+\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
+ resetColours();\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
+ Vector sel = new Vector();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ int height;\r
+ originalSequences = new Vector();\r
+ originalColours = new Hashtable();\r
+\r
+ if ( (sg != null) && (sg.getSize() >= 1))\r
+ {\r
+ height = sg.getSize();\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ sel.addElement(sg.getSequenceAt(i));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ height = ap.av.alignment.getHeight();\r
+ for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ {\r
+ sel.addElement(ap.av.alignment.getSequenceAt(i));\r
+ }\r
+ }\r
+\r
+ redundancy = new float[height];\r
+ for (int i = 0; i < height; i++)\r
+ {\r
+ redundancy[i] = 0f;\r
+ }\r
+\r
+\r
+ // long start = System.currentTimeMillis();\r
+\r
+ float pid;\r
+ SequenceI seqi, seqj;\r
+ for (int i = 0; i < sel.size(); i++)\r
+ {\r
+ originalSequences.addElement(sel.elementAt(i));\r
+ originalColours.put(sel.elementAt(i),\r
+ ((SequenceI) sel.elementAt(i)).getColor());\r
+\r
+ for (int j = 0; j < i; j++)\r
+ {\r
+ if(i==j)\r
+ continue;\r
+\r
+ seqi = (SequenceI) sel.elementAt(i);\r
+ seqj = (SequenceI) sel.elementAt(j);\r
+\r
+ if (sg != null)\r
+ pid = Comparison.PID( seqi,\r
+ seqj,\r
+ sg.getStartRes(), sg.getEndRes());\r
+ else\r
+ pid = Comparison.PID( seqi, seqj );\r
+\r
+\r
+ if(seqj.getLength() < seqi.getLength())\r
+ redundancy[j] = Math.max(pid, redundancy[j]);\r
+ else\r
+ redundancy[i] = Math.max(pid, redundancy[i]);\r
+\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("blob done "+ (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
+ ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
+ else\r
+ ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+ }\r
+\r
+ PaintRefresher.Refresh(null,ap.av.alignment);\r
+\r