/** DOCUMENT ME!! */
- public Vector vconsensus;
+ public Hashtable [] hconsensus;
AlignmentAnnotation consensus;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
boolean padGaps = false;
+ Rectangle explodedPosition;
+
+ String viewName;
+
+ String sequenceSetID;
+
+ boolean gatherViewsHere = false;
+
public AlignViewport(AlignmentI al, boolean dataset)
{
// 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)
if (globalColourScheme != null)
{
- globalColourScheme.setConsensus(vconsensus);
+ globalColourScheme.setConsensus(hconsensus);
}
}
}
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();
+
+ 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.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;
- Hashtable hash = null;
+ if (consensusThread == null || !consensusThread.isAlive())
+ {
+ consensusThread = new ConsensusThread(ap);
+ consensusThread.start();
+ }
+ else
+ {
+ consUpdateNeeded = true;
+ System.out.println("come back later");
+ }
+ }
- 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.
*/
public SequenceI getConsensusSeq() {
if (consensus==null)
- updateConsensus();
+ updateConsensus(null);
if (consensus==null)
return null;
StringBuffer seqs=new StringBuffer();
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);
// 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;
}
/**
{
showHiddenMarkers = show;
}
+
+ public String getSequenceSetId()
+ {
+ if(sequenceSetID==null)
+ sequenceSetID = alignment.hashCode()+"";
+
+ return sequenceSetID;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff