+ if (redundancy == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ float value = slider.getValue();\r
+\r
+ for (int i = 0; i < redundancy.length; i++)\r
+ {\r
+ if (value > redundancy[i])\r
+ {\r
+ redundantSeqs.removeElement(originalSequences[i]);\r
+ }\r
+ else if (!redundantSeqs.contains(originalSequences[i]))\r
+ {\r
+ redundantSeqs.addElement(originalSequences[i]);\r
+ }\r
+ }\r
+\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
+ PaintRefresher.Refresh(this,\r
+ ap.av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+\r
+ }\r
+\r
+ public void applyButton_actionPerformed()\r
+ {\r
+ Vector del = new Vector();\r
+\r
+ undoButton.setEnabled(true);\r
+\r
+ float value = slider.getValue();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ for (int i = 0; i < redundancy.length; i++)\r
+ {\r
+ if (value <= redundancy[i])\r
+ {\r
+ del.addElement(originalSequences[i]);\r
+ }\r
+ }\r
+\r
+ // This has to be done before the restoreHistoryItem method of alignFrame will\r
+ // actually restore these sequences.\r
+ if (del.size() > 0)\r
+ {\r
+ SequenceI[] deleted = new SequenceI[del.size()];\r
+\r
+ int width = 0;\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ deleted[i] = (SequenceI) del.elementAt(i);\r
+ if (deleted[i].getLength() > width)\r
+ {\r
+ width = deleted[i].getLength();\r
+ }\r
+ }\r
+\r
+ EditCommand cut = new EditCommand("Remove Redundancy",\r
+ EditCommand.CUT, deleted, 0, width,\r
+ ap.av.alignment);\r
+\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ ap.av.alignment.deleteSequence(deleted[i]);\r
+ PaintRefresher.Refresh(this,\r
+ ap.av.getSequenceSetId(),\r
+ true,\r
+ true);\r
+ if (sg != null)\r
+ {\r
+ sg.deleteSequence(deleted[i], false);\r
+ }\r
+ }\r
+\r
+ historyList.push(cut);\r
+\r
+ ap.alignFrame.addHistoryItem(cut);\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+ }\r
+\r