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Coverage Report

  1. Project Clover database Thu Nov 28 2024 18:06:40 GMT
  2. Package jalview.gui

File RedundancyPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
63% of files have more coverage

Code metrics

30
94
7
1
306
196
24
0.26
13.43
7
3.43

Classes

Class Line # Actions
RedundancyPanel 51 94 24
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.gui;
22   
23    import java.awt.event.ActionEvent;
24    import java.util.ArrayList;
25    import java.util.List;
26    import java.util.Stack;
27    import java.util.Vector;
28   
29    import javax.swing.JInternalFrame;
30    import javax.swing.JProgressBar;
31    import javax.swing.event.ChangeEvent;
32    import javax.swing.event.ChangeListener;
33    import javax.swing.event.InternalFrameAdapter;
34    import javax.swing.event.InternalFrameEvent;
35   
36    import jalview.analysis.AlignSeq;
37    import jalview.commands.CommandI;
38    import jalview.commands.EditCommand;
39    import jalview.commands.EditCommand.Action;
40    import jalview.datamodel.SequenceGroup;
41    import jalview.datamodel.SequenceI;
42    import jalview.jbgui.GSliderPanel;
43    import jalview.util.MessageManager;
44   
45    /**
46    * DOCUMENT ME!
47    *
48    * @author $author$
49    * @version $Revision$
50    */
 
51    public class RedundancyPanel extends GSliderPanel implements Runnable
52    {
53    AlignFrame af;
54   
55    AlignmentPanel ap;
56   
57    Stack<CommandI> historyList = new Stack<>();
58   
59    // simpler than synching with alignFrame.
60   
61    float[] redundancy;
62   
63    SequenceI[] originalSequences;
64   
65    JInternalFrame frame;
66   
67    Vector redundantSeqs;
68   
69    /**
70    * Creates a new RedundancyPanel object.
71    *
72    * @param ap
73    * DOCUMENT ME!
74    * @param af
75    * DOCUMENT ME!
76    */
 
77  0 toggle public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
78    {
79  0 this.ap = ap;
80  0 this.af = af;
81  0 redundantSeqs = new Vector();
82   
83  0 slider.addChangeListener(new ChangeListener()
84    {
 
85  0 toggle @Override
86    public void stateChanged(ChangeEvent evt)
87    {
88  0 valueField.setText(slider.getValue() + "");
89  0 sliderValueChanged();
90    }
91    });
92   
93  0 applyButton.setText(MessageManager.getString("action.remove"));
94  0 allGroupsCheck.setVisible(false);
95  0 slider.setMinimum(0);
96  0 slider.setMaximum(100);
97  0 slider.setValue(100);
98   
99  0 Thread worker = new Thread(this);
100  0 worker.start();
101   
102  0 frame = new JInternalFrame();
103  0 frame.setFrameIcon(null);
104  0 frame.setContentPane(this);
105  0 Desktop.addInternalFrame(frame,
106    MessageManager
107    .getString("label.redundancy_threshold_selection"),
108    true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
109  0 frame.addInternalFrameListener(new InternalFrameAdapter()
110    {
 
111  0 toggle @Override
112    public void internalFrameClosing(InternalFrameEvent evt)
113    {
114  0 ap.getIdPanel().getIdCanvas().setHighlighted(null);
115    }
116    });
117   
118    }
119   
120    /**
121    * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
122    * we dont want to remove redundancy, just calculate once so we can use the
123    * slider to dynamically hide redundant sequences
124    *
125    * @param threshold
126    * DOCUMENT ME!
127    * @param sel
128    * DOCUMENT ME!
129    *
130    * @return DOCUMENT ME!
131    */
 
132  0 toggle @Override
133    public void run()
134    {
135  0 JProgressBar progress = new JProgressBar();
136  0 progress.setIndeterminate(true);
137  0 southPanel.add(progress, java.awt.BorderLayout.SOUTH);
138   
139  0 label.setText(MessageManager.getString("label.calculating"));
140   
141  0 slider.setVisible(false);
142  0 applyButton.setEnabled(false);
143  0 valueField.setVisible(false);
144   
145  0 validate();
146   
147  0 String[] omitHidden = null;
148   
149  0 SequenceGroup sg = ap.av.getSelectionGroup();
150  0 int height;
151   
152  0 int start, end;
153   
154  0 if ((sg != null) && (sg.getSize() >= 1))
155    {
156  0 originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
157  0 start = sg.getStartRes();
158  0 end = sg.getEndRes();
159    }
160    else
161    {
162  0 originalSequences = ap.av.getAlignment().getSequencesArray();
163  0 start = 0;
164  0 end = ap.av.getAlignment().getWidth();
165    }
166   
167  0 height = originalSequences.length;
168  0 if (ap.av.hasHiddenColumns())
169    {
170  0 omitHidden = ap.av.getViewAsString(sg != null);
171    }
172  0 redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
173    omitHidden, start, end, false);
174   
175  0 progress.setIndeterminate(false);
176  0 progress.setVisible(false);
177  0 progress = null;
178   
179  0 label.setText(
180    MessageManager.getString("label.enter_redundancy_threshold"));
181  0 slider.setVisible(true);
182  0 applyButton.setEnabled(true);
183  0 valueField.setVisible(true);
184   
185  0 validate();
186  0 sliderValueChanged();
187    // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
188    }
189   
 
190  0 toggle void sliderValueChanged()
191    {
192  0 if (redundancy == null)
193    {
194  0 return;
195    }
196   
197  0 float value = slider.getValue();
198  0 List<SequenceI> redundantSequences = new ArrayList<>();
199  0 for (int i = 0; i < redundancy.length; i++)
200    {
201  0 if (value <= redundancy[i])
202    {
203  0 redundantSequences.add(originalSequences[i]);
204    }
205    }
206  0 ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
207    }
208   
209    /**
210    * DOCUMENT ME!
211    *
212    * @param e
213    * DOCUMENT ME!
214    */
 
215  0 toggle @Override
216    public void applyButton_actionPerformed(ActionEvent e)
217    {
218  0 List<SequenceI> del = new ArrayList<>();
219   
220  0 undoButton.setEnabled(true);
221   
222  0 float value = slider.getValue();
223  0 SequenceGroup sg = ap.av.getSelectionGroup();
224   
225  0 for (int i = 0; i < redundancy.length; i++)
226    {
227  0 if (value <= redundancy[i])
228    {
229  0 del.add(originalSequences[i]);
230    }
231    }
232   
233    // This has to be done before the restoreHistoryItem method of alignFrame
234    // will actually restore these sequences.
235  0 if (del.size() > 0)
236    {
237  0 SequenceI[] deleted = new SequenceI[del.size()];
238   
239  0 int width = 0;
240  0 for (int i = 0; i < del.size(); i++)
241    {
242  0 deleted[i] = del.get(i);
243  0 if (deleted[i].getLength() > width)
244    {
245  0 width = deleted[i].getLength();
246    }
247    }
248   
249  0 EditCommand cut = new EditCommand(
250    MessageManager.getString("action.remove_redundancy"),
251    Action.CUT, deleted, 0, width, ap.av.getAlignment());
252   
253  0 for (int i = 0; i < del.size(); i++)
254    {
255  0 ap.av.getAlignment().deleteSequence(deleted[i]);
256  0 if (sg != null)
257    {
258  0 sg.deleteSequence(deleted[i], false);
259    }
260    }
261   
262  0 historyList.push(cut);
263   
264  0 ap.alignFrame.addHistoryItem(cut);
265   
266  0 PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
267  0 ap.av.firePropertyChange("alignment", null,
268    ap.av.getAlignment().getSequences());
269    }
270   
271    }
272   
273    /**
274    * DOCUMENT ME!
275    *
276    * @param e
277    * DOCUMENT ME!
278    */
 
279  0 toggle @Override
280    public void undoButton_actionPerformed(ActionEvent e)
281    {
282  0 if (historyList == null || historyList.isEmpty())
283    {
284  0 undoButton.setEnabled(false);
285  0 return;
286    }
287   
288  0 CommandI command = historyList.pop();
289  0 if (ap.av.getHistoryList().contains(command))
290    {
291  0 command.undoCommand(af.getViewAlignments());
292  0 ap.av.getHistoryList().remove(command);
293  0 ap.av.firePropertyChange("alignment", null,
294    ap.av.getAlignment().getSequences());
295  0 af.updateEditMenuBar();
296    }
297   
298  0 ap.paintAlignment(true, true);
299   
300  0 if (historyList.size() == 0)
301    {
302  0 undoButton.setEnabled(false);
303    }
304    }
305   
306    }