+ AlignFrame af;\r
+ AlignmentPanel ap;\r
+ Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+ float [] redundancy;\r
+ SequenceI [] originalSequences;\r
+ JInternalFrame frame;\r
+ Vector redundantSeqs;\r
+\r
+ /**\r
+ * Creates a new RedundancyPanel object.\r
+ *\r
+ * @param ap DOCUMENT ME!\r
+ * @param af DOCUMENT ME!\r
+ */\r
+ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)\r
+ {\r
+ this.ap = ap;\r
+ this.af = af;\r
+ redundantSeqs = new Vector();\r
+\r
+ slider.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ sliderValueChanged();\r
+ }\r
+ });\r
+\r
+ applyButton.setText("Remove");\r
+ allGroupsCheck.setVisible(false);\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100);\r
+ slider.setValue(100);\r
+\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