\r
jalview.bin.JalviewLite applet;\r
\r
+ Hashtable sequenceColours;\r
+\r
boolean MAC = false;\r
\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
float value = 0;\r
if(ignoreGapsInConsensusCalculation)\r
- value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();\r
+ value = ((Float)hconsensus[i].get(AAFrequency.PID_NOGAPS)).floatValue();\r
else\r
- value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();\r
+ value = ((Float)hconsensus[i].get(AAFrequency.PID_GAPS)).floatValue();\r
\r
- String maxRes = hconsensus[i].get("maxResidue").toString();\r
- String mouseOver = hconsensus[i].get("maxResidue") + " ";\r
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();\r
+ String mouseOver = maxRes;\r
if (maxRes.length() > 1)\r
{\r
mouseOver = "[" + maxRes + "] ";\r
// object. Refactoring of Cigar and alignment view representation should\r
// be done to remove redundancy.\r
CigarArray aligview = getViewAsCigars(selectedOnly);\r
- if (aligview!=null)\r
- return new AlignmentView(aligview);\r
+ if (aligview!=null) {\r
+ return new AlignmentView(aligview,\r
+ (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);\r
+ }\r
return null;\r
}\r
/**\r
showHiddenMarkers = show;\r
}\r
\r
+ public Color getSequenceColour(SequenceI seq)\r
+ {\r
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))\r
+ return Color.white;\r
+ else\r
+ return (Color) sequenceColours.get(seq);\r
+ }\r
+\r
+ public void setSequenceColour(SequenceI seq, Color col)\r
+ {\r
+ if (sequenceColours == null)\r
+ sequenceColours = new Hashtable();\r
+\r
+ if (col == null)\r
+ sequenceColours.remove(seq);\r
+ else\r
+ sequenceColours.put(seq, col);\r
+ }\r
\r
}\r