Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GPCAPanel	47	113	34	0.6870748468.7%	Show methods

Class GPCAPanel

Class GPCAPanel	Line # 47	Total Statements 113	Complexity 34	TOTAL Coverage 0.6870748468.7%
GPCAPanel()   GPCAPanel()	7272	7.07	3.03	0.8888889 0.888888988.9%
GPCAPanel(int)   GPCAPanel(int)	9090	7.07	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	129129	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	138138	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	147147	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	158158	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	171171	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	200200	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	221221	1.01	1.01	0.0 0.00%
menuSelected(MenuEvent) : void   menuSelected(MenuEvent) : void	230230	1.01	1.01	0.0 0.00%
menuDeselected(MenuEvent) : void   menuDeselected(MenuEvent) : void	236236	0.00	1.01	-1.0 -1.0 -
menuCanceled(MenuEvent) : void   menuCanceled(MenuEvent) : void	241241	0.00	1.01	-1.0 -1.0 -
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	249249	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	259259	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	269269	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	108108	85.085	1.01	1.0 1.0100%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	312312	0.00	1.01	-1.0 -1.0 -
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	316316	0.00	1.01	-1.0 -1.0 -
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	320320	0.00	1.01	-1.0 -1.0 -
makePCAImage(TYPE) : void   makePCAImage(TYPE) : void	324324	0.00	1.01	-1.0 -1.0 -
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	328328	0.00	1.01	-1.0 -1.0 -
print_actionPerformed() : void   print_actionPerformed() : void	332332	0.00	1.01	-1.0 -1.0 -
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	336336	0.00	1.01	-1.0 -1.0 -
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	340340	0.00	1.01	-1.0 -1.0 -
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	344344	0.00	1.01	-1.0 -1.0 -
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	348348	0.00	1.01	-1.0 -1.0 -
doDimensionChange() : void   doDimensionChange() : void	352352	0.00	1.01	-1.0 -1.0 -

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.68707484	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		import jalview.util.Platform;
46
		68.7% Uncovered Elements: 46 (147) Complexity: 34 Complexity Density: 0.3
47		public class GPCAPanel extends JInternalFrame
48		{
49		private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
50
51		protected JComboBox<String> xCombobox = new JComboBox<>();
52
53		protected JComboBox<String> yCombobox = new JComboBox<>();
54
55		protected JComboBox<String> zCombobox = new JComboBox<>();
56
57		protected JMenu viewMenu = new JMenu();
58
59		protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
60
61		protected JMenu associateViewsMenu = new JMenu();
62
63		protected JLabel statusBar = new JLabel();
64
65		protected JPanel statusPanel = new JPanel();
66
67		protected JMenuItem originalSeqData;
68
69		/**
70		* Constructor
71		*/
		88.9% Uncovered Elements: 1 (9) Complexity: 3 Complexity Density: 0.43
72	2	public GPCAPanel()...
73		{
74	2	try
75		{
76	2	jbInit();
77		} catch (Exception e)
78		{
79	0	e.printStackTrace();
80		}
81
82	16	for (int i = 1; i < 8; i++)
83		{
84	14	xCombobox.addItem("dim " + i);
85	14	yCombobox.addItem("dim " + i);
86	14	zCombobox.addItem("dim " + i);
87		}
88		}
89
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
90	0	public GPCAPanel(int dim)...
91		{
92	0	try
93		{
94	0	jbInit();
95		} catch (Exception e)
96		{
97	0	e.printStackTrace();
98		}
99
100	0	for (int i = 1; i <= dim; i++)
101		{
102	0	xCombobox.addItem("dim " + i);
103	0	yCombobox.addItem("dim " + i);
104	0	zCombobox.addItem("dim " + i);
105		}
106		}
107
		100% Uncovered Elements: 0 (85) Complexity: 1 Complexity Density: 0.01
108	2	private void jbInit() throws Exception...
109		{
110	2	setFrameIcon(null);
111	2	setName(Platform.getAppID("pca"));
112	2	this.getContentPane().setLayout(new BorderLayout());
113	2	JPanel jPanel2 = new JPanel();
114	2	jPanel2.setLayout(new FlowLayout());
115	2	JLabel jLabel1 = new JLabel();
116	2	jLabel1.setFont(VERDANA_12);
117	2	jLabel1.setText("x=");
118	2	JLabel jLabel2 = new JLabel();
119	2	jLabel2.setFont(VERDANA_12);
120	2	jLabel2.setText("y=");
121	2	JLabel jLabel3 = new JLabel();
122	2	jLabel3.setFont(VERDANA_12);
123	2	jLabel3.setText("z=");
124	2	jPanel2.setBackground(Color.white);
125	2	jPanel2.setBorder(null);
126	2	zCombobox.setFont(VERDANA_12);
127	2	zCombobox.addActionListener(new ActionListener()
128		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
129	4	@Override...
130		public void actionPerformed(ActionEvent e)
131		{
132	4	doDimensionChange();
133		}
134		});
135	2	yCombobox.setFont(VERDANA_12);
136	2	yCombobox.addActionListener(new ActionListener()
137		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
138	4	@Override...
139		public void actionPerformed(ActionEvent e)
140		{
141	4	doDimensionChange();
142		}
143		});
144	2	xCombobox.setFont(VERDANA_12);
145	2	xCombobox.addActionListener(new ActionListener()
146		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
147	4	@Override...
148		public void actionPerformed(ActionEvent e)
149		{
150	4	doDimensionChange();
151		}
152		});
153	2	JButton resetButton = new JButton();
154	2	resetButton.setFont(VERDANA_12);
155	2	resetButton.setText(MessageManager.getString("action.reset"));
156	2	resetButton.addActionListener(new ActionListener()
157		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
158	0	@Override...
159		public void actionPerformed(ActionEvent e)
160		{
161	0	resetButton_actionPerformed();
162		}
163		});
164	2	JMenu fileMenu = new JMenu();
165	2	fileMenu.setText(MessageManager.getString("action.file"));
166	2	JMenu saveMenu = new JMenu();
167	2	saveMenu.setText(MessageManager.getString("action.save_as"));
168	2	JMenuItem eps = new JMenuItem("EPS");
169	2	eps.addActionListener(new ActionListener()
170		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
171	0	@Override...
172		public void actionPerformed(ActionEvent e)
173		{
174	0	makePCAImage(TYPE.EPS);
175		}
176		});
177	2	JMenuItem png = new JMenuItem("PNG");
178	2	png.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	makePCAImage(TYPE.PNG);
184		}
185		});
186	2	JMenuItem outputValues = new JMenuItem();
187	2	outputValues.setText(MessageManager.getString("label.output_values"));
188	2	outputValues.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	outputValues_actionPerformed();
194		}
195		});
196	2	JMenuItem outputPoints = new JMenuItem();
197	2	outputPoints.setText(MessageManager.getString("label.output_points"));
198	2	outputPoints.addActionListener(new ActionListener()
199		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
200	0	@Override...
201		public void actionPerformed(ActionEvent e)
202		{
203	0	outputPoints_actionPerformed();
204		}
205		});
206	2	JMenuItem outputProjPoints = new JMenuItem();
207	2	outputProjPoints.setText(
208		MessageManager.getString("label.output_transformed_points"));
209	2	outputProjPoints.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	outputProjPoints_actionPerformed();
215		}
216		});
217	2	JMenuItem print = new JMenuItem();
218	2	print.setText(MessageManager.getString("action.print"));
219	2	print.addActionListener(new ActionListener()
220		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
221	0	@Override...
222		public void actionPerformed(ActionEvent e)
223		{
224	0	print_actionPerformed();
225		}
226		});
227	2	viewMenu.setText(MessageManager.getString("action.view"));
228	2	viewMenu.addMenuListener(new MenuListener()
229		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
230	0	@Override...
231		public void menuSelected(MenuEvent e)
232		{
233	0	viewMenu_menuSelected();
234		}
235
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
236	0	@Override...
237		public void menuDeselected(MenuEvent e)
238		{
239		}
240
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
241	0	@Override...
242		public void menuCanceled(MenuEvent e)
243		{
244		}
245		});
246	2	showLabels.setText(MessageManager.getString("label.show_labels"));
247	2	showLabels.addActionListener(new ActionListener()
248		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
249	0	@Override...
250		public void actionPerformed(ActionEvent e)
251		{
252	0	showLabels_actionPerformed();
253		}
254		});
255	2	JMenuItem bgcolour = new JMenuItem();
256	2	bgcolour.setText(MessageManager.getString("action.background_colour"));
257	2	bgcolour.addActionListener(new ActionListener()
258		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
259	0	@Override...
260		public void actionPerformed(ActionEvent e)
261		{
262	0	bgcolour_actionPerformed();
263		}
264		});
265	2	originalSeqData = new JMenuItem();
266	2	originalSeqData.setText(MessageManager.getString("label.input_data"));
267	2	originalSeqData.addActionListener(new ActionListener()
268		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
269	0	@Override...
270		public void actionPerformed(ActionEvent e)
271		{
272	0	originalSeqData_actionPerformed();
273		}
274		});
275	2	associateViewsMenu.setText(
276		MessageManager.getString("label.associate_nodes_with"));
277
278	2	statusPanel.setLayout(new GridLayout());
279	2	statusBar.setFont(VERDANA_12);
280		// statusPanel.setBackground(Color.lightGray);
281		// statusBar.setBackground(Color.lightGray);
282		// statusPanel.add(statusBar, null);
283	2	JPanel panelBar = new JPanel(new BorderLayout());
284	2	panelBar.add(jPanel2, BorderLayout.NORTH);
285	2	panelBar.add(statusPanel, BorderLayout.SOUTH);
286	2	this.getContentPane().add(panelBar, BorderLayout.SOUTH);
287	2	jPanel2.add(jLabel1, null);
288	2	jPanel2.add(xCombobox, null);
289	2	jPanel2.add(jLabel2, null);
290	2	jPanel2.add(yCombobox, null);
291	2	jPanel2.add(jLabel3, null);
292	2	jPanel2.add(zCombobox, null);
293	2	jPanel2.add(resetButton, null);
294
295	2	JMenuBar jMenuBar1 = new JMenuBar();
296	2	jMenuBar1.add(fileMenu);
297	2	jMenuBar1.add(viewMenu);
298	2	setJMenuBar(jMenuBar1);
299	2	fileMenu.add(saveMenu);
300	2	fileMenu.add(outputValues);
301	2	fileMenu.add(print);
302	2	fileMenu.add(originalSeqData);
303	2	fileMenu.add(outputPoints);
304	2	fileMenu.add(outputProjPoints);
305	2	saveMenu.add(eps);
306	2	saveMenu.add(png);
307	2	viewMenu.add(showLabels);
308	2	viewMenu.add(bgcolour);
309	2	viewMenu.add(associateViewsMenu);
310		}
311
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
312	0	protected void resetButton_actionPerformed()...
313		{
314		}
315
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
316	0	protected void outputPoints_actionPerformed()...
317		{
318		}
319
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
320	0	protected void outputProjPoints_actionPerformed()...
321		{
322		}
323
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
324	0	public void makePCAImage(TYPE imageType)...
325		{
326		}
327
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
328	0	protected void outputValues_actionPerformed()...
329		{
330		}
331
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
332	0	protected void print_actionPerformed()...
333		{
334		}
335
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
336	0	protected void showLabels_actionPerformed()...
337		{
338		}
339
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
340	0	protected void bgcolour_actionPerformed()...
341		{
342		}
343
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
344	0	protected void originalSeqData_actionPerformed()...
345		{
346		}
347
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
348	0	protected void viewMenu_menuSelected()...
349		{
350		}
351
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
352	0	protected void doDimensionChange()...
353		{
354		}
355		}