- // 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
+ 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