Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GTreePanel	45	89	38	0.587301658.7%	Show methods

Class GTreePanel

Class GTreePanel	Line # 45	Total Statements 89	Complexity 38	TOTAL Coverage 0.587301658.7%
GTreePanel()   GTreePanel()	9999	4.04	2.02	0.75 0.7575%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	123123	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	132132	1.01	1.01	0.0 0.00%
menuSelected(MenuEvent) : void   menuSelected(MenuEvent) : void	141141	1.01	1.01	0.0 0.00%
menuDeselected(MenuEvent) : void   menuDeselected(MenuEvent) : void	147147	0.00	1.01	-1.0 -1.0 -
menuCanceled(MenuEvent) : void   menuCanceled(MenuEvent) : void	152152	0.00	1.01	-1.0 -1.0 -
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	189189	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	204204	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	214214	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	224224	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	236236	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	245245	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	254254	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	267267	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	276276	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	285285	1.01	1.01	0.0 0.00%
jbInit() : void   jbInit() : void	111111	69.069	1.01	1.0 1.0100%
printMenu_actionPerformed(ActionEvent) : void   printMenu_actionPerformed(ActionEvent) : void	317317	0.00	1.01	-1.0 -1.0 -
font_actionPerformed(ActionEvent) : void   font_actionPerformed(ActionEvent) : void	321321	0.00	1.01	-1.0 -1.0 -
distanceMenu_actionPerformed(ActionEvent) : void   distanceMenu_actionPerformed(ActionEvent) : void	325325	0.00	1.01	-1.0 -1.0 -
showSecondaryStructureProviderMenu_actionPerformed(ActionEvent) : void   showSecondaryStructureProviderMenu_actionPerformed(ActionEvent) : void	329329	0.00	1.01	-1.0 -1.0 -
hideStructureProviders_actionPerformed(ActionEvent) : void   hideStructureProviders_actionPerformed(ActionEvent) : void	333333	0.00	1.01	-1.0 -1.0 -
showStructureProviderColouredLines_actionPerformed(ActionEvent) : void   showStructureProviderColouredLines_actionPerformed(ActionEvent) : void	337337	0.00	1.01	-1.0 -1.0 -
showStructureProviderLabels_actionPerformed(ActionEvent) : void   showStructureProviderLabels_actionPerformed(ActionEvent) : void	341341	0.00	1.01	-1.0 -1.0 -
bootstrapMenu_actionPerformed(ActionEvent) : void   bootstrapMenu_actionPerformed(ActionEvent) : void	345345	0.00	1.01	-1.0 -1.0 -
fitToWindow_actionPerformed(ActionEvent) : void   fitToWindow_actionPerformed(ActionEvent) : void	349349	0.00	1.01	-1.0 -1.0 -
writeTreeImage(TYPE) : void   writeTreeImage(TYPE) : void	353353	0.00	1.01	-1.0 -1.0 -
saveAsNewick_actionPerformed(ActionEvent) : void   saveAsNewick_actionPerformed(ActionEvent) : void	357357	0.00	1.01	-1.0 -1.0 -
placeholdersMenu_actionPerformed(ActionEvent) : void   placeholdersMenu_actionPerformed(ActionEvent) : void	361361	0.00	1.01	-1.0 -1.0 -
textbox_actionPerformed(ActionEvent) : void   textbox_actionPerformed(ActionEvent) : void	365365	0.00	1.01	-1.0 -1.0 -
fullid_actionPerformed(ActionEvent) : void   fullid_actionPerformed(ActionEvent) : void	369369	0.00	1.01	-1.0 -1.0 -
originalSeqData_actionPerformed(ActionEvent) : void   originalSeqData_actionPerformed(ActionEvent) : void	374374	0.00	1.01	-1.0 -1.0 -
viewMenu_menuSelected() : void   viewMenu_menuSelected() : void	379379	0.00	1.01	-1.0 -1.0 -
sortByTree_actionPerformed() : void   sortByTree_actionPerformed() : void	383383	0.00	1.01	-1.0 -1.0 -

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5873016	jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere	1PASS
	0.5873016	jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation	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.event.ActionEvent;
26		import java.awt.event.ActionListener;
27		import java.awt.event.MouseAdapter;
28		import java.awt.event.MouseEvent;
29
30		import javax.swing.ButtonGroup;
31		import javax.swing.JCheckBoxMenuItem;
32		import javax.swing.JInternalFrame;
33		import javax.swing.JMenu;
34		import javax.swing.JMenuBar;
35		import javax.swing.JMenuItem;
36		import javax.swing.JRadioButtonMenuItem;
37		import javax.swing.JScrollPane;
38		import javax.swing.event.MenuEvent;
39		import javax.swing.event.MenuListener;
40
41		import jalview.util.ImageMaker.TYPE;
42		import jalview.util.MessageManager;
43
44		@SuppressWarnings("serial")
		58.7% Uncovered Elements: 52 (126) Complexity: 38 Complexity Density: 0.43
45		public class GTreePanel extends JInternalFrame
46		{
47		BorderLayout borderLayout1 = new BorderLayout();
48
49		public JScrollPane scrollPane = new JScrollPane();
50
51		JMenuBar jMenuBar1 = new JMenuBar();
52
53		JMenu fileMenu = new JMenu();
54
55		JMenuItem saveAsNewick = new JMenuItem();
56
57		JMenuItem printMenu = new JMenuItem();
58
59		protected JMenu viewMenu = new JMenu();
60
61		public JMenuItem font = new JMenuItem();
62
63		public JMenuItem sortAssocViews = new JMenuItem();
64
65		public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
66
67		public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
68
69		//Menu option for the user to select their preference in
70		//displaying secondary structure providers as labels.
71		//Visible only for secondary structure similarity.
72
73		public JMenu showSecondaryStructureProviderMenu = new JMenu();
74
75		ButtonGroup showSecondaryStructureProviderButtonGroup = new ButtonGroup();
76
77		public JRadioButtonMenuItem hideStructureProviders = new JRadioButtonMenuItem();
78
79		public JRadioButtonMenuItem showStructureProviderLabels = new JRadioButtonMenuItem();
80
81		public JRadioButtonMenuItem showStructureProviderColouredLines = new JRadioButtonMenuItem();
82
83		public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
84
85		public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
86
87		JMenuItem pngTree = new JMenuItem();
88
89		JMenuItem epsTree = new JMenuItem();
90
91		JMenu saveAsMenu = new JMenu();
92
93		JMenuItem textbox = new JMenuItem();
94
95		public JMenuItem originalSeqData = new JMenuItem();
96
97		protected JMenu associateLeavesMenu = new JMenu();
98
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 0.5
99	14	public GTreePanel()...
100		{
101	14	try
102		{
103	14	jbInit();
104	14	this.setJMenuBar(jMenuBar1);
105		} catch (Exception e)
106		{
107	0	e.printStackTrace();
108		}
109		}
110
		100% Uncovered Elements: 0 (69) Complexity: 1 Complexity Density: 0.01
111	14	private void jbInit() throws Exception...
112		{
113	14	setFrameIcon(null);
114	14	setName("jalview-tree");
115	14	this.getContentPane().setLayout(borderLayout1);
116	14	this.setBackground(Color.white);
117	14	this.setFont(new java.awt.Font("Verdana", 0, 12));
118	14	scrollPane.setOpaque(false);
119	14	fileMenu.setText(MessageManager.getString("action.file"));
120	14	saveAsNewick.setText(MessageManager.getString("label.newick_format"));
121	14	saveAsNewick.addActionListener(new ActionListener()
122		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
123	0	@Override...
124		public void actionPerformed(ActionEvent e)
125		{
126	0	saveAsNewick_actionPerformed(e);
127		}
128		});
129	14	printMenu.setText(MessageManager.getString("action.print"));
130	14	printMenu.addActionListener(new java.awt.event.ActionListener()
131		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
132	0	@Override...
133		public void actionPerformed(ActionEvent e)
134		{
135	0	printMenu_actionPerformed(e);
136		}
137		});
138	14	viewMenu.setText(MessageManager.getString("action.view"));
139	14	viewMenu.addMenuListener(new MenuListener()
140		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	@Override...
142		public void menuSelected(MenuEvent e)
143		{
144	0	viewMenu_menuSelected();
145		}
146
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
147	0	@Override...
148		public void menuDeselected(MenuEvent e)
149		{
150		}
151
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
152	0	@Override...
153		public void menuCanceled(MenuEvent e)
154		{
155		}
156		});
157	14	sortAssocViews.setText(
158		MessageManager.getString("label.sort_alignment_by_tree"));
159	14	sortAssocViews.addActionListener(new java.awt.event.ActionListener()
160		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
161	0	@Override...
162		public void actionPerformed(ActionEvent e)
163		{
164	0	sortByTree_actionPerformed();
165		}
166		});
167	14	font.setText(MessageManager.getString("action.font"));
168	14	font.addActionListener(new java.awt.event.ActionListener()
169		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
170	0	@Override...
171		public void actionPerformed(ActionEvent e)
172		{
173	0	font_actionPerformed(e);
174		}
175		});
176	14	bootstrapMenu.setText(
177		MessageManager.getString("label.show_bootstrap_values"));
178	14	bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
179		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
180	0	@Override...
181		public void actionPerformed(ActionEvent e)
182		{
183	0	bootstrapMenu_actionPerformed(e);
184		}
185		});
186	14	distanceMenu.setText(MessageManager.getString("label.show_distances"));
187	14	distanceMenu.addActionListener(new java.awt.event.ActionListener()
188		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
189	0	@Override...
190		public void actionPerformed(ActionEvent e)
191		{
192	0	distanceMenu_actionPerformed(e);
193		}
194		});
195
196	14	showSecondaryStructureProviderButtonGroup.add(hideStructureProviders);
197	14	showSecondaryStructureProviderButtonGroup.add(showStructureProviderLabels);
198	14	showSecondaryStructureProviderButtonGroup.add(showStructureProviderColouredLines);
199	14	showSecondaryStructureProviderMenu.setText(MessageManager.getString("label.show_secondary_structure_provider"));
200	14	hideStructureProviders.setText(MessageManager.getString("label.hide_structure_provider"));
201	14	hideStructureProviders.setSelected(true);
202	14	hideStructureProviders.addActionListener(new ActionListener()
203		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
204	0	@Override...
205		public void actionPerformed(ActionEvent e)
206		{
207	0	hideStructureProviders_actionPerformed(e);
208		}
209		});
210
211	14	showStructureProviderLabels.setText(MessageManager.getString("label.show_structure_provider_as_labels"));
212	14	showStructureProviderLabels.addActionListener(new ActionListener()
213		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
214	0	@Override...
215		public void actionPerformed(ActionEvent e)
216		{
217	0	showStructureProviderLabels_actionPerformed(e);
218		}
219		});
220
221	14	showStructureProviderColouredLines.setText(MessageManager.getString("label.show_structure_provider_as_coloured_lines"));
222	14	showStructureProviderColouredLines.addActionListener(new java.awt.event.ActionListener()
223		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
224	0	@Override...
225		public void actionPerformed(ActionEvent e)
226		{
227	0	showStructureProviderColouredLines_actionPerformed(e);
228		}
229
230		});
231
232	14	fitToWindow.setSelected(true);
233	14	fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
234	14	fitToWindow.addActionListener(new java.awt.event.ActionListener()
235		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
236	0	@Override...
237		public void actionPerformed(ActionEvent e)
238		{
239	0	fitToWindow_actionPerformed(e);
240		}
241		});
242	14	epsTree.setText("EPS");
243	14	epsTree.addActionListener(new java.awt.event.ActionListener()
244		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
245	0	@Override...
246		public void actionPerformed(ActionEvent e)
247		{
248	0	writeTreeImage(TYPE.EPS);
249		}
250		});
251	14	pngTree.setText("PNG");
252	14	pngTree.addActionListener(new java.awt.event.ActionListener()
253		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
254	0	@Override...
255		public void actionPerformed(ActionEvent e)
256		{
257	0	writeTreeImage(TYPE.PNG);
258		}
259		});
260	14	saveAsMenu.setText(MessageManager.getString("action.save_as"));
261	14	placeholdersMenu.setToolTipText(MessageManager.getString(
262		"label.marks_leaves_tree_not_associated_with_sequence"));
263	14	placeholdersMenu.setText(
264		MessageManager.getString("label.mark_unlinked_leaves"));
265	14	placeholdersMenu.addActionListener(new ActionListener()
266		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
267	0	@Override...
268		public void actionPerformed(ActionEvent e)
269		{
270	0	placeholdersMenu_actionPerformed(e);
271		}
272		});
273	14	textbox.setText(MessageManager.getString("label.out_to_textbox"));
274	14	textbox.addActionListener(new ActionListener()
275		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
276	0	@Override...
277		public void actionPerformed(ActionEvent e)
278		{
279	0	textbox_actionPerformed(e);
280		}
281		});
282	14	originalSeqData.setText(MessageManager.getString("label.input_data"));
283	14	originalSeqData.addActionListener(new ActionListener()
284		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
285	0	@Override...
286		public void actionPerformed(ActionEvent e)
287		{
288	0	originalSeqData_actionPerformed(e);
289		}
290		});
291	14	associateLeavesMenu.setText(
292		MessageManager.getString("label.associate_leaves_with"));
293	14	this.getContentPane().add(scrollPane, BorderLayout.CENTER);
294	14	jMenuBar1.add(fileMenu);
295	14	jMenuBar1.add(viewMenu);
296	14	fileMenu.add(saveAsMenu);
297	14	fileMenu.add(textbox);
298	14	fileMenu.add(printMenu);
299	14	fileMenu.add(originalSeqData);
300	14	viewMenu.add(fitToWindow);
301	14	viewMenu.add(font);
302	14	viewMenu.add(distanceMenu);
303	14	viewMenu.add(showSecondaryStructureProviderMenu);
304	14	viewMenu.add(bootstrapMenu);
305	14	viewMenu.add(placeholdersMenu);
306	14	viewMenu.add(sortAssocViews);
307	14	viewMenu.add(associateLeavesMenu);
308	14	saveAsMenu.add(saveAsNewick);
309	14	saveAsMenu.add(epsTree);
310	14	saveAsMenu.add(pngTree);
311	14	showSecondaryStructureProviderMenu.add(hideStructureProviders);
312	14	showSecondaryStructureProviderMenu.add(showStructureProviderLabels);
313	14	showSecondaryStructureProviderMenu.add(showStructureProviderColouredLines);
314
315		}
316
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
317	0	public void printMenu_actionPerformed(ActionEvent e)...
318		{
319		}
320
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
321	0	public void font_actionPerformed(ActionEvent e)...
322		{
323		}
324
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
325	0	public void distanceMenu_actionPerformed(ActionEvent e)...
326		{
327		}
328
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
329	0	public void showSecondaryStructureProviderMenu_actionPerformed(ActionEvent e)...
330		{
331		}
332
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
333	0	public void hideStructureProviders_actionPerformed(ActionEvent e)...
334		{
335		}
336
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
337	0	public void showStructureProviderColouredLines_actionPerformed(ActionEvent e)...
338		{
339		}
340
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
341	0	public void showStructureProviderLabels_actionPerformed(ActionEvent e)...
342		{
343		}
344
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
345	0	public void bootstrapMenu_actionPerformed(ActionEvent e)...
346		{
347		}
348
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
349	0	public void fitToWindow_actionPerformed(ActionEvent e)...
350		{
351		}
352
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
353	0	public void writeTreeImage(TYPE imageType)...
354		{
355		}
356
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
357	0	public void saveAsNewick_actionPerformed(ActionEvent e)...
358		{
359		}
360
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
361	0	public void placeholdersMenu_actionPerformed(ActionEvent e)...
362		{
363		}
364
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
365	0	public void textbox_actionPerformed(ActionEvent e)...
366		{
367		}
368
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
369	0	public void fullid_actionPerformed(ActionEvent e)...
370		{
371
372		}
373
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
374	0	public void originalSeqData_actionPerformed(ActionEvent e)...
375		{
376
377		}
378
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
379	0	public void viewMenu_menuSelected()...
380		{
381		}
382
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
383	0	public void sortByTree_actionPerformed()...
384		{
385
386		}
387
388		}