Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RedundancyPanel	51	94	24	0.00%	Show methods

Class RedundancyPanel

Class RedundancyPanel	Line # 51	Total Statements 94	Complexity 24	TOTAL Coverage 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	8585	2.02	1.01	0.0 0.00%
internalFrameClosing(InternalFrameEvent) : void   internalFrameClosing(InternalFrameEvent) : void	111111	1.01	1.01	0.0 0.00%
RedundancyPanel(AlignmentPanel,AlignFrame)   RedundancyPanel(AlignmentPanel,AlignFrame)	7777	16.016	1.01	0.0 0.00%
run() : void   run() : void	132132	32.032	4.04	0.0 0.00%
sliderValueChanged() : void   sliderValueChanged() : void	190190	8.08	4.04	0.0 0.00%
applyButton_actionPerformed(ActionEvent) : void   applyButton_actionPerformed(ActionEvent) : void	215215	23.023	8.08	0.0 0.00%
undoButton_actionPerformed(ActionEvent) : void   undoButton_actionPerformed(ActionEvent) : void	279279	12.012	5.05	0.0 0.00%

 

Contributing tests

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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		*/
		0% Uncovered Elements: 131 (131) 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: 16 (16) Complexity: 1 Complexity Density: 0.06
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.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		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
111	0	@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		*/
		0% Uncovered Elements: 36 (36) Complexity: 4 Complexity Density: 0.12
132	0	@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
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.5
190	0	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		*/
		0% Uncovered Elements: 37 (37) Complexity: 8 Complexity Density: 0.35
215	0	@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		*/
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.42
279	0	@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		}