boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
\r
+\r
+ boolean ignoreGapsInConsensusCalculation = false;\r
+\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
setAlignment(al);\r
for (int i = 0; i < alignment.getWidth(); i++)\r
{\r
hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = new Float(hash.get("maxCount").toString()).floatValue();\r
- value /= new Float(hash.get("size").toString()).floatValue();\r
+ float value = 0;\r
+ if(ignoreGapsInConsensusCalculation)\r
+ value = ((Float)hash.get("pid_nogaps")).floatValue();\r
+ else\r
+ value = ((Float)hash.get("pid_gaps")).floatValue();\r
\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue") + " ";\r
+ String maxRes = hash.get("maxResidue").toString();\r
String mouseOver = hash.get("maxResidue") + " ";\r
- if (maxRes.length() > 2)\r
+ if (maxRes.length() > 1)\r
{\r
mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+ ";\r
+ maxRes = "+";\r
}\r
\r
+\r
mouseOver += (int) value + "%";\r
annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
\r
scaleRightWrapped = b;\r
}\r
\r
+ public void setIgnoreGapsConsensus(boolean b)\r
+ {\r
+ ignoreGapsInConsensusCalculation = b;\r
+ updateConsensus();\r
+ if (globalColourScheme!=null && globalColourScheme instanceof ResidueColourScheme)\r
+ {\r
+ ( (ResidueColourScheme) globalColourScheme).setThreshold(\r
+ ( (ResidueColourScheme) globalColourScheme).getThreshold(),\r
+ ignoreGapsInConsensusCalculation);\r
+\r
+ }\r
+\r
+ }\r
+\r
+ public boolean getIgnoreGapsConsensus()\r
+ {\r
+ return ignoreGapsInConsensusCalculation;\r
+ }\r
+\r
+\r
}\r