Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GPCAPanel	46	115	34	0.7248322472.5%	Show methods

Class GPCAPanel

Class GPCAPanel	Line # 46	Total Statements 115	Complexity 34	TOTAL Coverage 0.7248322472.5%
GPCAPanel()   GPCAPanel()	7575	1.01	1.01	0.0 0.00%
GPCAPanel(int)   GPCAPanel(int)	8080	7.07	3.03	0.8888889 0.888888988.9%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	119119	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	128128	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	137137	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	148148	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	161161	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	170170	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	180180	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	190190	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	201201	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	211211	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	222222	1.01	1.01	0.0 0.00%
menuSelected(MenuEvent) : void   menuSelected(MenuEvent) : void	231231	1.01	1.01	0.0 0.00%
menuDeselected(MenuEvent) : void   menuDeselected(MenuEvent) : void	237237	0.00	1.01	-1.0 -1.0 -
menuCanceled(MenuEvent) : void   menuCanceled(MenuEvent) : void	242242	0.00	1.01	-1.0 -1.0 -
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	250250	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	260260	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	270270	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	9898	92.092	1.01	1.0 1.0100%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	318318	0.00	1.01	-1.0 -1.0 -
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	322322	0.00	1.01	-1.0 -1.0 -
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	326326	0.00	1.01	-1.0 -1.0 -
outputAlignment_actionPerformed() : void   outputAlignment_actionPerformed() : void	330330	0.00	1.01	-1.0 -1.0 -
makePCAImage(TYPE) : void   makePCAImage(TYPE) : void	334334	0.00	1.01	-1.0 -1.0 -
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	338338	0.00	1.01	-1.0 -1.0 -
print_actionPerformed() : void   print_actionPerformed() : void	342342	0.00	1.01	-1.0 -1.0 -
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	346346	0.00	1.01	-1.0 -1.0 -
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	350350	0.00	1.01	-1.0 -1.0 -
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	354354	0.00	1.01	-1.0 -1.0 -
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	358358	0.00	1.01	-1.0 -1.0 -
doDimensionChange() : void   doDimensionChange() : void	362362	0.00	1.01	-1.0 -1.0 -

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.72483224	jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation	1PASS

 

Source view

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.jbgui;
22
23		import java.awt.BorderLayout;
24		import java.awt.Color;
25		import java.awt.FlowLayout;
26		import java.awt.Font;
27		import java.awt.GridLayout;
28		import java.awt.event.ActionEvent;
29		import java.awt.event.ActionListener;
30
31		import javax.swing.JButton;
32		import javax.swing.JCheckBoxMenuItem;
33		import javax.swing.JComboBox;
34		import javax.swing.JInternalFrame;
35		import javax.swing.JLabel;
36		import javax.swing.JMenu;
37		import javax.swing.JMenuBar;
38		import javax.swing.JMenuItem;
39		import javax.swing.JPanel;
40		import javax.swing.event.MenuEvent;
41		import javax.swing.event.MenuListener;
42
43		import jalview.util.ImageMaker.TYPE;
44		import jalview.util.MessageManager;
45
		72.5% Uncovered Elements: 41 (149) Complexity: 34 Complexity Density: 0.3
46		public class GPCAPanel extends JInternalFrame
47		{
48		private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
49
50		protected JComboBox<String> xCombobox = new JComboBox<>();
51
52		protected JComboBox<String> yCombobox = new JComboBox<>();
53
54		protected JComboBox<String> zCombobox = new JComboBox<>();
55
56		protected JMenu viewMenu = new JMenu();
57
58		protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
59
60		protected JMenu associateViewsMenu = new JMenu();
61
62		protected JLabel statusBar = new JLabel();
63
64		protected JPanel statusPanel = new JPanel();
65
66		protected JMenuItem originalSeqData;
67
68		protected JMenuItem outputAlignment;
69
70		protected JMenu doClustering;
71
72		/**
73		* Constructor
74		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	public GPCAPanel()...
76		{
77	0	this(8);
78		}
79
		88.9% Uncovered Elements: 1 (9) Complexity: 3 Complexity Density: 0.43
80	2	public GPCAPanel(int dim)...
81		{
82	2	try
83		{
84	2	jbInit();
85		} catch (Exception e)
86		{
87	0	e.printStackTrace();
88		}
89
90	18	for (int i = 1; i <= dim; i++)
91		{
92	16	xCombobox.addItem("dim " + i);
93	16	yCombobox.addItem("dim " + i);
94	16	zCombobox.addItem("dim " + i);
95		}
96		}
97
		100% Uncovered Elements: 0 (92) Complexity: 1 Complexity Density: 0.01
98	2	private void jbInit() throws Exception...
99		{
100	2	setFrameIcon(null);
101	2	setName("jalview-"+this.getClass().getName());
102	2	this.getContentPane().setLayout(new BorderLayout());
103	2	JPanel jPanel2 = new JPanel();
104	2	jPanel2.setLayout(new FlowLayout());
105	2	JLabel jLabel1 = new JLabel();
106	2	jLabel1.setFont(VERDANA_12);
107	2	jLabel1.setText("x=");
108	2	JLabel jLabel2 = new JLabel();
109	2	jLabel2.setFont(VERDANA_12);
110	2	jLabel2.setText("y=");
111	2	JLabel jLabel3 = new JLabel();
112	2	jLabel3.setFont(VERDANA_12);
113	2	jLabel3.setText("z=");
114	2	jPanel2.setBackground(Color.white);
115	2	jPanel2.setBorder(null);
116	2	zCombobox.setFont(VERDANA_12);
117	2	zCombobox.addActionListener(new ActionListener()
118		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
119	4	@Override...
120		public void actionPerformed(ActionEvent e)
121		{
122	4	doDimensionChange();
123		}
124		});
125	2	yCombobox.setFont(VERDANA_12);
126	2	yCombobox.addActionListener(new ActionListener()
127		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
128	4	@Override...
129		public void actionPerformed(ActionEvent e)
130		{
131	4	doDimensionChange();
132		}
133		});
134	2	xCombobox.setFont(VERDANA_12);
135	2	xCombobox.addActionListener(new ActionListener()
136		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
137	4	@Override...
138		public void actionPerformed(ActionEvent e)
139		{
140	4	doDimensionChange();
141		}
142		});
143	2	JButton resetButton = new JButton();
144	2	resetButton.setFont(VERDANA_12);
145	2	resetButton.setText(MessageManager.getString("action.reset"));
146	2	resetButton.addActionListener(new ActionListener()
147		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
148	0	@Override...
149		public void actionPerformed(ActionEvent e)
150		{
151	0	resetButton_actionPerformed();
152		}
153		});
154	2	JMenu fileMenu = new JMenu();
155	2	fileMenu.setText(MessageManager.getString("action.file"));
156	2	JMenu saveMenu = new JMenu();
157	2	saveMenu.setText(MessageManager.getString("action.save_as"));
158	2	JMenuItem eps = new JMenuItem("EPS");
159	2	eps.addActionListener(new ActionListener()
160		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	@Override...
162		public void actionPerformed(ActionEvent e)
163		{
164	0	makePCAImage(TYPE.EPS);
165		}
166		});
167	2	JMenuItem png = new JMenuItem("PNG");
168	2	png.addActionListener(new ActionListener()
169		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@Override...
171		public void actionPerformed(ActionEvent e)
172		{
173	0	makePCAImage(TYPE.PNG);
174		}
175		});
176	2	JMenuItem outputValues = new JMenuItem();
177	2	outputValues.setText(MessageManager.getString("label.output_values"));
178	2	outputValues.addActionListener(new ActionListener()
179		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public void actionPerformed(ActionEvent e)
182		{
183	0	outputValues_actionPerformed();
184		}
185		});
186	2	JMenuItem outputPoints = new JMenuItem();
187	2	outputPoints.setText(MessageManager.getString("label.output_points"));
188	2	outputPoints.addActionListener(new ActionListener()
189		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
190	0	@Override...
191		public void actionPerformed(ActionEvent e)
192		{
193	0	outputPoints_actionPerformed();
194		}
195		});
196	2	JMenuItem outputProjPoints = new JMenuItem();
197	2	outputProjPoints.setText(
198		MessageManager.getString("label.output_transformed_points"));
199	2	outputProjPoints.addActionListener(new ActionListener()
200		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
201	0	@Override...
202		public void actionPerformed(ActionEvent e)
203		{
204	0	outputProjPoints_actionPerformed();
205		}
206		});
207	2	JMenuItem print = new JMenuItem();
208	2	print.setText(MessageManager.getString("action.print"));
209	2	print.addActionListener(new ActionListener()
210		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
211	0	@Override...
212		public void actionPerformed(ActionEvent e)
213		{
214	0	print_actionPerformed();
215		}
216		});
217	2	outputAlignment = new JMenuItem();
218	2	outputAlignment
219		.setText(MessageManager.getString("label.output_alignment"));
220	2	outputAlignment.addActionListener(new ActionListener()
221		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
222	0	@Override...
223		public void actionPerformed(ActionEvent e)
224		{
225	0	outputAlignment_actionPerformed();
226		}
227		});
228	2	viewMenu.setText(MessageManager.getString("action.view"));
229	2	viewMenu.addMenuListener(new MenuListener()
230		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
231	0	@Override...
232		public void menuSelected(MenuEvent e)
233		{
234	0	viewMenu_menuSelected();
235		}
236
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
237	0	@Override...
238		public void menuDeselected(MenuEvent e)
239		{
240		}
241
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
242	0	@Override...
243		public void menuCanceled(MenuEvent e)
244		{
245		}
246		});
247	2	showLabels.setText(MessageManager.getString("label.show_labels"));
248	2	showLabels.addActionListener(new ActionListener()
249		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
250	0	@Override...
251		public void actionPerformed(ActionEvent e)
252		{
253	0	showLabels_actionPerformed();
254		}
255		});
256	2	JMenuItem bgcolour = new JMenuItem();
257	2	bgcolour.setText(MessageManager.getString("action.background_colour"));
258	2	bgcolour.addActionListener(new ActionListener()
259		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
260	0	@Override...
261		public void actionPerformed(ActionEvent e)
262		{
263	0	bgcolour_actionPerformed();
264		}
265		});
266	2	originalSeqData = new JMenuItem();
267	2	originalSeqData.setText(MessageManager.getString("label.input_data"));
268	2	originalSeqData.addActionListener(new ActionListener()
269		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
270	0	@Override...
271		public void actionPerformed(ActionEvent e)
272		{
273	0	originalSeqData_actionPerformed();
274		}
275		});
276	2	associateViewsMenu.setText(
277		MessageManager.getString("label.associate_nodes_with"));
278
279	2	doClustering = new JMenu();
280	2	doClustering.setText(MessageManager.getString("label.cluster"));
281
282	2	statusPanel.setLayout(new GridLayout());
283	2	statusBar.setFont(VERDANA_12);
284		// statusPanel.setBackground(Color.lightGray);
285		// statusBar.setBackground(Color.lightGray);
286		// statusPanel.add(statusBar, null);
287	2	JPanel panelBar = new JPanel(new BorderLayout());
288	2	panelBar.add(jPanel2, BorderLayout.NORTH);
289	2	panelBar.add(statusPanel, BorderLayout.SOUTH);
290	2	this.getContentPane().add(panelBar, BorderLayout.SOUTH);
291	2	jPanel2.add(jLabel1, null);
292	2	jPanel2.add(xCombobox, null);
293	2	jPanel2.add(jLabel2, null);
294	2	jPanel2.add(yCombobox, null);
295	2	jPanel2.add(jLabel3, null);
296	2	jPanel2.add(zCombobox, null);
297	2	jPanel2.add(resetButton, null);
298
299	2	JMenuBar jMenuBar1 = new JMenuBar();
300	2	jMenuBar1.add(fileMenu);
301	2	jMenuBar1.add(viewMenu);
302	2	jMenuBar1.add(doClustering);
303	2	setJMenuBar(jMenuBar1);
304	2	fileMenu.add(saveMenu);
305	2	fileMenu.add(outputValues);
306	2	fileMenu.add(print);
307	2	fileMenu.add(originalSeqData);
308	2	fileMenu.add(outputPoints);
309	2	fileMenu.add(outputProjPoints);
310	2	fileMenu.add(outputAlignment);
311	2	saveMenu.add(eps);
312	2	saveMenu.add(png);
313	2	viewMenu.add(showLabels);
314	2	viewMenu.add(bgcolour);
315	2	viewMenu.add(associateViewsMenu);
316		}
317
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
318	0	protected void resetButton_actionPerformed()...
319		{
320		}
321
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
322	0	protected void outputPoints_actionPerformed()...
323		{
324		}
325
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
326	0	protected void outputProjPoints_actionPerformed()...
327		{
328		}
329
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
330	0	protected void outputAlignment_actionPerformed()...
331		{
332		}
333
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
334	0	public void makePCAImage(TYPE imageType)...
335		{
336		}
337
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
338	0	protected void outputValues_actionPerformed()...
339		{
340		}
341
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
342	0	protected void print_actionPerformed()...
343		{
344		}
345
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
346	0	protected void showLabels_actionPerformed()...
347		{
348		}
349
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
350	0	protected void bgcolour_actionPerformed()...
351		{
352		}
353
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
354	0	protected void originalSeqData_actionPerformed()...
355		{
356		}
357
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
358	0	protected void viewMenu_menuSelected()...
359		{
360		}
361
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
362	0	protected void doDimensionChange()...
363		{
364		}
365		}