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Coverage Report

  1. Project Clover database Thu Dec 4 2025 16:11:35 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
414
326
41
0.44
2.33
40
1.02

Classes

Class Line # Actions
GTreePanel 46 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    import jalview.util.Platform;
44   
45    @SuppressWarnings("serial")
 
46    public class GTreePanel extends JInternalFrame
47    {
48    BorderLayout borderLayout1 = new BorderLayout();
49   
50    public JScrollPane scrollPane = new JScrollPane();
51   
52    JMenuBar jMenuBar1 = new JMenuBar();
53   
54    JMenu fileMenu = new JMenu();
55   
56    JMenuItem saveAsNewick = new JMenuItem();
57   
58    JMenuItem printMenu = new JMenuItem();
59   
60    protected JMenu viewMenu = new JMenu();
61   
62    public JMenuItem font = new JMenuItem();
63   
64    public JMenuItem sortAssocViews = new JMenuItem();
65   
66    public JMenuItem sortAnnotationAssocViews = new JMenuItem();
67   
68    public JCheckBoxMenuItem bootstrapMenu = new JCheckBoxMenuItem();
69   
70    public JCheckBoxMenuItem distanceMenu = new JCheckBoxMenuItem();
71   
72    //Menu option for the user to select their preference in
73    //displaying secondary structure providers as labels.
74    //Visible only for secondary structure similarity.
75   
76    public JMenu showSecondaryStructureProviderMenu = new JMenu();
77   
78    ButtonGroup showSecondaryStructureProviderButtonGroup = new ButtonGroup();
79   
80    public JRadioButtonMenuItem hideStructureProviders = new JRadioButtonMenuItem();
81   
82    public JRadioButtonMenuItem showStructureProviderLabels = new JRadioButtonMenuItem();
83   
84    public JRadioButtonMenuItem showStructureProviderColouredLines = new JRadioButtonMenuItem();
85   
86    public JCheckBoxMenuItem fitToWindow = new JCheckBoxMenuItem();
87   
88    public JCheckBoxMenuItem placeholdersMenu = new JCheckBoxMenuItem();
89   
90    JMenuItem pngTree = new JMenuItem();
91   
92    JMenuItem epsTree = new JMenuItem();
93   
94    JMenu saveAsMenu = new JMenu();
95   
96    JMenuItem textbox = new JMenuItem();
97   
98    public JMenuItem originalSeqData = new JMenuItem();
99   
100    protected JMenu associateLeavesMenu = new JMenu();
101   
 
102  18 toggle public GTreePanel()
103    {
104  18 try
105    {
106  18 jbInit();
107  18 this.setJMenuBar(jMenuBar1);
108    } catch (Exception e)
109    {
110  0 e.printStackTrace();
111    }
112    }
113   
 
114  18 toggle private void jbInit() throws Exception
115    {
116  18 setFrameIcon(null);
117  18 setName(Platform.getAppID("tree"));
118  18 this.getContentPane().setLayout(borderLayout1);
119  18 this.setBackground(Color.white);
120  18 this.setFont(new java.awt.Font("Verdana", 0, 12));
121  18 scrollPane.setOpaque(false);
122  18 fileMenu.setText(MessageManager.getString("action.file"));
123  18 saveAsNewick.setText(MessageManager.getString("label.newick_format"));
124  18 saveAsNewick.addActionListener(new ActionListener()
125    {
 
126  0 toggle @Override
127    public void actionPerformed(ActionEvent e)
128    {
129  0 saveAsNewick_actionPerformed(e);
130    }
131    });
132  18 printMenu.setText(MessageManager.getString("action.print"));
133  18 printMenu.addActionListener(new java.awt.event.ActionListener()
134    {
 
135  0 toggle @Override
136    public void actionPerformed(ActionEvent e)
137    {
138  0 printMenu_actionPerformed(e);
139    }
140    });
141  18 viewMenu.setText(MessageManager.getString("action.view"));
142  18 viewMenu.addMenuListener(new MenuListener()
143    {
 
144  0 toggle @Override
145    public void menuSelected(MenuEvent e)
146    {
147  0 viewMenu_menuSelected();
148    }
149   
 
150  0 toggle @Override
151    public void menuDeselected(MenuEvent e)
152    {
153    }
154   
 
155  0 toggle @Override
156    public void menuCanceled(MenuEvent e)
157    {
158    }
159    });
160  18 sortAssocViews.setText(
161    MessageManager.getString("label.sort_alignment_by_tree"));
162  18 sortAssocViews.addActionListener(new java.awt.event.ActionListener()
163    {
 
164  0 toggle @Override
165    public void actionPerformed(ActionEvent e)
166    {
167  0 sortByTree_actionPerformed();
168    }
169    });
170  18 sortAnnotationAssocViews.setText(
171    MessageManager.getString("label.sort_annotation_by_tree"));
172  18 sortAnnotationAssocViews.addActionListener(new java.awt.event.ActionListener()
173    {
 
174  0 toggle @Override
175    public void actionPerformed(ActionEvent e)
176    {
177  0 sortAnnotationByTree_actionPerformed();
178   
179    }
180    });
181  18 font.setText(MessageManager.getString("action.font"));
182  18 font.addActionListener(new java.awt.event.ActionListener()
183    {
 
184  0 toggle @Override
185    public void actionPerformed(ActionEvent e)
186    {
187  0 font_actionPerformed(e);
188    }
189    });
190  18 bootstrapMenu.setText(
191    MessageManager.getString("label.show_bootstrap_values"));
192  18 bootstrapMenu.addActionListener(new java.awt.event.ActionListener()
193    {
 
194  0 toggle @Override
195    public void actionPerformed(ActionEvent e)
196    {
197  0 bootstrapMenu_actionPerformed(e);
198    }
199    });
200  18 distanceMenu.setText(MessageManager.getString("label.show_distances"));
201  18 distanceMenu.addActionListener(new java.awt.event.ActionListener()
202    {
 
203  0 toggle @Override
204    public void actionPerformed(ActionEvent e)
205    {
206  0 distanceMenu_actionPerformed(e);
207    }
208    });
209   
210  18 showSecondaryStructureProviderButtonGroup.add(hideStructureProviders);
211  18 showSecondaryStructureProviderButtonGroup.add(showStructureProviderLabels);
212  18 showSecondaryStructureProviderButtonGroup.add(showStructureProviderColouredLines);
213  18 showSecondaryStructureProviderMenu.setText(MessageManager.getString("label.show_secondary_structure_provider"));
214  18 hideStructureProviders.setText(MessageManager.getString("label.hide_structure_provider"));
215  18 hideStructureProviders.setSelected(true);
216  18 hideStructureProviders.addActionListener(new ActionListener()
217    {
 
218  0 toggle @Override
219    public void actionPerformed(ActionEvent e)
220    {
221  0 hideStructureProviders_actionPerformed(e);
222    }
223    });
224   
225  18 showStructureProviderLabels.setText(MessageManager.getString("label.show_structure_provider_as_labels"));
226  18 showStructureProviderLabels.addActionListener(new ActionListener()
227    {
 
228  0 toggle @Override
229    public void actionPerformed(ActionEvent e)
230    {
231  0 showStructureProviderLabels_actionPerformed(e);
232    }
233    });
234   
235  18 showStructureProviderColouredLines.setText(MessageManager.getString("label.show_structure_provider_as_coloured_lines"));
236  18 showStructureProviderColouredLines.addActionListener(new java.awt.event.ActionListener()
237    {
 
238  4 toggle @Override
239    public void actionPerformed(ActionEvent e)
240    {
241  4 showStructureProviderColouredLines_actionPerformed(e);
242    }
243   
244    });
245   
246  18 fitToWindow.setSelected(true);
247  18 fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
248  18 fitToWindow.addActionListener(new java.awt.event.ActionListener()
249    {
 
250  0 toggle @Override
251    public void actionPerformed(ActionEvent e)
252    {
253  0 fitToWindow_actionPerformed(e);
254    }
255    });
256  18 epsTree.setText("EPS");
257  18 epsTree.addActionListener(new java.awt.event.ActionListener()
258    {
 
259  0 toggle @Override
260    public void actionPerformed(ActionEvent e)
261    {
262  0 writeTreeImage(TYPE.EPS);
263    }
264    });
265  18 pngTree.setText("PNG");
266  18 pngTree.addActionListener(new java.awt.event.ActionListener()
267    {
 
268  0 toggle @Override
269    public void actionPerformed(ActionEvent e)
270    {
271  0 writeTreeImage(TYPE.PNG);
272    }
273    });
274  18 saveAsMenu.setText(MessageManager.getString("action.save_as"));
275  18 placeholdersMenu.setToolTipText(MessageManager.getString(
276    "label.marks_leaves_tree_not_associated_with_sequence"));
277  18 placeholdersMenu.setText(
278    MessageManager.getString("label.mark_unlinked_leaves"));
279  18 placeholdersMenu.addActionListener(new ActionListener()
280    {
 
281  0 toggle @Override
282    public void actionPerformed(ActionEvent e)
283    {
284  0 placeholdersMenu_actionPerformed(e);
285    }
286    });
287  18 textbox.setText(MessageManager.getString("label.out_to_textbox"));
288  18 textbox.addActionListener(new ActionListener()
289    {
 
290  0 toggle @Override
291    public void actionPerformed(ActionEvent e)
292    {
293  0 textbox_actionPerformed(e);
294    }
295    });
296  18 originalSeqData.setText(MessageManager.getString("label.input_data"));
297  18 originalSeqData.addActionListener(new ActionListener()
298    {
 
299  0 toggle @Override
300    public void actionPerformed(ActionEvent e)
301    {
302  0 originalSeqData_actionPerformed(e);
303    }
304    });
305  18 associateLeavesMenu.setText(
306    MessageManager.getString("label.associate_leaves_with"));
307  18 this.getContentPane().add(scrollPane, BorderLayout.CENTER);
308  18 jMenuBar1.add(fileMenu);
309  18 jMenuBar1.add(viewMenu);
310  18 fileMenu.add(saveAsMenu);
311  18 fileMenu.add(textbox);
312  18 fileMenu.add(printMenu);
313  18 fileMenu.add(originalSeqData);
314  18 viewMenu.add(fitToWindow);
315  18 viewMenu.add(font);
316  18 viewMenu.add(distanceMenu);
317  18 viewMenu.add(showSecondaryStructureProviderMenu);
318  18 viewMenu.add(bootstrapMenu);
319  18 viewMenu.add(placeholdersMenu);
320  18 viewMenu.add(sortAssocViews);
321  18 viewMenu.add(sortAnnotationAssocViews);
322  18 viewMenu.add(associateLeavesMenu);
323  18 saveAsMenu.add(saveAsNewick);
324  18 saveAsMenu.add(epsTree);
325  18 saveAsMenu.add(pngTree);
326  18 showSecondaryStructureProviderMenu.add(hideStructureProviders);
327  18 showSecondaryStructureProviderMenu.add(showStructureProviderLabels);
328  18 showSecondaryStructureProviderMenu.add(showStructureProviderColouredLines);
329   
330    }
331   
 
332  0 toggle public void printMenu_actionPerformed(ActionEvent e)
333    {
334    }
335   
 
336  0 toggle public void font_actionPerformed(ActionEvent e)
337    {
338    }
339   
 
340  0 toggle public void distanceMenu_actionPerformed(ActionEvent e)
341    {
342    }
343   
 
344  0 toggle public void showSecondaryStructureProviderMenu_actionPerformed(ActionEvent e)
345    {
346    }
347   
 
348  0 toggle public void hideStructureProviders_actionPerformed(ActionEvent e)
349    {
350    }
351   
 
352  0 toggle public void showStructureProviderColouredLines_actionPerformed(ActionEvent e)
353    {
354    }
355   
 
356  0 toggle public void showStructureProviderLabels_actionPerformed(ActionEvent e)
357    {
358    }
359   
 
360  0 toggle public void bootstrapMenu_actionPerformed(ActionEvent e)
361    {
362    }
363   
 
364  0 toggle public void fitToWindow_actionPerformed(ActionEvent e)
365    {
366    }
367   
 
368  0 toggle public void writeTreeImage(TYPE imageType)
369    {
370    }
371   
 
372  0 toggle public void saveAsNewick_actionPerformed(ActionEvent e)
373    {
374    }
375   
 
376  0 toggle public void placeholdersMenu_actionPerformed(ActionEvent e)
377    {
378    }
379   
 
380  0 toggle public void textbox_actionPerformed(ActionEvent e)
381    {
382    }
383   
 
384  0 toggle public void fullid_actionPerformed(ActionEvent e)
385    {
386   
387    }
388   
 
389  0 toggle public void originalSeqData_actionPerformed(ActionEvent e)
390    {
391   
392    }
393   
 
394  0 toggle public void viewMenu_menuSelected()
395    {
396    }
397   
 
398  0 toggle public void sortByTree_actionPerformed()
399    {
400   
401    }
 
402  0 toggle public void sortAnnotationByTree_actionPerformed()
403    {
404   
405    }
406   
 
407  0 toggle public void toggleOffStructureProviderColouredLine_actionPerformed(
408    ActionEvent e)
409    {
410    // TODO Auto-generated method stub
411   
412    }
413   
414    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 16:21:53 GMT using coverage data from Thu Dec 4 2025 16:21:39 GMT.
  • OpenClover is free and open-source software.