2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
19 package jalview.gui;
\r
23 import java.awt.event.*;
\r
24 import javax.swing.event.*;
\r
26 import jalview.datamodel.*;
\r
27 import jalview.jbgui.*;
\r
29 public class RedundancyPanel
\r
30 extends GSliderPanel
\r
34 Stack historyList = new Stack(); // simpler than synching with alignFrame.
\r
36 public RedundancyPanel(AlignmentPanel ap, AlignFrame af)
\r
40 label.setText("Enter the redundancy threshold");
\r
42 slider.addChangeListener(new ChangeListener()
\r
44 public void stateChanged(ChangeEvent evt)
\r
46 valueField.setText(slider.getValue() + "");
\r
50 slider.setMinimum(0);
\r
51 slider.setMaximum(100);
\r
52 slider.setValue(100);
\r
55 public void applyButton_actionPerformed(ActionEvent e)
\r
57 float threshold = slider.getValue();
\r
60 historyList.push(it = new HistoryItem("Remove redundancy",
\r
61 ap.av.alignment, HistoryItem.HIDE));
\r
63 if ( (historyList.size() == 1) ||
\r
64 !af.historyList.contains(historyList.firstElement()))
\r
66 af.addHistoryItem( (HistoryItem) historyList.firstElement());
\r
67 af.updateEditMenuBar();
\r
70 undoButton.setEnabled(true);
\r
72 SequenceGroup sg = ap.av.getSelectionGroup();
\r
74 if ( (sg != null) && (sg.getSize() >= 1))
\r
76 del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);
\r
78 for (int i = 0; i < del.size(); i++)
\r
80 if (sg.sequences.contains( (SequenceI) del.elementAt(i)))
\r
82 sg.deleteSequence( (SequenceI) del.elementAt(i), true);
\r
88 Vector s = new Vector();
\r
91 while (i < ap.av.alignment.getHeight())
\r
93 s.addElement(ap.av.alignment.getSequenceAt(i));
\r
97 del = ap.av.alignment.removeRedundancy(threshold, s);
\r
100 // This has to be done before the restoreHistoryItem method of alignFrame will
\r
101 // actually restore these sequences.
\r
102 if (del.size() > 0)
\r
104 for (int i = 0, j = del.size(); i < j; i++)
\r
106 SequenceI sq = (SequenceI) del.elementAt(i);
\r
107 sq.deleteChars(0, sq.getLength());
\r
111 ap.av.firePropertyChange("alignment", null,
\r
112 ap.av.getAlignment().getSequences());
\r
113 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
\r
115 if (ap.av.getAlignment().getHeight() < 1)
\r
119 af.setClosed(true);
\r
121 catch (Exception ex)
\r
126 ap.av.updateConservation();
\r
127 ap.av.updateConsensus();
\r
128 af.updateEditMenuBar();
\r
132 public void undoButton_actionPerformed(ActionEvent e)
\r
134 HistoryItem hi = (HistoryItem) historyList.pop();
\r
135 af.restoreHistoryItem(hi);
\r
137 if (historyList.size() == 0)
\r
139 undoButton.setEnabled(false);
\r
141 if (af.historyList.contains(hi))
\r
143 af.historyList.remove(hi);
\r
144 af.updateEditMenuBar();
\r
149 public void valueField_actionPerformed(ActionEvent e)
\r
153 int i = Integer.parseInt(valueField.getText());
\r
154 slider.setValue(i);
\r
156 catch (Exception ex)
\r
158 valueField.setText(slider.getValue() + "");
\r