Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
RedundancyPanel	51	93	24	130	0.00%	Show methods

Class RedundancyPanel

Class RedundancyPanel	Line # 51	Total Statements 93	Complexity 24	Uncovered Elements 130	TOTAL Coverage 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	8585	2.02	1.01	2.02	0.0 0.00%
internalFrameClosing(InternalFrameEvent) : void   internalFrameClosing(InternalFrameEvent) : void	110110	1.01	1.01	1.01	0.0 0.00%
RedundancyPanel(AlignmentPanel,AlignFrame)   RedundancyPanel(AlignmentPanel,AlignFrame)	7777	15.015	1.01	15.015	0.0 0.00%
run() : void   run() : void	131131	32.032	4.04	36.036	0.0 0.00%
sliderValueChanged() : void   sliderValueChanged() : void	189189	8.08	4.04	14.014	0.0 0.00%
applyButton_actionPerformed(ActionEvent) : void   applyButton_actionPerformed(ActionEvent) : void	214214	23.023	8.08	37.037	0.0 0.00%
undoButton_actionPerformed(ActionEvent) : void   undoButton_actionPerformed(ActionEvent) : void	278278	12.012	5.05	18.018	0.0 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 jalview.analysis.AlignSeq;
24		import jalview.commands.CommandI;
25		import jalview.commands.EditCommand;
26		import jalview.commands.EditCommand.Action;
27		import jalview.datamodel.SequenceGroup;
28		import jalview.datamodel.SequenceI;
29		import jalview.jbgui.GSliderPanel;
30		import jalview.util.MessageManager;
31
32		import java.awt.event.ActionEvent;
33		import java.util.ArrayList;
34		import java.util.List;
35		import java.util.Stack;
36		import java.util.Vector;
37
38		import javax.swing.JInternalFrame;
39		import javax.swing.JProgressBar;
40		import javax.swing.event.ChangeEvent;
41		import javax.swing.event.ChangeListener;
42		import javax.swing.event.InternalFrameAdapter;
43		import javax.swing.event.InternalFrameEvent;
44
45		/**
46		* DOCUMENT ME!
47		*
48		* @author $author$
49		* @version $Revision$
50		*/
		0% Uncovered Elements: 130 (130) Complexity: 24 Complexity Density: 0.26
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		*/
		0% Uncovered Elements: 15 (15) Complexity: 1 Complexity Density: 0.07
77	0	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		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
85	0	@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.setContentPane(this);
104	0	Desktop.addInternalFrame(frame,
105		MessageManager
106		.getString("label.redundancy_threshold_selection"),
107		true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
108	0	frame.addInternalFrameListener(new InternalFrameAdapter()
109		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public void internalFrameClosing(InternalFrameEvent evt)
112		{
113	0	ap.getIdPanel().getIdCanvas().setHighlighted(null);
114		}
115		});
116
117		}
118
119		/**
120		* This is a copy of remove redundancy in jalivew.datamodel.Alignment except
121		* we dont want to remove redundancy, just calculate once so we can use the
122		* slider to dynamically hide redundant sequences
123		*
124		* @param threshold
125		* DOCUMENT ME!
126		* @param sel
127		* DOCUMENT ME!
128		*
129		* @return DOCUMENT ME!
130		*/
		0% Uncovered Elements: 36 (36) Complexity: 4 Complexity Density: 0.12
131	0	@Override...
132		public void run()
133		{
134	0	JProgressBar progress = new JProgressBar();
135	0	progress.setIndeterminate(true);
136	0	southPanel.add(progress, java.awt.BorderLayout.SOUTH);
137
138	0	label.setText(MessageManager.getString("label.calculating"));
139
140	0	slider.setVisible(false);
141	0	applyButton.setEnabled(false);
142	0	valueField.setVisible(false);
143
144	0	validate();
145
146	0	String[] omitHidden = null;
147
148	0	SequenceGroup sg = ap.av.getSelectionGroup();
149	0	int height;
150
151	0	int start, end;
152
153	0	if ((sg != null) && (sg.getSize() >= 1))
154		{
155	0	originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
156	0	start = sg.getStartRes();
157	0	end = sg.getEndRes();
158		}
159		else
160		{
161	0	originalSequences = ap.av.getAlignment().getSequencesArray();
162	0	start = 0;
163	0	end = ap.av.getAlignment().getWidth();
164		}
165
166	0	height = originalSequences.length;
167	0	if (ap.av.hasHiddenColumns())
168		{
169	0	omitHidden = ap.av.getViewAsString(sg != null);
170		}
171	0	redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
172		omitHidden, start, end, false);
173
174	0	progress.setIndeterminate(false);
175	0	progress.setVisible(false);
176	0	progress = null;
177
178	0	label.setText(
179		MessageManager.getString("label.enter_redundancy_threshold"));
180	0	slider.setVisible(true);
181	0	applyButton.setEnabled(true);
182	0	valueField.setVisible(true);
183
184	0	validate();
185	0	sliderValueChanged();
186		// System.out.println((System.currentTimeMillis()-start));
187		}
188
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.5
189	0	void sliderValueChanged()...
190		{
191	0	if (redundancy == null)
192		{
193	0	return;
194		}
195
196	0	float value = slider.getValue();
197	0	List<SequenceI> redundantSequences = new ArrayList<>();
198	0	for (int i = 0; i < redundancy.length; i++)
199		{
200	0	if (value <= redundancy[i])
201		{
202	0	redundantSequences.add(originalSequences[i]);
203		}
204		}
205	0	ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
206		}
207
208		/**
209		* DOCUMENT ME!
210		*
211		* @param e
212		* DOCUMENT ME!
213		*/
		0% Uncovered Elements: 37 (37) Complexity: 8 Complexity Density: 0.35
214	0	@Override...
215		public void applyButton_actionPerformed(ActionEvent e)
216		{
217	0	List<SequenceI> del = new ArrayList<>();
218
219	0	undoButton.setEnabled(true);
220
221	0	float value = slider.getValue();
222	0	SequenceGroup sg = ap.av.getSelectionGroup();
223
224	0	for (int i = 0; i < redundancy.length; i++)
225		{
226	0	if (value <= redundancy[i])
227		{
228	0	del.add(originalSequences[i]);
229		}
230		}
231
232		// This has to be done before the restoreHistoryItem method of alignFrame
233		// will actually restore these sequences.
234	0	if (del.size() > 0)
235		{
236	0	SequenceI[] deleted = new SequenceI[del.size()];
237
238	0	int width = 0;
239	0	for (int i = 0; i < del.size(); i++)
240		{
241	0	deleted[i] = del.get(i);
242	0	if (deleted[i].getLength() > width)
243		{
244	0	width = deleted[i].getLength();
245		}
246		}
247
248	0	EditCommand cut = new EditCommand(
249		MessageManager.getString("action.remove_redundancy"),
250		Action.CUT, deleted, 0, width, ap.av.getAlignment());
251
252	0	for (int i = 0; i < del.size(); i++)
253		{
254	0	ap.av.getAlignment().deleteSequence(deleted[i]);
255	0	if (sg != null)
256		{
257	0	sg.deleteSequence(deleted[i], false);
258		}
259		}
260
261	0	historyList.push(cut);
262
263	0	ap.alignFrame.addHistoryItem(cut);
264
265	0	PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
266	0	ap.av.firePropertyChange("alignment", null,
267		ap.av.getAlignment().getSequences());
268		}
269
270		}
271
272		/**
273		* DOCUMENT ME!
274		*
275		* @param e
276		* DOCUMENT ME!
277		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
278	0	@Override...
279		public void undoButton_actionPerformed(ActionEvent e)
280		{
281	0	if (historyList == null || historyList.isEmpty())
282		{
283	0	undoButton.setEnabled(false);
284	0	return;
285		}
286
287	0	CommandI command = historyList.pop();
288	0	if (ap.av.getHistoryList().contains(command))
289		{
290	0	command.undoCommand(af.getViewAlignments());
291	0	ap.av.getHistoryList().remove(command);
292	0	ap.av.firePropertyChange("alignment", null,
293		ap.av.getAlignment().getSequences());
294	0	af.updateEditMenuBar();
295		}
296
297	0	ap.paintAlignment(true, true);
298
299	0	if (historyList.size() == 0)
300		{
301	0	undoButton.setEnabled(false);
302		}
303		}
304
305		}