- // long start = System.currentTimeMillis();\r
-\r
- float pid;\r
- String seqi, seqj;\r
- for (int i = 0; i < height; i++)\r
- {\r
- originalColours.put(originalSequences[i],\r
- originalSequences[i].getColor());\r
-\r
- for (int j = 0; j < i; j++)\r
- {\r
- if(i==j)\r
- continue;\r
-\r
- if(omitHidden==null)\r
- {\r
- seqi = originalSequences[i].getSequence(start, end);\r
- seqj = originalSequences[j].getSequence(start, end);\r
- }\r
- else\r
- {\r
- seqi = omitHidden[i];\r
- seqj = omitHidden[j];\r
- }\r
-\r
- pid = Comparison.PID( seqi, seqj );\r
-\r
- if(seqj.length() < seqi.length())\r
- redundancy[j] = Math.max(pid, redundancy[j]);\r
- else\r
- redundancy[i] = Math.max(pid, redundancy[i]);\r
-\r
- }\r
- }\r
-\r
- progress.setIndeterminate(false);\r
- progress.setVisible(false);\r
- progress = null;\r