+/*\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
-public class RedundancyPanel extends GSliderPanel\r
+import jalview.datamodel.*;\r
+import jalview.jbgui.*;\r
+\r
+public class RedundancyPanel\r
+ extends GSliderPanel\r
{\r
+ AlignFrame af;\r
AlignmentPanel ap;\r
+ Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
\r
- SequenceI[] oldAlignment;\r
-\r
-\r
- public RedundancyPanel(AlignmentPanel ap)\r
+ public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
{\r
this.ap = ap;\r
-\r
+ this.af = af;\r
label.setText("Enter the redundancy threshold");\r
\r
slider.addChangeListener(new ChangeListener()\r
{\r
public void stateChanged(ChangeEvent evt)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
});\r
\r
slider.setMinimum(0);\r
slider.setMaximum(100);\r
- slider.setValue(100 );\r
-\r
+ slider.setValue(100);\r
}\r
\r
public void applyButton_actionPerformed(ActionEvent e)\r
{\r
- float threshold = slider.getValue();\r
- Vector del;\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
+\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
+\r
+ if ( (sg != null) && (sg.getSize() >= 1))\r
+ {\r
+ del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
\r
- oldAlignment = new SequenceI[ap.av.alignment.getHeight()];\r
- for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
{\r
- oldAlignment[i] = new Sequence(ap.av.alignment.getSequenceAt(i).getName(),\r
- ap.av.alignment.getSequenceAt(i).\r
- getSequence());\r
+ sg.deleteSequence( (SequenceI) del.elementAt(i), true);\r
}\r
+ }\r
+ }\r
+ else\r
+ {\r
+ Vector s = new Vector();\r
+ int i = 0;\r
\r
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg != null && sg.getSize() > 1)\r
- {\r
-\r
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
- for (int i = 0; i < del.size(); i++)\r
- if (sg.sequences.contains( (SequenceI) del.elementAt(i)))\r
- sg.deleteSequence( (SequenceI) del.elementAt(i));\r
-\r
- }\r
- else\r
- {\r
- Vector s = new Vector();\r
- int i=0;\r
- while(i < ap.av.alignment.getHeight())\r
- {\r
- s.addElement( ap.av.alignment.getSequenceAt(i) );\r
- i++;\r
- }\r
- del = ap.av.alignment.removeRedundancy(threshold,s);\r
- for (int j=0; j < del.size(); j++)\r
- {\r
- if (sg.sequences.contains((SequenceI)del.elementAt(j)))\r
- sg.deleteSequence((SequenceI)del.elementAt(j));\r
-\r
- }\r
- }\r
-\r
- ap.repaint();\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
+ 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,\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
+ {\r
+ af.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ ap.av.updateConservation();\r
+ ap.av.updateConsensus();\r
+ af.updateEditMenuBar();\r
+ ap.repaint();\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
- ap.av.setAlignment( new Alignment(oldAlignment) );\r
- oldAlignment = null;\r
- ap.repaint();\r
- }\r
\r
+ if (af.historyList.contains(hi))\r
+ {\r
+ af.historyList.remove(hi);\r
+ af.updateEditMenuBar();\r
+ }\r
+ }\r
+ }\r
\r
public void valueField_actionPerformed(ActionEvent e)\r
{\r
- try{\r
+ try\r
+ {\r
int i = Integer.parseInt(valueField.getText());\r
slider.setValue(i);\r
}\r
- catch(Exception ex)\r
+ catch (Exception ex)\r
{\r
- valueField.setText( slider.getValue()+"" );\r
+ valueField.setText(slider.getValue() + "");\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff