+ else\r
+ {\r
+ originalSequences = ap.av.alignment.getSequencesArray();\r
+ start = 0;\r
+ end = ap.av.alignment.getWidth();\r
+ }\r
+\r
+ height = originalSequences.length;\r
+\r
+ redundancy = new float[height];\r
+ for (int i = 0; i < height; i++)\r
+ {\r
+ redundancy[i] = 0f;\r
+ }\r
+\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ omitHidden = ap.av.getViewAsString(sg!=null);\r
+ }\r
+\r
+\r
+ // long start = System.currentTimeMillis();\r
+\r
+ float pid;\r
+ String seqi, seqj;\r
+ for (int i = 0; i < height; i++)\r
+ {\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
+\r
+ label.setText("Enter the redundancy threshold");\r
+ slider.setVisible(true);\r
+ applyButton.setEnabled(true);\r
+ valueField.setVisible(true);\r
+\r
+ validate();\r
+ // System.out.println((System.currentTimeMillis()-start));\r