this.pidColours = ResidueProperties.pidColours;\r
this.thresholds = ResidueProperties.pidThresholds;\r
}\r
this.pidColours = ResidueProperties.pidColours;\r
this.thresholds = ResidueProperties.pidThresholds;\r
}\r
public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
Color c = Color.white;\r
Hashtable hash = null;\r
\r
public Color findColour(SequenceI seq,String s, int j,Vector aa) {\r
Color c = Color.white;\r
Hashtable hash = null;\r
\r
- if (((Integer)hash.get("maxCount")).intValue() != -1 && hash.contains(s)) {\r
- sc = ((Integer)hash.get(s)).intValue()*100.0/Integer.parseInt((String)hash.get("maxResidue"));\r
-\r
- // MC Should be isGap\r
- if ( !s.equals("-") && !s.equals(".") && !s.equals(" ")) {\r
- for (int i=0; i < thresholds.length; i++) {\r
- if (sc > thresholds[i]) {\r
- c = pidColours[i];\r
- break;\r
- }\r
- }\r
- } else {\r
- c = Color.white;\r
- }\r
+ if ( Integer.parseInt( hash.get("maxCount").toString() ) != -1 && hash.contains(s))\r
+ {\r
+\r
+ sc = ( (Integer) hash.get(s)).intValue() * 100.0 / ((Integer)hash.get("size")).intValue() ;\r
+ // MC Should be isGap\r
+ if (!s.equals("-") && !s.equals(".") && !s.equals(" "))\r
+ {\r
+ for (int i = 0; i < thresholds.length; i++)\r
+ {\r
+ if (sc > thresholds[i])\r
+ {\r
+ c = pidColours[i];\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ else\r
+ c = Color.white;\r