\r
boolean MAC = false;\r
\r
+ Stack historyList = new Stack();\r
+ Stack redoList = new Stack();\r
+\r
+ String sequenceSetID;\r
+\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
this.applet = applet;\r
}\r
\r
}\r
- // We must set conservation and consensus before setting colour,\r
- // as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
-\r
\r
if (applet != null)\r
{\r
applet.getParameter("userDefinedColour"));\r
}\r
\r
+ if(hconsensus==null)\r
+ {\r
+ if(!alignment.isNucleotide())\r
+ {\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps",\r
+ new Annotation[1], 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ conservation.hasText = true;\r
+\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
+ if (showQuality)\r
+ {\r
+ quality = new AlignmentAnnotation("Quality",\r
+ "Alignment Quality based on Blosum62 scores",\r
+ new Annotation[1],\r
+ 0f,\r
+ 11f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ quality.hasText = true;\r
+\r
+ alignment.addAnnotation(quality);\r
+ }\r
+ }\r
\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ new Annotation[1], 0f, 100f,\r
+ AlignmentAnnotation.BAR_GRAPH);\r
+ consensus.hasText = true;\r
+\r
+ if (showConsensus)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
}\r
}\r
\r
}\r
\r
\r
- public void updateConservation()\r
+ class ConservationThread extends Thread\r
{\r
- if(alignment.isNucleotide())\r
- return;\r
+ AlignmentPanel ap;\r
+ public ConservationThread(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ }\r
\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth() - 1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\r
- int alWidth = alignment.getWidth();\r
- Annotation[] annotations = new Annotation[alWidth];\r
- Annotation[] qannotations = new Annotation[alWidth];\r
- String sequence = cons.getConsSequence().getSequence();\r
- float minR, minG, minB, maxR, maxG, maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f - minR;\r
- maxG = 0.9f - minG;\r
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
- float min = 0f;\r
- float max = 11f;\r
- float qmin = cons.qualityRange[0].floatValue();\r
- float qmax = cons.qualityRange[1].floatValue();\r
-\r
- for (int i = 0; i < alWidth; i++)\r
+ public void run()\r
{\r
- float value = 0;\r
try\r
{\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- if (sequence.charAt(i) == '*')\r
+ updatingConservation = true;\r
+\r
+ while (UPDATING_CONSERVATION)\r
{\r
- value = 11;\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
- if (sequence.charAt(i) == '+')\r
+\r
+ UPDATING_CONSERVATION = true;\r
+\r
+\r
+ int alWidth = alignment.getWidth();\r
+ if(alWidth<0)\r
+ return;\r
+\r
+ Conservation cons = new jalview.analysis.Conservation("All",\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0, alWidth -1);\r
+\r
+ cons.calculate();\r
+ cons.verdict(false, ConsPercGaps);\r
+\r
+ if (quality!=null)\r
{\r
- value = 10;\r
+ cons.findQuality();\r
}\r
- }\r
- float vprop = value - min;\r
- vprop /= max;\r
-\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value,\r
- new Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- // Quality calc\r
- value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value,\r
- new\r
- Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- }\r
\r
- if (conservation == null)\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showConservation)\r
+ String sequence = cons.getConsSequence().getSequence();\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
+ minR = 0.3f;\r
+ minG = 0.0f;\r
+ minB = 0f;\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
+ float min = 0f;\r
+ float max = 11f;\r
+ float qmin = 0f;\r
+ float qmax = 0f;\r
+\r
+ char c;\r
+\r
+ conservation.annotations = new Annotation[alWidth];\r
+\r
+ if (quality!=null)\r
+ {\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
+ quality.annotations = new Annotation[alWidth];\r
+ qmin = cons.qualityRange[0].floatValue();\r
+ qmax = cons.qualityRange[1].floatValue();\r
+ }\r
+\r
+ for (int i = 0; i < alWidth; i++)\r
+ {\r
+ float value = 0;\r
+\r
+ c = sequence.charAt(i);\r
+\r
+ if (Character.isDigit(c))\r
+ value = (int) (c - '0');\r
+ else if (c == '*')\r
+ value = 11;\r
+ else if (c == '+')\r
+ value = 10;\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ conservation.annotations[i] =\r
+ new Annotation(String.valueOf(c),\r
+ String.valueOf(value), ' ', value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
+ // Quality calc\r
+ if (quality!=null)\r
+ {\r
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
+ vprop = value - qmin;\r
+ vprop /= qmax;\r
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop),\r
+ minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+ }\r
+ }\r
+ }\r
+ catch (OutOfMemoryError error)\r
{\r
- alignment.addAnnotation(conservation);\r
+ System.out.println("Out of memory calculating conservation!!");\r
+ conservation = null;\r
+ quality = null;\r
+ System.gc();\r
}\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores",\r
- qannotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showQuality)\r
+\r
+ UPDATING_CONSERVATION = false;\r
+ updatingConservation = false;\r
+\r
+ if(ap!=null)\r
{\r
- alignment.addAnnotation(quality);\r
+ ap.repaint();\r
}\r
- }\r
- else\r
- {\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
- }\r
\r
+ }\r
}\r
\r
- public void updateConsensus()\r
- {\r
- // this routine prevents vconsensus becoming a new object each time\r
- // consenus is calculated. Important for speed of Blosum62\r
- // and PID colouring of alignment\r
- int aWidth = alignment.getWidth();\r
\r
- Annotation[] annotations = new Annotation[aWidth];\r
+ ConservationThread conservationThread;\r
\r
- hconsensus = new Hashtable[aWidth];\r
- AAFrequency.calculate(alignment.getSequencesArray(),\r
- 0, aWidth,\r
- hconsensus);\r
+ ConsensusThread consensusThread;\r
\r
- for (int i = 0; i < aWidth; i++)\r
- {\r
- float value = 0;\r
- if(ignoreGapsInConsensusCalculation)\r
- value = ((Float)hconsensus[i].get(AAFrequency.PID_NOGAPS)).floatValue();\r
- else\r
- value = ((Float)hconsensus[i].get(AAFrequency.PID_GAPS)).floatValue();\r
+ boolean consUpdateNeeded = false;\r
\r
- String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
- String mouseOver = maxRes;\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
+ static boolean UPDATING_CONSENSUS = false;\r
\r
+ static boolean UPDATING_CONSERVATION = false;\r
\r
- mouseOver += (int) value + "%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ boolean updatingConsensus = false;\r
\r
- }\r
+ boolean updatingConservation = false;\r
\r
- if (consensus == null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConservation(final AlignmentPanel ap)\r
+ {\r
+ if (alignment.isNucleotide() || conservation==null)\r
+ return;\r
+\r
+ conservationThread = new ConservationThread(ap);\r
+ conservationThread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConsensus(final AlignmentPanel ap)\r
+ {\r
+ consensusThread = new ConsensusThread(ap);\r
+ consensusThread.start();\r
+ }\r
+\r
+\r
+ class ConsensusThread extends Thread\r
+ {\r
+ AlignmentPanel ap;\r
+ public ConsensusThread(AlignmentPanel ap)\r
{\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
- if (showConsensus)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
+ this.ap = ap;\r
}\r
- else\r
+ public void run()\r
{\r
- consensus.annotations = annotations;\r
- }\r
+ updatingConsensus = true;\r
+ while (UPDATING_CONSENSUS)\r
+ {\r
+ try\r
+ {\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+\r
+ Thread.sleep(200);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+\r
+ UPDATING_CONSENSUS = true;\r
+\r
+ try\r
+ {\r
+ int aWidth = alignment.getWidth();\r
+ if(aWidth<0)\r
+ return;\r
+\r
+ consensus.annotations = null;\r
+ consensus.annotations = new Annotation[aWidth];\r
+\r
\r
- if(globalColourScheme!=null)\r
+ hconsensus = new Hashtable[aWidth];\r
+ AAFrequency.calculate(alignment.getSequencesArray(),\r
+ 0,\r
+ alignment.getWidth(),\r
+ hconsensus);\r
+\r
+ for (int i = 0; i < aWidth; i++)\r
+ {\r
+ float value = 0;\r
+ if (ignoreGapsInConsensusCalculation)\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).\r
+ floatValue();\r
+ else\r
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).\r
+ floatValue();\r
+\r
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";\r
+\r
+ if (maxRes.length() > 1)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+";\r
+ }\r
+\r
+ mouseOver += ( (int) value + "%");\r
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ }\r
+\r
+\r
+ if (globalColourScheme != null)\r
globalColourScheme.setConsensus(hconsensus);\r
\r
+ }\r
+ catch (OutOfMemoryError error)\r
+ {\r
+ alignment.deleteAnnotation(consensus);\r
+\r
+ consensus = null;\r
+ hconsensus = null;\r
+ System.out.println("Out of memory calculating consensus!!");\r
+ System.gc();\r
+ }\r
+ UPDATING_CONSENSUS = false;\r
+ updatingConsensus = false;\r
+\r
+ if (ap != null)\r
+ {\r
+ ap.repaint();\r
+ }\r
+ }\r
}\r
+\r
/**\r
* get the consensus sequence as displayed under the PID consensus annotation row.\r
* @return consensus sequence as a new sequence object\r
* get the consensus sequence as displayed under the PID consensus annotation row.\r
* @return consensus sequence as a new sequence object\r
*/\r
- public SequenceI getConsensusSeq() {\r
- if (consensus==null)\r
- updateConsensus();\r
+ public SequenceI getConsensusSeq()\r
+ {\r
if (consensus==null)\r
return null;\r
StringBuffer seqs=new StringBuffer();\r
public void setIgnoreGapsConsensus(boolean b)\r
{\r
ignoreGapsInConsensusCalculation = b;\r
- updateConsensus();\r
+ updateConsensus(null);\r
if (globalColourScheme!=null)\r
{\r
globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
sequenceColours.put(seq, col);\r
}\r
\r
+ public String getSequenceSetId()\r
+ {\r
+ if (sequenceSetID == null)\r
+ sequenceSetID = alignment.hashCode() + "";\r
+\r
+ return sequenceSetID;\r
+ }\r
+\r
+ public void alignmentChanged(AlignmentPanel ap)\r
+ {\r
+ alignment.padGaps();\r
+\r
+ if (hconsensus != null && autocalculateConsensus)\r
+ {\r
+ updateConsensus(ap);\r
+ updateConservation(ap);\r
+ }\r
+\r
+ //Reset endRes of groups if beyond alignment width\r
+ int alWidth = alignment.getWidth();\r
+ Vector groups = alignment.getGroups();\r
+ if(groups!=null)\r
+ {\r
+ for(int i=0; i<groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if(sg.getEndRes()>alWidth)\r
+ sg.setEndRes(alWidth-1);\r
+ }\r
+ }\r
+\r
+ if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)\r
+ selectionGroup.setEndRes(alWidth-1);\r
+\r
+ resetAllColourSchemes();\r
+\r
+ alignment.adjustSequenceAnnotations();\r
+ }\r
+\r
+ void resetAllColourSchemes()\r
+ {\r
+ ColourSchemeI cs = globalColourScheme;\r
+ if(cs!=null)\r
+ {\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) cs).\r
+ resetClustalX(alignment.getSequences(),\r
+ alignment.getWidth());\r
+ }\r
+\r
+ cs.setConsensus(hconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, ConsPercGaps);\r
+\r
+ cs.setConservation(c);\r
+ }\r
+ }\r
+\r
+ int s, sSize = alignment.getGroups().size();\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);\r
+ if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ {\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ sg.getSequences(true), sg.getWidth());\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ }\r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff