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Coverage Report

  1. Project Clover database Wed Nov 12 2025 09:00:47 GMT
  2. Package jalview.jbgui

File GTreePanel.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
37% of files have more coverage

Code metrics

0
93
40
1
413
325
41
0.44
2.33
40
1.02

Classes

Class Line # Actions
GTreePanel 45 93 41
0.5939849659.4%
 

Contributing tests

This file is covered by 10 tests. .

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")
 
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 JMenuItem sortAnnotationAssocViews = new JMenuItem();
66   
67    public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
68   
69    public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
70   
71    //Menu option for the user to select their preference in
72    //displaying secondary structure providers as labels.
73    //Visible only for secondary structure similarity.
74   
75    public JMenu showSecondaryStructureProviderMenu = new JMenu();
76   
77    ButtonGroup showSecondaryStructureProviderButtonGroup = new ButtonGroup();
78   
79    public JRadioButtonMenuItem hideStructureProviders = new JRadioButtonMenuItem();
80   
81    public JRadioButtonMenuItem showStructureProviderLabels = new JRadioButtonMenuItem();
82   
83    public JRadioButtonMenuItem showStructureProviderColouredLines = new JRadioButtonMenuItem();
84   
85    public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
86   
87    public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
88   
89    JMenuItem pngTree = new JMenuItem();
90   
91    JMenuItem epsTree = new JMenuItem();
92   
93    JMenu saveAsMenu = new JMenu();
94   
95    JMenuItem textbox = new JMenuItem();
96   
97    public JMenuItem originalSeqData = new JMenuItem();
98   
99    protected JMenu associateLeavesMenu = new JMenu();
100   
 
101  18 toggle public GTreePanel()
102    {
103  18 try
104    {
105  18 jbInit();
106  18 this.setJMenuBar(jMenuBar1);
107    } catch (Exception e)
108    {
109  0 e.printStackTrace();
110    }
111    }
112   
 
113  18 toggle private void jbInit() throws Exception
114    {
115  18 setFrameIcon(null);
116  18 setName("jalview-tree");
117  18 this.getContentPane().setLayout(borderLayout1);
118  18 this.setBackground(Color.white);
119  18 this.setFont(new java.awt.Font("Verdana", 0, 12));
120  18 scrollPane.setOpaque(false);
121  18 fileMenu.setText(MessageManager.getString("action.file"));
122  18 saveAsNewick.setText(MessageManager.getString("label.newick_format"));
123  18 saveAsNewick.addActionListener(new ActionListener()
124    {
 
125  0 toggle @Override
126    public void actionPerformed(ActionEvent e)
127    {
128  0 saveAsNewick_actionPerformed(e);
129    }
130    });
131  18 printMenu.setText(MessageManager.getString("action.print"));
132  18 printMenu.addActionListener(new java.awt.event.ActionListener()
133    {
 
134  0 toggle @Override
135    public void actionPerformed(ActionEvent e)
136    {
137  0 printMenu_actionPerformed(e);
138    }
139    });
140  18 viewMenu.setText(MessageManager.getString("action.view"));
141  18 viewMenu.addMenuListener(new MenuListener()
142    {
 
143  0 toggle @Override
144    public void menuSelected(MenuEvent e)
145    {
146  0 viewMenu_menuSelected();
147    }
148   
 
149  0 toggle @Override
150    public void menuDeselected(MenuEvent e)
151    {
152    }
153   
 
154  0 toggle @Override
155    public void menuCanceled(MenuEvent e)
156    {
157    }
158    });
159  18 sortAssocViews.setText(
160    MessageManager.getString("label.sort_alignment_by_tree"));
161  18 sortAssocViews.addActionListener(new java.awt.event.ActionListener()
162    {
 
163  0 toggle @Override
164    public void actionPerformed(ActionEvent e)
165    {
166  0 sortByTree_actionPerformed();
167    }
168    });
169  18 sortAnnotationAssocViews.setText(
170    MessageManager.getString("label.sort_annotation_by_tree"));
171  18 sortAnnotationAssocViews.addActionListener(new java.awt.event.ActionListener()
172    {
 
173  0 toggle @Override
174    public void actionPerformed(ActionEvent e)
175    {
176  0 sortAnnotationByTree_actionPerformed();
177   
178    }
179    });
180  18 font.setText(MessageManager.getString("action.font"));
181  18 font.addActionListener(new java.awt.event.ActionListener()
182    {
 
183  0 toggle @Override
184    public void actionPerformed(ActionEvent e)
185    {
186  0 font_actionPerformed(e);
187    }
188    });
189  18 bootstrapMenu.setText(
190    MessageManager.getString("label.show_bootstrap_values"));
191  18 bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
192    {
 
193  0 toggle @Override
194    public void actionPerformed(ActionEvent e)
195    {
196  0 bootstrapMenu_actionPerformed(e);
197    }
198    });
199  18 distanceMenu.setText(MessageManager.getString("label.show_distances"));
200  18 distanceMenu.addActionListener(new java.awt.event.ActionListener()
201    {
 
202  0 toggle @Override
203    public void actionPerformed(ActionEvent e)
204    {
205  0 distanceMenu_actionPerformed(e);
206    }
207    });
208   
209  18 showSecondaryStructureProviderButtonGroup.add(hideStructureProviders);
210  18 showSecondaryStructureProviderButtonGroup.add(showStructureProviderLabels);
211  18 showSecondaryStructureProviderButtonGroup.add(showStructureProviderColouredLines);
212  18 showSecondaryStructureProviderMenu.setText(MessageManager.getString("label.show_secondary_structure_provider"));
213  18 hideStructureProviders.setText(MessageManager.getString("label.hide_structure_provider"));
214  18 hideStructureProviders.setSelected(true);
215  18 hideStructureProviders.addActionListener(new ActionListener()
216    {
 
217  0 toggle @Override
218    public void actionPerformed(ActionEvent e)
219    {
220  0 hideStructureProviders_actionPerformed(e);
221    }
222    });
223   
224  18 showStructureProviderLabels.setText(MessageManager.getString("label.show_structure_provider_as_labels"));
225  18 showStructureProviderLabels.addActionListener(new ActionListener()
226    {
 
227  0 toggle @Override
228    public void actionPerformed(ActionEvent e)
229    {
230  0 showStructureProviderLabels_actionPerformed(e);
231    }
232    });
233   
234  18 showStructureProviderColouredLines.setText(MessageManager.getString("label.show_structure_provider_as_coloured_lines"));
235  18 showStructureProviderColouredLines.addActionListener(new java.awt.event.ActionListener()
236    {
 
237  4 toggle @Override
238    public void actionPerformed(ActionEvent e)
239    {
240  4 showStructureProviderColouredLines_actionPerformed(e);
241    }
242   
243    });
244   
245  18 fitToWindow.setSelected(true);
246  18 fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
247  18 fitToWindow.addActionListener(new java.awt.event.ActionListener()
248    {
 
249  0 toggle @Override
250    public void actionPerformed(ActionEvent e)
251    {
252  0 fitToWindow_actionPerformed(e);
253    }
254    });
255  18 epsTree.setText("EPS");
256  18 epsTree.addActionListener(new java.awt.event.ActionListener()
257    {
 
258  0 toggle @Override
259    public void actionPerformed(ActionEvent e)
260    {
261  0 writeTreeImage(TYPE.EPS);
262    }
263    });
264  18 pngTree.setText("PNG");
265  18 pngTree.addActionListener(new java.awt.event.ActionListener()
266    {
 
267  0 toggle @Override
268    public void actionPerformed(ActionEvent e)
269    {
270  0 writeTreeImage(TYPE.PNG);
271    }
272    });
273  18 saveAsMenu.setText(MessageManager.getString("action.save_as"));
274  18 placeholdersMenu.setToolTipText(MessageManager.getString(
275    "label.marks_leaves_tree_not_associated_with_sequence"));
276  18 placeholdersMenu.setText(
277    MessageManager.getString("label.mark_unlinked_leaves"));
278  18 placeholdersMenu.addActionListener(new ActionListener()
279    {
 
280  0 toggle @Override
281    public void actionPerformed(ActionEvent e)
282    {
283  0 placeholdersMenu_actionPerformed(e);
284    }
285    });
286  18 textbox.setText(MessageManager.getString("label.out_to_textbox"));
287  18 textbox.addActionListener(new ActionListener()
288    {
 
289  0 toggle @Override
290    public void actionPerformed(ActionEvent e)
291    {
292  0 textbox_actionPerformed(e);
293    }
294    });
295  18 originalSeqData.setText(MessageManager.getString("label.input_data"));
296  18 originalSeqData.addActionListener(new ActionListener()
297    {
 
298  0 toggle @Override
299    public void actionPerformed(ActionEvent e)
300    {
301  0 originalSeqData_actionPerformed(e);
302    }
303    });
304  18 associateLeavesMenu.setText(
305    MessageManager.getString("label.associate_leaves_with"));
306  18 this.getContentPane().add(scrollPane, BorderLayout.CENTER);
307  18 jMenuBar1.add(fileMenu);
308  18 jMenuBar1.add(viewMenu);
309  18 fileMenu.add(saveAsMenu);
310  18 fileMenu.add(textbox);
311  18 fileMenu.add(printMenu);
312  18 fileMenu.add(originalSeqData);
313  18 viewMenu.add(fitToWindow);
314  18 viewMenu.add(font);
315  18 viewMenu.add(distanceMenu);
316  18 viewMenu.add(showSecondaryStructureProviderMenu);
317  18 viewMenu.add(bootstrapMenu);
318  18 viewMenu.add(placeholdersMenu);
319  18 viewMenu.add(sortAssocViews);
320  18 viewMenu.add(sortAnnotationAssocViews);
321  18 viewMenu.add(associateLeavesMenu);
322  18 saveAsMenu.add(saveAsNewick);
323  18 saveAsMenu.add(epsTree);
324  18 saveAsMenu.add(pngTree);
325  18 showSecondaryStructureProviderMenu.add(hideStructureProviders);
326  18 showSecondaryStructureProviderMenu.add(showStructureProviderLabels);
327  18 showSecondaryStructureProviderMenu.add(showStructureProviderColouredLines);
328   
329    }
330   
 
331  0 toggle public void printMenu_actionPerformed(ActionEvent e)
332    {
333    }
334   
 
335  0 toggle public void font_actionPerformed(ActionEvent e)
336    {
337    }
338   
 
339  0 toggle public void distanceMenu_actionPerformed(ActionEvent e)
340    {
341    }
342   
 
343  0 toggle public void showSecondaryStructureProviderMenu_actionPerformed(ActionEvent e)
344    {
345    }
346   
 
347  0 toggle public void hideStructureProviders_actionPerformed(ActionEvent e)
348    {
349    }
350   
 
351  0 toggle public void showStructureProviderColouredLines_actionPerformed(ActionEvent e)
352    {
353    }
354   
 
355  0 toggle public void showStructureProviderLabels_actionPerformed(ActionEvent e)
356    {
357    }
358   
 
359  0 toggle public void bootstrapMenu_actionPerformed(ActionEvent e)
360    {
361    }
362   
 
363  0 toggle public void fitToWindow_actionPerformed(ActionEvent e)
364    {
365    }
366   
 
367  0 toggle public void writeTreeImage(TYPE imageType)
368    {
369    }
370   
 
371  0 toggle public void saveAsNewick_actionPerformed(ActionEvent e)
372    {
373    }
374   
 
375  0 toggle public void placeholdersMenu_actionPerformed(ActionEvent e)
376    {
377    }
378   
 
379  0 toggle public void textbox_actionPerformed(ActionEvent e)
380    {
381    }
382   
 
383  0 toggle public void fullid_actionPerformed(ActionEvent e)
384    {
385   
386    }
387   
 
388  0 toggle public void originalSeqData_actionPerformed(ActionEvent e)
389    {
390   
391    }
392   
 
393  0 toggle public void viewMenu_menuSelected()
394    {
395    }
396   
 
397  0 toggle public void sortByTree_actionPerformed()
398    {
399   
400    }
 
401  0 toggle public void sortAnnotationByTree_actionPerformed()
402    {
403   
404    }
405   
 
406  0 toggle public void toggleOffStructureProviderColouredLine_actionPerformed(
407    ActionEvent e)
408    {
409    // TODO Auto-generated method stub
410   
411    }
412   
413    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 09:10:40 GMT using coverage data from Wed Nov 12 2025 09:10:27 GMT.
  • OpenClover is free and open-source software.