Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GStructureViewer	42	67	21	0.689655269%	Show methods

Class GStructureViewer

Class GStructureViewer	Line # 42	Total Statements 67	Complexity 21	TOTAL Coverage 0.689655269%
GStructureViewer()   GStructureViewer()	7878	3.03	2.02	0.6666667 0.666666766.7%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	109109	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	120120	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	131131	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	142142	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	159159	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	182182	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	8989	56.056	1.01	1.0 1.0100%
fitToWindow_actionPerformed() : void   fitToWindow_actionPerformed() : void	215215	1.01	1.01	0.0 0.00%
highlightSelection_actionPerformed() : void   highlightSelection_actionPerformed() : void	220220	0.00	1.01	-1.0 -1.0 -
viewerColour_actionPerformed() : void   viewerColour_actionPerformed() : void	224224	0.00	1.01	-1.0 -1.0 -
pdbFile_actionPerformed() : void   pdbFile_actionPerformed() : void	230230	0.00	1.01	-1.0 -1.0 -
makePDBImage(TYPE) : void   makePDBImage(TYPE) : void	235235	0.00	1.01	-1.0 -1.0 -
viewMapping_actionPerformed() : void   viewMapping_actionPerformed() : void	240240	0.00	1.01	-1.0 -1.0 -
seqColour_actionPerformed() : void   seqColour_actionPerformed() : void	245245	0.00	1.01	-1.0 -1.0 -
chainColour_actionPerformed() : void   chainColour_actionPerformed() : void	250250	0.00	1.01	-1.0 -1.0 -
chargeColour_actionPerformed() : void   chargeColour_actionPerformed() : void	255255	0.00	1.01	-1.0 -1.0 -
background_actionPerformed() : void   background_actionPerformed() : void	260260	0.00	1.01	-1.0 -1.0 -
showHelp_actionPerformed() : void   showHelp_actionPerformed() : void	265265	0.00	1.01	-1.0 -1.0 -

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6896552	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.6896552	jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol	1PASS
	0.6896552	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.6896552	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.6896552	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	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.GridLayout;
25		import java.awt.event.ActionEvent;
26		import java.awt.event.ActionListener;
27
28		import javax.swing.JInternalFrame;
29		import javax.swing.JLabel;
30		import javax.swing.JMenu;
31		import javax.swing.JMenuBar;
32		import javax.swing.JMenuItem;
33		import javax.swing.JPanel;
34		import javax.swing.JRadioButtonMenuItem;
35
36		import jalview.api.structures.JalviewStructureDisplayI;
37		import jalview.gui.ColourMenuHelper.ColourChangeListener;
38		import jalview.util.ImageMaker.TYPE;
39		import jalview.util.MessageManager;
40
41		@SuppressWarnings("serial")
		69% Uncovered Elements: 27 (87) Complexity: 21 Complexity Density: 0.31
42		public abstract class GStructureViewer extends JInternalFrame
43		implements JalviewStructureDisplayI, ColourChangeListener
44		{
45		// private AAStructureBindingModel bindingModel;
46
47		protected JMenu savemenu;
48
49		protected JMenu viewMenu;
50
51		protected JMenu colourMenu;
52
53		protected JMenu chainMenu;
54
55		protected JMenu viewerActionMenu;
56
57		protected JMenuItem alignStructs;
58
59		protected JMenuItem fitToWindow;
60
61		protected JRadioButtonMenuItem seqColour;
62
63		protected JRadioButtonMenuItem chainColour;
64
65		protected JRadioButtonMenuItem chargeColour;
66
67		protected JRadioButtonMenuItem viewerColour;
68
69		protected JMenuItem helpItem;
70
71		protected JLabel statusBar;
72
73		protected JPanel statusPanel;
74
75		/**
76		* Constructor
77		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 0.67
78	7	public GStructureViewer()...
79		{
80	7	try
81		{
82	7	jbInit();
83		} catch (Exception ex)
84		{
85	0	ex.printStackTrace();
86		}
87		}
88
		100% Uncovered Elements: 0 (56) Complexity: 1 Complexity Density: 0.02
89	7	private void jbInit() throws Exception...
90		{
91
92	7	setName("jalview-structureviewer");
93
94	7	JMenuBar menuBar = new JMenuBar();
95	7	this.setJMenuBar(menuBar);
96
97	7	JMenu fileMenu = new JMenu();
98	7	fileMenu.setText(MessageManager.getString("action.file"));
99
100	7	savemenu = new JMenu();
101	7	savemenu.setActionCommand(
102		MessageManager.getString("action.save_image"));
103	7	savemenu.setText(MessageManager.getString("action.save_as"));
104
105	7	JMenuItem pdbFile = new JMenuItem();
106	7	pdbFile.setText(MessageManager.getString("label.pdb_file"));
107	7	pdbFile.addActionListener(new ActionListener()
108		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
109	0	@Override...
110		public void actionPerformed(ActionEvent actionEvent)
111		{
112	0	pdbFile_actionPerformed();
113		}
114		});
115
116	7	JMenuItem png = new JMenuItem();
117	7	png.setText("PNG");
118	7	png.addActionListener(new ActionListener()
119		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
120	0	@Override...
121		public void actionPerformed(ActionEvent actionEvent)
122		{
123	0	makePDBImage(TYPE.PNG);
124		}
125		});
126
127	7	JMenuItem eps = new JMenuItem();
128	7	eps.setText("EPS");
129	7	eps.addActionListener(new ActionListener()
130		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	@Override...
132		public void actionPerformed(ActionEvent actionEvent)
133		{
134	0	makePDBImage(TYPE.EPS);
135		}
136		});
137
138	7	JMenuItem viewMapping = new JMenuItem();
139	7	viewMapping.setText(MessageManager.getString("label.view_mapping"));
140	7	viewMapping.addActionListener(new ActionListener()
141		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
142	0	@Override...
143		public void actionPerformed(ActionEvent actionEvent)
144		{
145	0	viewMapping_actionPerformed();
146		}
147		});
148
149	7	viewMenu = new JMenu();
150	7	viewMenu.setText(MessageManager.getString("action.view"));
151
152	7	chainMenu = new JMenu();
153	7	chainMenu.setText(MessageManager.getString("action.show_chain"));
154
155	7	fitToWindow = new JMenuItem();
156	7	fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
157	7	fitToWindow.addActionListener(new ActionListener()
158		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
159	0	@Override...
160		public void actionPerformed(ActionEvent actionEvent)
161		{
162	0	fitToWindow_actionPerformed();
163		}
164		});
165
166	7	JMenu helpMenu = new JMenu();
167	7	helpMenu.setText(MessageManager.getString("action.help"));
168	7	helpItem = new JMenuItem();
169	7	helpItem.addActionListener(new ActionListener()
170		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
171	0	@Override...
172		public void actionPerformed(ActionEvent actionEvent)
173		{
174	0	showHelp_actionPerformed();
175		}
176		});
177	7	alignStructs = new JMenuItem();
178	7	alignStructs.setText(
179		MessageManager.getString("label.superpose_structures"));
180	7	alignStructs.addActionListener(new ActionListener()
181		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
182	0	@Override...
183		public void actionPerformed(ActionEvent actionEvent)
184		{
185	0	alignStructsWithAllAlignPanels();
186		}
187		});
188
189	7	viewerActionMenu = new JMenu(); // text set in sub-classes
190	7	viewerActionMenu.setVisible(false);
191	7	viewerActionMenu.add(alignStructs);
192	7	colourMenu = new JMenu();
193	7	colourMenu.setText(MessageManager.getString("label.colours"));
194	7	fileMenu.add(savemenu);
195	7	fileMenu.add(viewMapping);
196	7	savemenu.add(pdbFile);
197	7	savemenu.add(png);
198	7	savemenu.add(eps);
199	7	viewMenu.add(chainMenu);
200	7	helpMenu.add(helpItem);
201
202	7	menuBar.add(fileMenu);
203	7	menuBar.add(viewMenu);
204	7	menuBar.add(colourMenu);
205	7	menuBar.add(viewerActionMenu);
206	7	menuBar.add(helpMenu);
207
208	7	statusPanel = new JPanel();
209	7	statusPanel.setLayout(new GridLayout());
210	7	this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
211	7	statusBar = new JLabel();
212	7	statusPanel.add(statusBar, null);
213		}
214
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
215	0	protected void fitToWindow_actionPerformed()...
216		{
217	0	getBinding().focusView();
218		}
219
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
220	0	protected void highlightSelection_actionPerformed()...
221		{
222		}
223
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
224	0	protected void viewerColour_actionPerformed()...
225		{
226		}
227
228		protected abstract String alignStructsWithAllAlignPanels();
229
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
230	0	public void pdbFile_actionPerformed()...
231		{
232
233		}
234
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
235	0	public void makePDBImage(TYPE imageType)...
236		{
237
238		}
239
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
240	0	public void viewMapping_actionPerformed()...
241		{
242
243		}
244
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
245	0	public void seqColour_actionPerformed()...
246		{
247
248		}
249
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
250	0	public void chainColour_actionPerformed()...
251		{
252
253		}
254
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
255	0	public void chargeColour_actionPerformed()...
256		{
257
258		}
259
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
260	0	public void background_actionPerformed()...
261		{
262
263		}
264
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
265	0	public void showHelp_actionPerformed()...
266		{
267
268		}
269		}