showSequenceFeatures = b;\r
}\r
\r
+ public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
AlignmentAnnotation quality;\r
\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+\r
public void updateConservation()\r
{\r
- int percGaps = 100; // JBPNote : This should be a scalable property!\r
Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 1,\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
alignment.getSequences(), 0,\r
- alignment.getWidth());\r
+ alignment.getWidth()-1);\r
cons.calculate();\r
- cons.verdict(false, percGaps);\r
+ cons.verdict(false, ConsPercGaps);\r
cons.findQuality();\r
int alWidth = alignment.getWidth();\r
Annotation [] annotations = new Annotation[alWidth];\r
value = ((Double) cons.quality.get(i)).floatValue();\r
vprop = value - qmin;\r
vprop/=qmax;\r
- qannotations[i] = new Annotation(sequence.charAt(i) + "",\r
- new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+ qannotations[i] = new Annotation(" ",\r
+ String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
}\r
\r
if(conservation==null)\r
{\r
conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+percGaps+"% gaps",\r
+ "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
annotations,\r
0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
{\r
Annotation [] annotations = new Annotation[alignment.getWidth()];\r
\r
- Vector cons = alignment.getAAFrequency();\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
+ if(vconsensus == null)\r
+ vconsensus = alignment.getAAFrequency();\r
+ else\r
+ {\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
+ Enumeration e = temp.elements();\r
+ while(e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
+ }\r
Hashtable hash = null;\r
- for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; i++)\r
+ for (int i = 0; i<alignment.getWidth(); i++)\r
{\r
- hash = (Hashtable) cons.elementAt(i);\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
float value = Float.parseFloat(hash.get("maxCount").toString());\r
value /= Float.parseFloat(hash.get("size").toString());\r
\r
\r
}\r
\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
-\r
- String visibleConsensus;\r
- Vector consensusV = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensusV.size()<1)\r
- {\r
- consensusV = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0, sz=consensusV.size(); i < sz; i++)\r
- {\r
- hash = (Hashtable) consensusV.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensusV;\r
- }\r
-\r
\r
public SequenceGroup getSelectionGroup()\r
{\r