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Coverage Report

  1. Project Clover database Wed Jun 18 2025 15:09:16 BST
  2. Package jalview.appletgui

File TreePanel.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
59% of files have more coverage

Code metrics

26
111
15
2
368
273
32
0.29
7.4
7.5
2.13

Classes

Class Line # Actions
TreePanel 48 91 27
0.00%
TreePanel.TreeLoader 173 20 5
0.00%
 

Contributing tests

No tests hitting this source file were found.

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.appletgui;
22   
23    import jalview.analysis.AverageDistanceTree;
24    import jalview.analysis.NJTree;
25    import jalview.analysis.TreeBuilder;
26    import jalview.analysis.TreeModel;
27    import jalview.analysis.scoremodels.ScoreModels;
28    import jalview.analysis.scoremodels.SimilarityParams;
29    import jalview.api.analysis.ScoreModelI;
30    import jalview.datamodel.Alignment;
31    import jalview.datamodel.HiddenColumns;
32    import jalview.datamodel.SequenceI;
33    import jalview.io.NewickFile;
34    import jalview.util.MessageManager;
35   
36    import java.awt.BorderLayout;
37    import java.awt.CheckboxMenuItem;
38    import java.awt.Color;
39    import java.awt.Menu;
40    import java.awt.MenuBar;
41    import java.awt.MenuItem;
42    import java.awt.ScrollPane;
43    import java.awt.event.ActionEvent;
44    import java.awt.event.ActionListener;
45    import java.awt.event.ItemEvent;
46    import java.awt.event.ItemListener;
47   
 
48    public class TreePanel extends EmbmenuFrame
49    implements ActionListener, ItemListener, AutoCloseable
50    {
51    SequenceI[] seq;
52   
53    String type;
54   
55    String pwtype;
56   
57    int start;
58   
59    int end;
60   
61    TreeCanvas treeCanvas;
62   
63    TreeModel tree;
64   
65    AlignmentPanel ap;
66   
67    AlignViewport av;
68   
 
69  0 toggle public TreeModel getTree()
70    {
71  0 return tree;
72    }
73   
 
74  0 toggle @Override
75    public void close()
76    {
77  0 ap = null;
78  0 av = null;
79  0 super.close();
80    }
81   
82    /**
83    * Creates a new TreePanel object.
84    */
 
85  0 toggle public TreePanel(AlignmentPanel alignPanel, String type, String pwtype)
86    {
87  0 try
88    {
89  0 jbInit();
90  0 this.setMenuBar(jMenuBar1);
91    } catch (Exception ex)
92    {
93  0 ex.printStackTrace();
94    }
95   
96  0 initTreePanel(alignPanel, type, pwtype, null);
97    }
98   
99    /**
100    * Creates a new TreePanel object.
101    *
102    */
 
103  0 toggle public TreePanel(AlignmentPanel ap, String type, String pwtype,
104    NewickFile newtree)
105    {
106  0 try
107    {
108  0 jbInit();
109  0 this.setMenuBar(jMenuBar1);
110    } catch (Exception e)
111    {
112  0 e.printStackTrace();
113    }
114   
115  0 initTreePanel(ap, type, pwtype, newtree);
116    }
117   
 
118  0 toggle void initTreePanel(AlignmentPanel ap, String type, String pwtype,
119    NewickFile newTree)
120    {
121   
122  0 this.ap = ap;
123  0 this.av = ap.av;
124  0 this.type = type;
125  0 this.pwtype = pwtype;
126   
127  0 treeCanvas = new TreeCanvas(ap, scrollPane);
128  0 TreeLoader tl = new TreeLoader(newTree);
129  0 tl.start();
130  0 embedMenuIfNeeded(treeCanvas);
131  0 scrollPane.add(treeCanvas, BorderLayout.CENTER);
132    }
133   
 
134  0 toggle void showOriginalData()
135    {
136    // decide if av alignment is sufficiently different to original data to
137    // warrant a new window to be created
138    // create new alignmnt window with hidden regions (unhiding hidden regions
139    // yields unaligned seqs)
140    // or create a selection box around columns in alignment view
141    // test Alignment(SeqCigar[])
142  0 if (tree.getOriginalData() != null)
143    {
144  0 char gc = '-';
145  0 try
146    {
147    // we try to get the associated view's gap character
148    // but this may fail if the view was closed...
149  0 gc = av.getGapCharacter();
150    } catch (Exception ex)
151    {
152    }
153   
154  0 Object[] alAndColsel = tree.getOriginalData()
155    .getAlignmentAndHiddenColumns(gc);
156   
157  0 if (alAndColsel != null && alAndColsel[0] != null)
158    {
159  0 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
160  0 AlignFrame af = new AlignFrame(al, av.applet,
161    "Original Data for Tree", false);
162   
163  0 af.viewport.getAlignment()
164    .setHiddenColumns((HiddenColumns) alAndColsel[1]);
165    }
166    }
167    else
168    {
169  0 jalview.bin.Console.outPrintln("Original Tree Data not available");
170    }
171    }
172   
 
173    class TreeLoader extends Thread
174    {
175    NewickFile newtree;
176   
177    jalview.datamodel.AlignmentView odata = null;
178   
 
179  0 toggle public TreeLoader(NewickFile newtree)
180    {
181  0 this.newtree = newtree;
182    }
183   
 
184  0 toggle @Override
185    public void run()
186    {
187  0 if (newtree != null)
188    {
189  0 tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
190    newtree);
191    }
192    else
193    {
194  0 ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype,
195    treeCanvas.ap);
196  0 ScoreModelI sm = sm1;
197  0 TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING)
198    ? new NJTree(av, sm, SimilarityParams.Jalview)
199    : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
200  0 tree = new TreeModel(njtree);
201    }
202   
203  0 tree.reCount(tree.getTopNode());
204  0 tree.findHeight(tree.getTopNode());
205  0 treeCanvas.setTree(tree);
206  0 if (newtree != null)
207    {
208    // Set default view, paying lip service to any overriding tree view
209    // parameter settings
210  0 boolean showDist = newtree.HasDistances()
211    && av.applet.getDefaultParameter("showTreeDistances",
212    newtree.HasDistances());
213  0 boolean showBoots = newtree.HasBootstrap()
214    && av.applet.getDefaultParameter("showTreeBootstraps",
215    newtree.HasBootstrap());
216  0 distanceMenu.setState(showDist);
217  0 bootstrapMenu.setState(showBoots);
218  0 treeCanvas.setShowBootstrap(showBoots);
219  0 treeCanvas.setShowDistances(showDist);
220  0 treeCanvas.setMarkPlaceholders(av.applet
221    .getDefaultParameter("showUnlinkedTreeNodes", false));
222    }
223   
224  0 treeCanvas.repaint();
225   
226  0 av.setCurrentTree(tree);
227   
228    }
229    }
230   
 
231  0 toggle @Override
232    public void actionPerformed(ActionEvent evt)
233    {
234  0 if (evt.getSource() == newickOutput)
235    {
236  0 newickOutput_actionPerformed();
237    }
238  0 else if (evt.getSource() == fontSize)
239    {
240  0 fontSize_actionPerformed();
241    }
242  0 else if (evt.getSource() == inputData)
243    {
244  0 showOriginalData();
245    }
246    }
247   
 
248  0 toggle @Override
249    public void itemStateChanged(ItemEvent evt)
250    {
251  0 if (evt.getSource() == fitToWindow)
252    {
253  0 treeCanvas.fitToWindow = fitToWindow.getState();
254    }
255   
256  0 else if (evt.getSource() == distanceMenu)
257    {
258  0 treeCanvas.setShowDistances(distanceMenu.getState());
259    }
260   
261  0 else if (evt.getSource() == bootstrapMenu)
262    {
263  0 treeCanvas.setShowBootstrap(bootstrapMenu.getState());
264    }
265   
266  0 else if (evt.getSource() == placeholdersMenu)
267    {
268  0 treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());
269    }
270   
271  0 treeCanvas.repaint();
272    }
273   
 
274  0 toggle public void newickOutput_actionPerformed()
275    {
276  0 jalview.io.NewickFile fout = new jalview.io.NewickFile(
277    tree.getTopNode());
278  0 String output = fout.print(false, true);
279  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
280  0 cap.setText(output);
281  0 java.awt.Frame frame = new java.awt.Frame();
282  0 frame.add(cap);
283  0 jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
284    }
285   
 
286  0 toggle public java.awt.Font getTreeFont()
287    {
288  0 return treeCanvas.font;
289    }
290   
 
291  0 toggle public void setTreeFont(java.awt.Font font)
292    {
293  0 treeCanvas.font = font;
294  0 treeCanvas.repaint();
295    }
296   
 
297  0 toggle protected void fontSize_actionPerformed()
298    {
299  0 if (treeCanvas == null)
300    {
301  0 return;
302    }
303   
304  0 new FontChooser(this);
305    }
306   
307    BorderLayout borderLayout1 = new BorderLayout();
308   
309    protected ScrollPane scrollPane = new ScrollPane();
310   
311    MenuBar jMenuBar1 = new MenuBar();
312   
313    Menu jMenu2 = new Menu();
314   
315    protected MenuItem fontSize = new MenuItem();
316   
317    protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();
318   
319    protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();
320   
321    protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();
322   
323    protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();
324   
325    Menu fileMenu = new Menu();
326   
327    MenuItem newickOutput = new MenuItem();
328   
329    MenuItem inputData = new MenuItem();
330   
 
331  0 toggle private void jbInit() throws Exception
332    {
333  0 setLayout(borderLayout1);
334  0 this.setBackground(Color.white);
335  0 this.setFont(new java.awt.Font("Verdana", 0, 12));
336  0 jMenu2.setLabel(MessageManager.getString("action.view"));
337  0 fontSize.setLabel(MessageManager.getString("action.font"));
338  0 fontSize.addActionListener(this);
339  0 bootstrapMenu.setLabel(
340    MessageManager.getString("label.show_bootstrap_values"));
341  0 bootstrapMenu.addItemListener(this);
342  0 distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
343  0 distanceMenu.addItemListener(this);
344  0 placeholdersMenu.setLabel(
345    MessageManager.getString("label.mark_unassociated_leaves"));
346  0 placeholdersMenu.addItemListener(this);
347  0 fitToWindow.setState(true);
348  0 fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
349  0 fitToWindow.addItemListener(this);
350  0 fileMenu.setLabel(MessageManager.getString("action.file"));
351  0 newickOutput.setLabel(MessageManager.getString("label.newick_format"));
352  0 newickOutput.addActionListener(this);
353  0 inputData.setLabel(MessageManager.getString("label.input_data"));
354   
355  0 add(scrollPane, BorderLayout.CENTER);
356  0 jMenuBar1.add(fileMenu);
357  0 jMenuBar1.add(jMenu2);
358  0 jMenu2.add(fitToWindow);
359  0 jMenu2.add(fontSize);
360  0 jMenu2.add(distanceMenu);
361  0 jMenu2.add(bootstrapMenu);
362  0 jMenu2.add(placeholdersMenu);
363  0 fileMenu.add(newickOutput);
364  0 fileMenu.add(inputData);
365  0 inputData.addActionListener(this);
366    }
367   
368    }
  • Report generated by OpenClover v 4.4.1 on Wed Jun 18 2025 15:16:08 BST using coverage data from Wed Jun 18 2025 15:15:57 BST.
  • OpenClover is free and open-source software.