Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
RedundancyPanel	43	92	29	0.00%	Show methods

Class RedundancyPanel

Class RedundancyPanel	Line # 43	Total Statements 92	Complexity 29	TOTAL Coverage 0.00%
adjustmentValueChanged(AdjustmentEvent) : void   adjustmentValueChanged(AdjustmentEvent) : void	7777	2.02	1.01	0.0 0.00%
RedundancyPanel(AlignmentPanel)   RedundancyPanel(AlignmentPanel)	5656	19.019	1.01	0.0 0.00%
run() : void   run() : void	108108	24.024	3.03	0.0 0.00%
sliderValueChanged() : void   sliderValueChanged() : void	155155	9.09	4.04	0.0 0.00%
applyButton_actionPerformed() : void   applyButton_actionPerformed() : void	178178	24.024	8.08	0.0 0.00%
undoButton_actionPerformed() : void   undoButton_actionPerformed() : void	237237	9.09	3.03	0.0 0.00%
valueField_actionPerformed(ActionEvent) : void   valueField_actionPerformed(ActionEvent) : void	259259	4.04	2.02	0.0 0.00%
windowOpened(WindowEvent) : void   windowOpened(WindowEvent) : void	271271	0.00	1.01	-1.0 -1.0 -
windowClosing(WindowEvent) : void   windowClosing(WindowEvent) : void	276276	1.01	1.01	0.0 0.00%
windowClosed(WindowEvent) : void   windowClosed(WindowEvent) : void	282282	0.00	1.01	-1.0 -1.0 -
windowActivated(WindowEvent) : void   windowActivated(WindowEvent) : void	287287	0.00	1.01	-1.0 -1.0 -
windowDeactivated(WindowEvent) : void   windowDeactivated(WindowEvent) : void	292292	0.00	1.01	-1.0 -1.0 -
windowIconified(WindowEvent) : void   windowIconified(WindowEvent) : void	297297	0.00	1.01	-1.0 -1.0 -
windowDeiconified(WindowEvent) : void   windowDeiconified(WindowEvent) : void	302302	0.00	1.01	-1.0 -1.0 -

 

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.appletgui;
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.AlignmentI;
28		import jalview.datamodel.SequenceGroup;
29		import jalview.datamodel.SequenceI;
30		import jalview.util.MessageManager;
31
32		import java.awt.Frame;
33		import java.awt.event.ActionEvent;
34		import java.awt.event.AdjustmentEvent;
35		import java.awt.event.AdjustmentListener;
36		import java.awt.event.WindowEvent;
37		import java.awt.event.WindowListener;
38		import java.util.ArrayList;
39		import java.util.List;
40		import java.util.Stack;
41		import java.util.Vector;
42
		0% Uncovered Elements: 132 (132) Complexity: 29 Complexity Density: 0.32
43		public class RedundancyPanel extends SliderPanel
44		implements Runnable, WindowListener
45		{
46		Stack historyList = new Stack(); // simpler than synching with alignFrame.
47
48		float[] redundancy;
49
50		SequenceI[] originalSequences;
51
52		Frame frame;
53
54		Vector redundantSeqs;
55
		0% Uncovered Elements: 19 (19) Complexity: 1 Complexity Density: 0.05
56	0	public RedundancyPanel(AlignmentPanel ap)...
57		{
58	0	super(ap, 0, false, null);
59
60	0	redundantSeqs = new Vector();
61	0	this.ap = ap;
62	0	undoButton.setVisible(true);
63	0	applyButton.setVisible(true);
64	0	allGroupsCheck.setVisible(false);
65
66	0	label.setText(
67		MessageManager.getString("label.enter_redundancy_threshold"));
68	0	valueField.setText("100");
69
70	0	slider.setVisibleAmount(1);
71	0	slider.setMinimum(0);
72	0	slider.setMaximum(100 + slider.getVisibleAmount());
73	0	slider.setValue(100);
74
75	0	slider.addAdjustmentListener(new AdjustmentListener()
76		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
77	0	@Override...
78		public void adjustmentValueChanged(AdjustmentEvent evt)
79		{
80	0	valueField.setText(String.valueOf(slider.getValue()));
81	0	sliderValueChanged();
82		}
83		});
84
85	0	frame = new Frame();
86	0	frame.add(this);
87	0	jalview.bin.JalviewLite.addFrame(frame, MessageManager
88		.getString("label.redundancy_threshold_selection"), 400, 100);
89
90	0	frame.addWindowListener(this);
91
92	0	Thread worker = new Thread(this);
93	0	worker.start();
94		}
95
96		/**
97		* This is a copy of remove redundancy in jalivew.datamodel.Alignment except
98		* we dont want to remove redundancy, just calculate once so we can use the
99		* slider to dynamically hide redundant sequences
100		*
101		* @param threshold
102		* DOCUMENT ME!
103		* @param sel
104		* DOCUMENT ME!
105		*
106		* @return DOCUMENT ME!
107		*/
		0% Uncovered Elements: 26 (26) Complexity: 3 Complexity Density: 0.12
108	0	@Override...
109		public void run()
110		{
111	0	label.setText(MessageManager.getString("label.calculating"));
112
113	0	slider.setVisible(false);
114	0	applyButton.setEnabled(false);
115	0	valueField.setVisible(false);
116
117	0	validate();
118
119	0	String[] omitHidden = null;
120
121	0	SequenceGroup sg = ap.av.getSelectionGroup();
122	0	int height;
123
124	0	int start, end;
125
126	0	if ((sg != null) && (sg.getSize() >= 1))
127		{
128	0	originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
129	0	start = sg.getStartRes();
130	0	end = sg.getEndRes();
131		}
132		else
133		{
134	0	originalSequences = ap.av.getAlignment().getSequencesArray();
135	0	start = 0;
136	0	end = ap.av.getAlignment().getWidth();
137		}
138
139	0	height = originalSequences.length;
140
141	0	redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
142		omitHidden, start, end, false);
143	0	label.setText(
144		MessageManager.getString("label.enter_redundancy_threshold"));
145	0	slider.setVisible(true);
146	0	applyButton.setEnabled(true);
147	0	valueField.setVisible(true);
148
149	0	validate();
150	0	sliderValueChanged();
151		// jalview.bin.Console.outPrintln("blob done "+
152		// (System.currentTimeMillis()-start));
153		}
154
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.44
155	0	void sliderValueChanged()...
156		{
157	0	if (redundancy == null)
158		{
159	0	return;
160		}
161
162	0	float value = slider.getValue();
163
164	0	List<SequenceI> redundantSequences = new ArrayList<>();
165	0	for (int i = 0; i < redundancy.length; i++)
166		{
167	0	if (value <= redundancy[i])
168		{
169	0	redundantSequences.add(originalSequences[i]);
170		}
171		}
172
173	0	ap.idPanel.idCanvas.setHighlighted(redundantSequences);
174	0	PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
175
176		}
177
		0% Uncovered Elements: 38 (38) Complexity: 8 Complexity Density: 0.33
178	0	@Override...
179		public void applyButton_actionPerformed()
180		{
181	0	Vector del = new Vector();
182
183	0	undoButton.setEnabled(true);
184
185	0	float value = slider.getValue();
186	0	SequenceGroup sg = ap.av.getSelectionGroup();
187
188	0	for (int i = 0; i < redundancy.length; i++)
189		{
190	0	if (value <= redundancy[i])
191		{
192	0	del.addElement(originalSequences[i]);
193		}
194		}
195
196		// This has to be done before the restoreHistoryItem method of alignFrame
197		// will
198		// actually restore these sequences.
199	0	if (del.size() > 0)
200		{
201	0	SequenceI[] deleted = new SequenceI[del.size()];
202
203	0	int width = 0;
204	0	for (int i = 0; i < del.size(); i++)
205		{
206	0	deleted[i] = (SequenceI) del.elementAt(i);
207	0	if (deleted[i].getLength() > width)
208		{
209	0	width = deleted[i].getLength();
210		}
211		}
212
213	0	EditCommand cut = new EditCommand(
214		MessageManager.getString("action.remove_redundancy"),
215		Action.CUT, deleted, 0, width, ap.av.getAlignment());
216	0	AlignmentI alignment = ap.av.getAlignment();
217	0	for (int i = 0; i < del.size(); i++)
218		{
219	0	alignment.deleteSequence(deleted[i]);
220	0	if (sg != null)
221		{
222	0	sg.deleteSequence(deleted[i], false);
223		}
224		}
225
226	0	historyList.push(cut);
227
228	0	ap.alignFrame.addHistoryItem(cut);
229
230	0	PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
231	0	ap.av.firePropertyChange("alignment", null,
232		ap.av.getAlignment().getSequences());
233		}
234
235		}
236
		0% Uncovered Elements: 13 (13) Complexity: 3 Complexity Density: 0.33
237	0	@Override...
238		public void undoButton_actionPerformed()
239		{
240	0	CommandI command = (CommandI) historyList.pop();
241	0	command.undoCommand(null);
242
243	0	if (ap.av.getHistoryList().contains(command))
244		{
245	0	ap.av.getHistoryList().remove(command);
246	0	ap.alignFrame.updateEditMenuBar();
247	0	ap.av.firePropertyChange("alignment", null,
248		ap.av.getAlignment().getSequences());
249		}
250
251	0	ap.paintAlignment(true, true);
252
253	0	if (historyList.size() == 0)
254		{
255	0	undoButton.setEnabled(false);
256		}
257		}
258
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 0.5
259	0	public void valueField_actionPerformed(ActionEvent e)...
260		{
261	0	try
262		{
263	0	int i = Integer.parseInt(valueField.getText());
264	0	slider.setValue(i);
265		} catch (Exception ex)
266		{
267	0	valueField.setText(slider.getValue() + "");
268		}
269		}
270
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
271	0	@Override...
272		public void windowOpened(WindowEvent evt)
273		{
274		}
275
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
276	0	@Override...
277		public void windowClosing(WindowEvent evt)
278		{
279	0	ap.idPanel.idCanvas.setHighlighted(null);
280		}
281
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
282	0	@Override...
283		public void windowClosed(WindowEvent evt)
284		{
285		}
286
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
287	0	@Override...
288		public void windowActivated(WindowEvent evt)
289		{
290		}
291
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
292	0	@Override...
293		public void windowDeactivated(WindowEvent evt)
294		{
295		}
296
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
297	0	@Override...
298		public void windowIconified(WindowEvent evt)
299		{
300		}
301
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
302	0	@Override...
303		public void windowDeiconified(WindowEvent evt)
304		{
305		}
306		}