+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.jbgui.*;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
+\r
+import java.awt.event.*;\r
import javax.swing.event.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+\r
public class RedundancyPanel\r
extends GSliderPanel\r
{\r
slider.setMinimum(0);\r
slider.setMaximum(100);\r
slider.setValue(100);\r
-\r
}\r
\r
public void applyButton_actionPerformed(ActionEvent e)\r
float threshold = slider.getValue();\r
Vector del;\r
HistoryItem it;\r
- historyList.push(it=new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
- if (historyList.size()==1\r
- || !af.historyList.contains(historyList.firstElement())) {\r
- af.addHistoryItem((HistoryItem) historyList.firstElement());\r
+ historyList.push(it = new HistoryItem("Remove redundancy",\r
+ ap.av.alignment, HistoryItem.HIDE));\r
+\r
+ if ( (historyList.size() == 1) ||\r
+ !af.historyList.contains(historyList.firstElement()))\r
+ {\r
+ af.addHistoryItem( (HistoryItem) historyList.firstElement());\r
af.updateEditMenuBar();\r
}\r
+\r
undoButton.setEnabled(true);\r
+\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null && sg.getSize() >= 1)\r
- {\r
\r
+ if ( (sg != null) && (sg.getSize() >= 1))\r
+ {\r
del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
+\r
for (int i = 0; i < del.size(); i++)\r
{\r
if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
{\r
- sg.deleteSequence( (SequenceI) del.elementAt(i));\r
+ sg.deleteSequence( (SequenceI) del.elementAt(i), true);\r
}\r
}\r
-\r
}\r
else\r
{\r
Vector s = new Vector();\r
int i = 0;\r
+\r
while (i < ap.av.alignment.getHeight())\r
{\r
s.addElement(ap.av.alignment.getSequenceAt(i));\r
i++;\r
}\r
+\r
del = ap.av.alignment.removeRedundancy(threshold, s);\r
}\r
\r
// This has to be done before the restoreHistoryItem method of alignFrame will\r
// actually restore these sequences.\r
-\r
- if (del.size()>0)\r
- for (int i=0,j=del.size(); i<j; i++) {\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
+ sq.deleteChars(0, sq.getLength());\r
}\r
+ }\r
\r
ap.av.firePropertyChange("alignment", null,\r
ap.av.getAlignment().getSequences());\r
ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
+\r
if (ap.av.getAlignment().getHeight() < 1)\r
{\r
try\r
af.setClosed(true);\r
}\r
catch (Exception ex)\r
- {}\r
+ {\r
+ }\r
}\r
+\r
ap.av.updateConservation();\r
ap.av.updateConsensus();\r
af.updateEditMenuBar();\r
ap.repaint();\r
-\r
}\r
\r
public void undoButton_actionPerformed(ActionEvent e)\r
{\r
HistoryItem hi = (HistoryItem) historyList.pop();\r
af.restoreHistoryItem(hi);\r
+\r
if (historyList.size() == 0)\r
{\r
undoButton.setEnabled(false);\r
+\r
if (af.historyList.contains(hi))\r
{\r
af.historyList.remove(hi);\r
}\r
}\r
}\r
+\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
try\r