+ ap.idPanel.idCanvas.setHighlighted(redundantSeqs);\r
+\r
+ PaintRefresher.Refresh(null,ap.av.alignment);\r
+\r
+ }\r
+ public void applyButton_actionPerformed()\r
+ {\r
+ historyList.push(new HistoryItem("Remove redundancy",\r
+ ap.av.alignment, HistoryItem.HIDE));\r
+\r
+ if ((historyList.size() == 1) ||\r
+ !ap.alignFrame.historyList.contains(historyList.firstElement()))\r
+ {\r
+ ap.alignFrame.addHistoryItem((HistoryItem) historyList.firstElement());\r
+ ap.alignFrame.updateEditMenuBar();\r
+ }\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
+ SequenceI seq = originalSequences[i];\r
+ ap.av.alignment.deleteSequence(seq);\r
+ del.addElement(seq);\r
+ if (sg != null)\r
+ {\r
+ sg.deleteSequence(seq, false);\r
+ }\r
+ }\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
+ for (int i = 0, j = del.size(); i < j; i++)\r
+ {\r
+ SequenceI sq = (SequenceI) del.elementAt(i);\r
+ sq.deleteChars(0, sq.getLength());\r
+ }\r
+ }\r
+\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+ ap.alignFrame.updateEditMenuBar();\r