ 4 files changed, 291 insertions(+), 173 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 77f1e41..27503f9 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -415,6 +415,9 @@ public class AlignFrame tabbedPane.addTab(ap.av.viewName==null?"Original":ap.av.viewName, ap); } + ap.av.updateConsensus(ap); + ap.av.updateConservation(ap); + ap.av.addPropertyChangeListener(new PropertyChangeListener() { @@ -1616,8 +1619,9 @@ public class AlignFrame if (av.hconsensus != null && av.autoCalculateConsensus) { - av.updateConsensus(); - av.updateConservation(); + av.updateConsensus(ap); + av.updateConservation(ap); + ap.annotationPanel.repaint(); } resetAllColourSchemes(); diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 84cbe76..ddb871e 100755 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -189,8 +189,44 @@ 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 (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) @@ -228,216 +264,271 @@ 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; + long t = System.currentTimeMillis(); + + Conservation cons = new jalview.analysis.Conservation("All", + jalview.schemes.ResidueProperties.propHash, 3, + alignment.getSequences(), 0, alignment.getWidth() - 1); + + cons.calculate(); + cons.verdict(false, ConsPercGaps); - try + if (showQuality) { - value = Integer.parseInt(sequence.charAt(i) + ""); + cons.findQuality(); } - catch (Exception ex) + + System.out.println("Conservation took " + (System.currentTimeMillis() - t) + + "ms"); + + int alWidth = alignment.getWidth(); + 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 (showQuality) { - if (sequence.charAt(i) == '*') - { + 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 (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.annotationPanel.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); - } - }); + } + + + ConservationThread conservationThread; + + ConsensusThread consensusThread; + + boolean consUpdateNeeded = false; + + boolean updatingConsensus = false; + + boolean updatingConservation = false; + + /** + * DOCUMENT ME! + */ + public void updateConservation(AlignmentPanel ap) + { + if (alignment.isNucleotide()) + return; - System.out.println("Conservation calculation: " + error); - System.gc(); + updatingConservation = true; + if (conservationThread == null || !conservationThread.isAlive()) + { + conservationThread = new ConservationThread(ap); + conservationThread.start(); + } + else + { + consUpdateNeeded = true; + System.out.println("come back later"); } } - /** * DOCUMENT ME! */ - public void updateConsensus() + public void updateConsensus(AlignmentPanel ap) { - try{ - int aWidth = alignment.getWidth(); + updatingConsensus = true; - Annotation[] annotations = new Annotation[aWidth]; + if (consensusThread == null || !consensusThread.isAlive()) + { + consensusThread = new ConsensusThread(ap); + consensusThread.start(); + } + else + { + consUpdateNeeded = true; + System.out.println("come back later"); + } + } - hconsensus = new Hashtable[aWidth]; - AAFrequency.calculate(alignment.getSequencesArray(), - 0, - alignment.getWidth(), - hconsensus); - for (int i = 0; i < aWidth; i++) + class ConsensusThread extends Thread + { + AlignmentPanel ap; + public ConsensusThread(AlignmentPanel ap) + { + this.ap = ap; + } + public void run() + { + try { - float value = 0; - if (ignoreGapsInConsensusCalculation) - value = ( (Float) hconsensus[i].get("pid_nogaps")).floatValue(); - else - value = ( (Float) hconsensus[i].get("pid_gaps")).floatValue(); + int aWidth = alignment.getWidth(); - String maxRes = hconsensus[i].get("maxResidue").toString(); - String mouseOver = hconsensus[i].get("maxResidue") + " "; + consensus.annotations = null; + consensus.annotations = new Annotation[aWidth]; - if (maxRes.length() > 1) + 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++) { - 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(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.annotationPanel.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 +536,7 @@ public class AlignViewport */ public SequenceI getConsensusSeq() { if (consensus==null) - updateConsensus(); + updateConsensus(null); if (consensus==null) return null; StringBuffer seqs=new StringBuffer(); @@ -1090,10 +1181,10 @@ 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); diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 63d7c53..f32a350 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -217,7 +217,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, SequenceI cons=av.getConsensusSeq(); if (cons!=null) copy_annotseqtoclipboard(cons); - + } ap.annotationPanel.adjustPanelHeight(); @@ -387,8 +387,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, cbmi.addActionListener(new ActionListener() {public void actionPerformed(ActionEvent e) { - ap.av.setIgnoreGapsConsensus(cbmi.getState()); - ap.repaint(); + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } }); pop.add(cbmi); @@ -442,7 +441,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, region[1]}); } } - + Desktop.jalviewClipboard = new Object[]{ seqs, ds, // what is the dataset of a consensus sequence ? need to flag sequence as special. hiddenColumns}; diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index fb48794..dbc1c92 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -667,6 +667,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); int x = 0, y = 0; @@ -689,6 +690,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, continue; } + lastSS = ' '; lastSSX = 0; @@ -706,6 +708,28 @@ public class AnnotationPanel extends JPanel implements MouseListener, } } + if (av.updatingConsensus && aa[i].label.equals("Consensus")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Consensus....", 20, y - 5); + y += av.charHeight; + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Conservation")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Conservation.....", 20, y - 5); + y += av.charHeight; + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Quality")) + { + g.setColor(Color.darkGray); + g.drawString("Recalculating Quality....", 20, y - 5); + continue; + } + + if (row.hasText) { iconOffset = av.charHeight / 2 + 4; -- 1.7.10.2