+\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
+ 100, false);\r
+ frame.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosing(InternalFrameEvent evt)\r
+ {\r
+ ap.idPanel.idCanvas.setHighlighted(null);\r
+ }\r
+ }\r
+ );\r
+\r
+ }\r
+\r
+\r
+ /**\r
+ * This is a copy of remove redundancy in jalivew.datamodel.Alignment\r
+ * except we dont want to remove redundancy, just calculate once\r
+ * so we can use the slider to dynamically hide redundant sequences\r
+ *\r
+ * @param threshold DOCUMENT ME!\r
+ * @param sel DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ JProgressBar progress = new JProgressBar();\r
+ progress.setIndeterminate(true);\r
+ southPanel.add(progress, java.awt.BorderLayout.SOUTH);\r
+\r
+ label.setText("Calculating....");\r
+\r
+ slider.setVisible(false);\r
+ applyButton.setEnabled(false);\r
+ valueField.setVisible(false);\r
+\r
+ validate();\r
+\r
+ String[] omitHidden = null;\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ int height;\r
+\r
+ int start, end;\r
+\r
+ if ( (sg != null) && (sg.getSize(false) >= 1))\r
+ {\r
+ originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
+ start = sg.getStartRes();\r
+ end = sg.getEndRes();\r
+ }\r
+ 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
+ }\r
+\r
+ void sliderValueChanged()\r
+ {\r
+ if(redundancy==null)\r
+ return;\r
+\r
+ float value = slider.getValue();\r
+\r
+ for(int i=0; i<redundancy.length; i++)\r
+ {\r
+ if (value > redundancy[i])\r
+ redundantSeqs.remove(originalSequences[i]);\r
+ else if(!redundantSeqs.contains(originalSequences[i]))\r
+ redundantSeqs.add(originalSequences[i]);\r
+\r
+ }\r
+\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r