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Coverage Report

  1. Project Clover database Wed Sep 17 2025 10:52:37 BST
  2. Package jalview.appletgui

File PCAPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

34
149
12
1
392
305
33
0.22
12.42
12
2.75

Classes

Class Line # Actions
PCAPanel 51 149 33
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.scoremodels.ScoreModels;
24    import jalview.analysis.scoremodels.SimilarityParams;
25    import jalview.api.analysis.ScoreModelI;
26    import jalview.datamodel.Alignment;
27    import jalview.datamodel.AlignmentView;
28    import jalview.datamodel.HiddenColumns;
29    import jalview.datamodel.SeqCigar;
30    import jalview.datamodel.SequenceI;
31    import jalview.util.MessageManager;
32    import jalview.viewmodel.PCAModel;
33   
34    import java.awt.BorderLayout;
35    import java.awt.Button;
36    import java.awt.CheckboxMenuItem;
37    import java.awt.Choice;
38    import java.awt.Color;
39    import java.awt.FlowLayout;
40    import java.awt.Frame;
41    import java.awt.Label;
42    import java.awt.Menu;
43    import java.awt.MenuBar;
44    import java.awt.MenuItem;
45    import java.awt.Panel;
46    import java.awt.event.ActionEvent;
47    import java.awt.event.ActionListener;
48    import java.awt.event.ItemEvent;
49    import java.awt.event.ItemListener;
50   
 
51    public class PCAPanel extends EmbmenuFrame
52    implements Runnable, ActionListener, ItemListener
53    {
54    RotatableCanvas rc;
55   
56    AlignViewport av;
57   
58    PCAModel pcaModel;
59   
60    int top = 0;
61   
 
62  0 toggle public PCAPanel(AlignViewport viewport)
63    {
64  0 try
65    {
66  0 jbInit();
67    } catch (Exception e)
68    {
69  0 e.printStackTrace();
70    }
71   
72  0 for (int i = 1; i < 8; i++)
73    {
74  0 xCombobox.addItem("dim " + i);
75  0 yCombobox.addItem("dim " + i);
76  0 zCombobox.addItem("dim " + i);
77    }
78   
79  0 this.av = viewport;
80  0 boolean selected = viewport.getSelectionGroup() != null
81    && viewport.getSelectionGroup().getSize() > 0;
82  0 AlignmentView seqstrings = viewport.getAlignmentView(selected);
83  0 boolean nucleotide = viewport.getAlignment().isNucleotide();
84  0 SequenceI[] seqs;
85  0 if (!selected)
86    {
87  0 seqs = viewport.getAlignment().getSequencesArray();
88    }
89    else
90    {
91  0 seqs = viewport.getSelectionGroup()
92    .getSequencesInOrder(viewport.getAlignment());
93    }
94  0 SeqCigar sq[] = seqstrings.getSequences();
95  0 int length = sq[0].getWidth();
96   
97  0 for (int i = 0; i < seqs.length; i++)
98    {
99  0 if (sq[i].getWidth() != length)
100    {
101  0 System.out
102    .println("Sequences must be equal length for PCA analysis");
103  0 return;
104    }
105    }
106   
107  0 ScoreModelI scoreModel = ScoreModels.getInstance()
108    .getDefaultModel(!nucleotide);
109  0 pcaModel = new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
110    SimilarityParams.SeqSpace);
111   
112  0 rc = new RotatableCanvas(viewport);
113  0 embedMenuIfNeeded(rc);
114  0 add(rc, BorderLayout.CENTER);
115   
116  0 jalview.bin.JalviewLite.addFrame(this,
117    MessageManager.getString("label.principal_component_analysis"),
118    475, 400);
119   
120  0 Thread worker = new Thread(this);
121  0 worker.start();
122    }
123   
124    /**
125    * DOCUMENT ME!
126    */
 
127  0 toggle @Override
128    public void run()
129    {
130    // TODO progress indicator
131  0 calcSettings.setEnabled(false);
132  0 rc.setEnabled(false);
133  0 try
134    {
135  0 nuclSetting.setState(pcaModel.isNucleotide());
136  0 protSetting.setState(!pcaModel.isNucleotide());
137  0 pcaModel.calculate();
138    // ////////////////
139  0 xCombobox.select(0);
140  0 yCombobox.select(1);
141  0 zCombobox.select(2);
142   
143  0 pcaModel.updateRc(rc);
144    // rc.invalidate();
145  0 top = pcaModel.getTop();
146    } catch (OutOfMemoryError x)
147    {
148  0 jalview.bin.Console.errPrintln("Out of memory when calculating PCA.");
149  0 return;
150    }
151  0 calcSettings.setEnabled(true);
152   
153    // TODO revert progress indicator
154  0 rc.setEnabled(true);
155  0 rc.repaint();
156  0 this.repaint();
157    }
158   
 
159  0 toggle void doDimensionChange()
160    {
161  0 if (top == 0)
162    {
163  0 return;
164    }
165   
166  0 int dim1 = top - xCombobox.getSelectedIndex();
167  0 int dim2 = top - yCombobox.getSelectedIndex();
168  0 int dim3 = top - zCombobox.getSelectedIndex();
169  0 pcaModel.updateRcView(dim1, dim2, dim3);
170  0 rc.resetView();
171  0 rc.paint(rc.getGraphics());
172    }
173   
 
174  0 toggle @Override
175    public void actionPerformed(ActionEvent evt)
176    {
177  0 if (evt.getSource() == inputData)
178    {
179  0 showOriginalData();
180    }
181  0 if (evt.getSource() == resetButton)
182    {
183  0 xCombobox.select(0);
184  0 yCombobox.select(1);
185  0 zCombobox.select(2);
186  0 doDimensionChange();
187    }
188  0 if (evt.getSource() == values)
189    {
190  0 values_actionPerformed();
191    }
192    }
193   
 
194  0 toggle @Override
195    public void itemStateChanged(ItemEvent evt)
196    {
197  0 if (evt.getSource() == xCombobox)
198    {
199  0 xCombobox_actionPerformed();
200    }
201  0 else if (evt.getSource() == yCombobox)
202    {
203  0 yCombobox_actionPerformed();
204    }
205  0 else if (evt.getSource() == zCombobox)
206    {
207  0 zCombobox_actionPerformed();
208    }
209  0 else if (evt.getSource() == labels)
210    {
211  0 labels_itemStateChanged(evt);
212    }
213  0 else if (evt.getSource() == nuclSetting)
214    {
215  0 if (!pcaModel.isNucleotide())
216    {
217  0 pcaModel.setNucleotide(true);
218  0 ScoreModelI scoreModel = ScoreModels.getInstance()
219    .getDefaultModel(false);
220  0 pcaModel.setScoreModel(scoreModel);
221  0 new Thread(this).start();
222    }
223    }
224  0 else if (evt.getSource() == protSetting)
225    {
226  0 if (pcaModel.isNucleotide())
227    {
228  0 pcaModel.setNucleotide(false);
229  0 ScoreModelI scoreModel = ScoreModels.getInstance()
230    .getDefaultModel(true);
231  0 pcaModel.setScoreModel(scoreModel);
232  0 new Thread(this).start();
233    }
234    }
235    }
236   
 
237  0 toggle protected void xCombobox_actionPerformed()
238    {
239  0 doDimensionChange();
240    }
241   
 
242  0 toggle protected void yCombobox_actionPerformed()
243    {
244  0 doDimensionChange();
245    }
246   
 
247  0 toggle protected void zCombobox_actionPerformed()
248    {
249  0 doDimensionChange();
250    }
251   
 
252  0 toggle public void values_actionPerformed()
253    {
254   
255  0 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
256  0 Frame frame = new Frame();
257  0 frame.add(cap);
258  0 jalview.bin.JalviewLite.addFrame(frame,
259    MessageManager.getString("label.pca_details"), 500, 500);
260   
261  0 cap.setText(pcaModel.getDetails());
262    }
263   
 
264  0 toggle void showOriginalData()
265    {
266    // decide if av alignment is sufficiently different to original data to
267    // warrant a new window to be created
268    // create new alignmnt window with hidden regions (unhiding hidden regions
269    // yields unaligned seqs)
270    // or create a selection box around columns in alignment view
271    // test Alignment(SeqCigar[])
272  0 char gc = '-';
273  0 try
274    {
275    // we try to get the associated view's gap character
276    // but this may fail if the view was closed...
277  0 gc = av.getGapCharacter();
278    } catch (Exception ex)
279    {
280    }
281  0 ;
282  0 Object[] alAndColsel = pcaModel.getInputData()
283    .getAlignmentAndHiddenColumns(gc);
284   
285  0 if (alAndColsel != null && alAndColsel[0] != null)
286    {
287  0 Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
288  0 AlignFrame af = new AlignFrame(al, av.applet, "Original Data for PCA",
289    false);
290   
291  0 af.viewport.getAlignment()
292    .setHiddenColumns((HiddenColumns) alAndColsel[1]);
293    }
294    }
295   
 
296  0 toggle public void labels_itemStateChanged(ItemEvent itemEvent)
297    {
298  0 rc.showLabels(labels.getState());
299    }
300   
301    Panel jPanel2 = new Panel();
302   
303    Label jLabel1 = new Label();
304   
305    Label jLabel2 = new Label();
306   
307    Label jLabel3 = new Label();
308   
309    protected Choice xCombobox = new Choice();
310   
311    protected Choice yCombobox = new Choice();
312   
313    protected Choice zCombobox = new Choice();
314   
315    protected Button resetButton = new Button();
316   
317    FlowLayout flowLayout1 = new FlowLayout();
318   
319    BorderLayout borderLayout1 = new BorderLayout();
320   
321    MenuBar menuBar1 = new MenuBar();
322   
323    Menu menu1 = new Menu();
324   
325    Menu menu2 = new Menu();
326   
327    Menu calcSettings = new Menu();
328   
329    protected CheckboxMenuItem labels = new CheckboxMenuItem();
330   
331    protected CheckboxMenuItem protSetting = new CheckboxMenuItem();
332   
333    protected CheckboxMenuItem nuclSetting = new CheckboxMenuItem();
334   
335    MenuItem values = new MenuItem();
336   
337    MenuItem inputData = new MenuItem();
338   
 
339  0 toggle private void jbInit() throws Exception
340    {
341  0 this.setLayout(borderLayout1);
342  0 jPanel2.setLayout(flowLayout1);
343  0 jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
344  0 jLabel1.setText("x=");
345  0 jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));
346  0 jLabel2.setText("y=");
347  0 jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));
348  0 jLabel3.setText("z=");
349  0 jPanel2.setBackground(Color.white);
350  0 zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
351  0 zCombobox.addItemListener(this);
352  0 yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
353  0 yCombobox.addItemListener(this);
354  0 xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));
355  0 xCombobox.addItemListener(this);
356  0 resetButton.setFont(new java.awt.Font("Verdana", 0, 12));
357  0 resetButton.setLabel(MessageManager.getString("action.reset"));
358  0 resetButton.addActionListener(this);
359  0 this.setMenuBar(menuBar1);
360  0 menu1.setLabel(MessageManager.getString("action.file"));
361  0 menu2.setLabel(MessageManager.getString("action.view"));
362  0 calcSettings.setLabel(MessageManager.getString("action.change_params"));
363  0 labels.setLabel(MessageManager.getString("label.labels"));
364  0 labels.addItemListener(this);
365  0 values.setLabel(MessageManager.getString("label.output_values"));
366  0 values.addActionListener(this);
367  0 inputData.setLabel(MessageManager.getString("label.input_data"));
368  0 nuclSetting
369    .setLabel(MessageManager.getString("label.nucleotide_matrix"));
370  0 nuclSetting.addItemListener(this);
371  0 protSetting.setLabel(MessageManager.getString("label.protein_matrix"));
372  0 protSetting.addItemListener(this);
373  0 this.add(jPanel2, BorderLayout.SOUTH);
374  0 jPanel2.add(jLabel1, null);
375  0 jPanel2.add(xCombobox, null);
376  0 jPanel2.add(jLabel2, null);
377  0 jPanel2.add(yCombobox, null);
378  0 jPanel2.add(jLabel3, null);
379  0 jPanel2.add(zCombobox, null);
380  0 jPanel2.add(resetButton, null);
381  0 menuBar1.add(menu1);
382  0 menuBar1.add(menu2);
383  0 menuBar1.add(calcSettings);
384  0 menu2.add(labels);
385  0 menu1.add(values);
386  0 menu1.add(inputData);
387  0 calcSettings.add(nuclSetting);
388  0 calcSettings.add(protSetting);
389  0 inputData.addActionListener(this);
390    }
391   
392    }
  • Report generated by OpenClover v 4.4.1 on Wed Sep 17 2025 11:01:30 BST using coverage data from Wed Sep 17 2025 11:01:17 BST.
  • OpenClover is free and open-source software.