Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GPCAPanel	46	113	34	0.6870748468.7%	Show methods

Class GPCAPanel

Class GPCAPanel	Line # 46	Total Statements 113	Complexity 34	TOTAL Coverage 0.6870748468.7%
GPCAPanel()   GPCAPanel()	7171	7.07	3.03	0.8888889 0.888888988.9%
GPCAPanel(int)   GPCAPanel(int)	8989	7.07	3.03	0.0 0.00%
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	146146	1.01	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	157157	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	179179	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	189189	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	199199	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	210210	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	220220	1.01	1.01	0.0 0.00%
menuSelected(MenuEvent) : void   menuSelected(MenuEvent) : void	229229	1.01	1.01	0.0 0.00%
menuDeselected(MenuEvent) : void   menuDeselected(MenuEvent) : void	235235	0.00	1.01	-1.0 -1.0 -
menuCanceled(MenuEvent) : void   menuCanceled(MenuEvent) : void	240240	0.00	1.01	-1.0 -1.0 -
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	248248	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	258258	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	268268	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	107107	85.085	1.01	1.0 1.0100%
resetButton_actionPerformed() : void   resetButton_actionPerformed() : void	311311	0.00	1.01	-1.0 -1.0 -
outputPoints_actionPerformed() : void   outputPoints_actionPerformed() : void	315315	0.00	1.01	-1.0 -1.0 -
outputProjPoints_actionPerformed() : void   outputProjPoints_actionPerformed() : void	319319	0.00	1.01	-1.0 -1.0 -
makePCAImage(TYPE) : void   makePCAImage(TYPE) : void	323323	0.00	1.01	-1.0 -1.0 -
outputValues_actionPerformed() : void   outputValues_actionPerformed() : void	327327	0.00	1.01	-1.0 -1.0 -
print_actionPerformed() : void   print_actionPerformed() : void	331331	0.00	1.01	-1.0 -1.0 -
showLabels_actionPerformed() : void   showLabels_actionPerformed() : void	335335	0.00	1.01	-1.0 -1.0 -
bgcolour_actionPerformed() : void   bgcolour_actionPerformed() : void	339339	0.00	1.01	-1.0 -1.0 -
originalSeqData_actionPerformed() : void   originalSeqData_actionPerformed() : void	343343	0.00	1.01	-1.0 -1.0 -
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	347347	0.00	1.01	-1.0 -1.0 -
doDimensionChange() : void   doDimensionChange() : void	351351	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
		68.7% Uncovered Elements: 46 (147) 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		/**
69		* Constructor
70		*/
		88.9% Uncovered Elements: 1 (9) Complexity: 3 Complexity Density: 0.43
71	2	public GPCAPanel()...
72		{
73	2	try
74		{
75	2	jbInit();
76		} catch (Exception e)
77		{
78	0	e.printStackTrace();
79		}
80
81	16	for (int i = 1; i < 8; i++)
82		{
83	14	xCombobox.addItem("dim " + i);
84	14	yCombobox.addItem("dim " + i);
85	14	zCombobox.addItem("dim " + i);
86		}
87		}
88
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
89	0	public GPCAPanel(int dim)...
90		{
91	0	try
92		{
93	0	jbInit();
94		} catch (Exception e)
95		{
96	0	e.printStackTrace();
97		}
98
99	0	for (int i = 1; i <= dim; i++)
100		{
101	0	xCombobox.addItem("dim " + i);
102	0	yCombobox.addItem("dim " + i);
103	0	zCombobox.addItem("dim " + i);
104		}
105		}
106
		100% Uncovered Elements: 0 (85) Complexity: 1 Complexity Density: 0.01
107	2	private void jbInit() throws Exception...
108		{
109	2	setFrameIcon(null);
110	2	setName("jalview-pca");
111	2	this.getContentPane().setLayout(new BorderLayout());
112	2	JPanel jPanel2 = new JPanel();
113	2	jPanel2.setLayout(new FlowLayout());
114	2	JLabel jLabel1 = new JLabel();
115	2	jLabel1.setFont(VERDANA_12);
116	2	jLabel1.setText("x=");
117	2	JLabel jLabel2 = new JLabel();
118	2	jLabel2.setFont(VERDANA_12);
119	2	jLabel2.setText("y=");
120	2	JLabel jLabel3 = new JLabel();
121	2	jLabel3.setFont(VERDANA_12);
122	2	jLabel3.setText("z=");
123	2	jPanel2.setBackground(Color.white);
124	2	jPanel2.setBorder(null);
125	2	zCombobox.setFont(VERDANA_12);
126	2	zCombobox.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	yCombobox.setFont(VERDANA_12);
135	2	yCombobox.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	xCombobox.setFont(VERDANA_12);
144	2	xCombobox.addActionListener(new ActionListener()
145		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
146	4	@Override...
147		public void actionPerformed(ActionEvent e)
148		{
149	4	doDimensionChange();
150		}
151		});
152	2	JButton resetButton = new JButton();
153	2	resetButton.setFont(VERDANA_12);
154	2	resetButton.setText(MessageManager.getString("action.reset"));
155	2	resetButton.addActionListener(new ActionListener()
156		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
157	0	@Override...
158		public void actionPerformed(ActionEvent e)
159		{
160	0	resetButton_actionPerformed();
161		}
162		});
163	2	JMenu fileMenu = new JMenu();
164	2	fileMenu.setText(MessageManager.getString("action.file"));
165	2	JMenu saveMenu = new JMenu();
166	2	saveMenu.setText(MessageManager.getString("action.save_as"));
167	2	JMenuItem eps = new JMenuItem("EPS");
168	2	eps.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.EPS);
174		}
175		});
176	2	JMenuItem png = new JMenuItem("PNG");
177	2	png.addActionListener(new ActionListener()
178		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
179	0	@Override...
180		public void actionPerformed(ActionEvent e)
181		{
182	0	makePCAImage(TYPE.PNG);
183		}
184		});
185	2	JMenuItem outputValues = new JMenuItem();
186	2	outputValues.setText(MessageManager.getString("label.output_values"));
187	2	outputValues.addActionListener(new ActionListener()
188		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
189	0	@Override...
190		public void actionPerformed(ActionEvent e)
191		{
192	0	outputValues_actionPerformed();
193		}
194		});
195	2	JMenuItem outputPoints = new JMenuItem();
196	2	outputPoints.setText(MessageManager.getString("label.output_points"));
197	2	outputPoints.addActionListener(new ActionListener()
198		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
199	0	@Override...
200		public void actionPerformed(ActionEvent e)
201		{
202	0	outputPoints_actionPerformed();
203		}
204		});
205	2	JMenuItem outputProjPoints = new JMenuItem();
206	2	outputProjPoints.setText(
207		MessageManager.getString("label.output_transformed_points"));
208	2	outputProjPoints.addActionListener(new ActionListener()
209		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
210	0	@Override...
211		public void actionPerformed(ActionEvent e)
212		{
213	0	outputProjPoints_actionPerformed();
214		}
215		});
216	2	JMenuItem print = new JMenuItem();
217	2	print.setText(MessageManager.getString("action.print"));
218	2	print.addActionListener(new ActionListener()
219		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
220	0	@Override...
221		public void actionPerformed(ActionEvent e)
222		{
223	0	print_actionPerformed();
224		}
225		});
226	2	viewMenu.setText(MessageManager.getString("action.view"));
227	2	viewMenu.addMenuListener(new MenuListener()
228		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
229	0	@Override...
230		public void menuSelected(MenuEvent e)
231		{
232	0	viewMenu_menuSelected();
233		}
234
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
235	0	@Override...
236		public void menuDeselected(MenuEvent e)
237		{
238		}
239
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
240	0	@Override...
241		public void menuCanceled(MenuEvent e)
242		{
243		}
244		});
245	2	showLabels.setText(MessageManager.getString("label.show_labels"));
246	2	showLabels.addActionListener(new ActionListener()
247		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
248	0	@Override...
249		public void actionPerformed(ActionEvent e)
250		{
251	0	showLabels_actionPerformed();
252		}
253		});
254	2	JMenuItem bgcolour = new JMenuItem();
255	2	bgcolour.setText(MessageManager.getString("action.background_colour"));
256	2	bgcolour.addActionListener(new ActionListener()
257		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	@Override...
259		public void actionPerformed(ActionEvent e)
260		{
261	0	bgcolour_actionPerformed();
262		}
263		});
264	2	originalSeqData = new JMenuItem();
265	2	originalSeqData.setText(MessageManager.getString("label.input_data"));
266	2	originalSeqData.addActionListener(new ActionListener()
267		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
268	0	@Override...
269		public void actionPerformed(ActionEvent e)
270		{
271	0	originalSeqData_actionPerformed();
272		}
273		});
274	2	associateViewsMenu.setText(
275		MessageManager.getString("label.associate_nodes_with"));
276
277	2	statusPanel.setLayout(new GridLayout());
278	2	statusBar.setFont(VERDANA_12);
279		// statusPanel.setBackground(Color.lightGray);
280		// statusBar.setBackground(Color.lightGray);
281		// statusPanel.add(statusBar, null);
282	2	JPanel panelBar = new JPanel(new BorderLayout());
283	2	panelBar.add(jPanel2, BorderLayout.NORTH);
284	2	panelBar.add(statusPanel, BorderLayout.SOUTH);
285	2	this.getContentPane().add(panelBar, BorderLayout.SOUTH);
286	2	jPanel2.add(jLabel1, null);
287	2	jPanel2.add(xCombobox, null);
288	2	jPanel2.add(jLabel2, null);
289	2	jPanel2.add(yCombobox, null);
290	2	jPanel2.add(jLabel3, null);
291	2	jPanel2.add(zCombobox, null);
292	2	jPanel2.add(resetButton, null);
293
294	2	JMenuBar jMenuBar1 = new JMenuBar();
295	2	jMenuBar1.add(fileMenu);
296	2	jMenuBar1.add(viewMenu);
297	2	setJMenuBar(jMenuBar1);
298	2	fileMenu.add(saveMenu);
299	2	fileMenu.add(outputValues);
300	2	fileMenu.add(print);
301	2	fileMenu.add(originalSeqData);
302	2	fileMenu.add(outputPoints);
303	2	fileMenu.add(outputProjPoints);
304	2	saveMenu.add(eps);
305	2	saveMenu.add(png);
306	2	viewMenu.add(showLabels);
307	2	viewMenu.add(bgcolour);
308	2	viewMenu.add(associateViewsMenu);
309		}
310
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
311	0	protected void resetButton_actionPerformed()...
312		{
313		}
314
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
315	0	protected void outputPoints_actionPerformed()...
316		{
317		}
318
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
319	0	protected void outputProjPoints_actionPerformed()...
320		{
321		}
322
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
323	0	public void makePCAImage(TYPE imageType)...
324		{
325		}
326
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
327	0	protected void outputValues_actionPerformed()...
328		{
329		}
330
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
331	0	protected void print_actionPerformed()...
332		{
333		}
334
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
335	0	protected void showLabels_actionPerformed()...
336		{
337		}
338
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
339	0	protected void bgcolour_actionPerformed()...
340		{
341		}
342
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
343	0	protected void originalSeqData_actionPerformed()...
344		{
345		}
346
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
347	0	protected void viewMenu_menuSelected()...
348		{
349		}
350
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
351	0	protected void doDimensionChange()...
352		{
353		}
354		}