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Coverage Report

  1. Project Clover database Mon Nov 11 2024 17:27:16 GMT
  2. Package jalview.jbgui

File GPCAPanel.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

4
113
30
1
354
295
34
0.3
3.77
30
1.13

Classes

Class Line # Actions
GPCAPanel 46 113 34
0.6870748468.7%
 

Contributing tests

This file is covered by 1 test. .

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.FlowLayout;
26    import java.awt.Font;
27    import java.awt.GridLayout;
28    import java.awt.event.ActionEvent;
29    import java.awt.event.ActionListener;
30   
31    import javax.swing.JButton;
32    import javax.swing.JCheckBoxMenuItem;
33    import javax.swing.JComboBox;
34    import javax.swing.JInternalFrame;
35    import javax.swing.JLabel;
36    import javax.swing.JMenu;
37    import javax.swing.JMenuBar;
38    import javax.swing.JMenuItem;
39    import javax.swing.JPanel;
40    import javax.swing.event.MenuEvent;
41    import javax.swing.event.MenuListener;
42   
43    import jalview.util.ImageMaker.TYPE;
44    import jalview.util.MessageManager;
45   
 
46    public class GPCAPanel extends JInternalFrame
47    {
48    private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
49   
50    protected JComboBox<String> xCombobox = new JComboBox<>();
51   
52    protected JComboBox<String> yCombobox = new JComboBox<>();
53   
54    protected JComboBox<String> zCombobox = new JComboBox<>();
55   
56    protected JMenu viewMenu = new JMenu();
57   
58    protected JCheckBoxMenuItem showLabels = new JCheckBoxMenuItem();
59   
60    protected JMenu associateViewsMenu = new JMenu();
61   
62    protected JLabel statusBar = new JLabel();
63   
64    protected JPanel statusPanel = new JPanel();
65   
66    protected JMenuItem originalSeqData;
67   
68    /**
69    * Constructor
70    */
 
71  2 toggle public GPCAPanel()
72    {
73  2 try
74    {
75  2 jbInit();
76    } catch (Exception e)
77    {
78  0 e.printStackTrace();
79    }
80   
81  16 for (int i = 1; i < 8; i++)
82    {
83  14 xCombobox.addItem("dim " + i);
84  14 yCombobox.addItem("dim " + i);
85  14 zCombobox.addItem("dim " + i);
86    }
87    }
88   
 
89  0 toggle public GPCAPanel(int dim)
90    {
91  0 try
92    {
93  0 jbInit();
94    } catch (Exception e)
95    {
96  0 e.printStackTrace();
97    }
98   
99  0 for (int i = 1; i <= dim; i++)
100    {
101  0 xCombobox.addItem("dim " + i);
102  0 yCombobox.addItem("dim " + i);
103  0 zCombobox.addItem("dim " + i);
104    }
105    }
106   
 
107  2 toggle private void jbInit() throws Exception
108    {
109  2 setFrameIcon(null);
110  2 setName("jalview-pca");
111  2 this.getContentPane().setLayout(new BorderLayout());
112  2 JPanel jPanel2 = new JPanel();
113  2 jPanel2.setLayout(new FlowLayout());
114  2 JLabel jLabel1 = new JLabel();
115  2 jLabel1.setFont(VERDANA_12);
116  2 jLabel1.setText("x=");
117  2 JLabel jLabel2 = new JLabel();
118  2 jLabel2.setFont(VERDANA_12);
119  2 jLabel2.setText("y=");
120  2 JLabel jLabel3 = new JLabel();
121  2 jLabel3.setFont(VERDANA_12);
122  2 jLabel3.setText("z=");
123  2 jPanel2.setBackground(Color.white);
124  2 jPanel2.setBorder(null);
125  2 zCombobox.setFont(VERDANA_12);
126  2 zCombobox.addActionListener(new ActionListener()
127    {
 
128  4 toggle @Override
129    public void actionPerformed(ActionEvent e)
130    {
131  4 doDimensionChange();
132    }
133    });
134  2 yCombobox.setFont(VERDANA_12);
135  2 yCombobox.addActionListener(new ActionListener()
136    {
 
137  4 toggle @Override
138    public void actionPerformed(ActionEvent e)
139    {
140  4 doDimensionChange();
141    }
142    });
143  2 xCombobox.setFont(VERDANA_12);
144  2 xCombobox.addActionListener(new ActionListener()
145    {
 
146  4 toggle @Override
147    public void actionPerformed(ActionEvent e)
148    {
149  4 doDimensionChange();
150    }
151    });
152  2 JButton resetButton = new JButton();
153  2 resetButton.setFont(VERDANA_12);
154  2 resetButton.setText(MessageManager.getString("action.reset"));
155  2 resetButton.addActionListener(new ActionListener()
156    {
 
157  0 toggle @Override
158    public void actionPerformed(ActionEvent e)
159    {
160  0 resetButton_actionPerformed();
161    }
162    });
163  2 JMenu fileMenu = new JMenu();
164  2 fileMenu.setText(MessageManager.getString("action.file"));
165  2 JMenu saveMenu = new JMenu();
166  2 saveMenu.setText(MessageManager.getString("action.save_as"));
167  2 JMenuItem eps = new JMenuItem("EPS");
168  2 eps.addActionListener(new ActionListener()
169    {
 
170  0 toggle @Override
171    public void actionPerformed(ActionEvent e)
172    {
173  0 makePCAImage(TYPE.EPS);
174    }
175    });
176  2 JMenuItem png = new JMenuItem("PNG");
177  2 png.addActionListener(new ActionListener()
178    {
 
179  0 toggle @Override
180    public void actionPerformed(ActionEvent e)
181    {
182  0 makePCAImage(TYPE.PNG);
183    }
184    });
185  2 JMenuItem outputValues = new JMenuItem();
186  2 outputValues.setText(MessageManager.getString("label.output_values"));
187  2 outputValues.addActionListener(new ActionListener()
188    {
 
189  0 toggle @Override
190    public void actionPerformed(ActionEvent e)
191    {
192  0 outputValues_actionPerformed();
193    }
194    });
195  2 JMenuItem outputPoints = new JMenuItem();
196  2 outputPoints.setText(MessageManager.getString("label.output_points"));
197  2 outputPoints.addActionListener(new ActionListener()
198    {
 
199  0 toggle @Override
200    public void actionPerformed(ActionEvent e)
201    {
202  0 outputPoints_actionPerformed();
203    }
204    });
205  2 JMenuItem outputProjPoints = new JMenuItem();
206  2 outputProjPoints.setText(
207    MessageManager.getString("label.output_transformed_points"));
208  2 outputProjPoints.addActionListener(new ActionListener()
209    {
 
210  0 toggle @Override
211    public void actionPerformed(ActionEvent e)
212    {
213  0 outputProjPoints_actionPerformed();
214    }
215    });
216  2 JMenuItem print = new JMenuItem();
217  2 print.setText(MessageManager.getString("action.print"));
218  2 print.addActionListener(new ActionListener()
219    {
 
220  0 toggle @Override
221    public void actionPerformed(ActionEvent e)
222    {
223  0 print_actionPerformed();
224    }
225    });
226  2 viewMenu.setText(MessageManager.getString("action.view"));
227  2 viewMenu.addMenuListener(new MenuListener()
228    {
 
229  0 toggle @Override
230    public void menuSelected(MenuEvent e)
231    {
232  0 viewMenu_menuSelected();
233    }
234   
 
235  0 toggle @Override
236    public void menuDeselected(MenuEvent e)
237    {
238    }
239   
 
240  0 toggle @Override
241    public void menuCanceled(MenuEvent e)
242    {
243    }
244    });
245  2 showLabels.setText(MessageManager.getString("label.show_labels"));
246  2 showLabels.addActionListener(new ActionListener()
247    {
 
248  0 toggle @Override
249    public void actionPerformed(ActionEvent e)
250    {
251  0 showLabels_actionPerformed();
252    }
253    });
254  2 JMenuItem bgcolour = new JMenuItem();
255  2 bgcolour.setText(MessageManager.getString("action.background_colour"));
256  2 bgcolour.addActionListener(new ActionListener()
257    {
 
258  0 toggle @Override
259    public void actionPerformed(ActionEvent e)
260    {
261  0 bgcolour_actionPerformed();
262    }
263    });
264  2 originalSeqData = new JMenuItem();
265  2 originalSeqData.setText(MessageManager.getString("label.input_data"));
266  2 originalSeqData.addActionListener(new ActionListener()
267    {
 
268  0 toggle @Override
269    public void actionPerformed(ActionEvent e)
270    {
271  0 originalSeqData_actionPerformed();
272    }
273    });
274  2 associateViewsMenu.setText(
275    MessageManager.getString("label.associate_nodes_with"));
276   
277  2 statusPanel.setLayout(new GridLayout());
278  2 statusBar.setFont(VERDANA_12);
279    // statusPanel.setBackground(Color.lightGray);
280    // statusBar.setBackground(Color.lightGray);
281    // statusPanel.add(statusBar, null);
282  2 JPanel panelBar = new JPanel(new BorderLayout());
283  2 panelBar.add(jPanel2, BorderLayout.NORTH);
284  2 panelBar.add(statusPanel, BorderLayout.SOUTH);
285  2 this.getContentPane().add(panelBar, BorderLayout.SOUTH);
286  2 jPanel2.add(jLabel1, null);
287  2 jPanel2.add(xCombobox, null);
288  2 jPanel2.add(jLabel2, null);
289  2 jPanel2.add(yCombobox, null);
290  2 jPanel2.add(jLabel3, null);
291  2 jPanel2.add(zCombobox, null);
292  2 jPanel2.add(resetButton, null);
293   
294  2 JMenuBar jMenuBar1 = new JMenuBar();
295  2 jMenuBar1.add(fileMenu);
296  2 jMenuBar1.add(viewMenu);
297  2 setJMenuBar(jMenuBar1);
298  2 fileMenu.add(saveMenu);
299  2 fileMenu.add(outputValues);
300  2 fileMenu.add(print);
301  2 fileMenu.add(originalSeqData);
302  2 fileMenu.add(outputPoints);
303  2 fileMenu.add(outputProjPoints);
304  2 saveMenu.add(eps);
305  2 saveMenu.add(png);
306  2 viewMenu.add(showLabels);
307  2 viewMenu.add(bgcolour);
308  2 viewMenu.add(associateViewsMenu);
309    }
310   
 
311  0 toggle protected void resetButton_actionPerformed()
312    {
313    }
314   
 
315  0 toggle protected void outputPoints_actionPerformed()
316    {
317    }
318   
 
319  0 toggle protected void outputProjPoints_actionPerformed()
320    {
321    }
322   
 
323  0 toggle public void makePCAImage(TYPE imageType)
324    {
325    }
326   
 
327  0 toggle protected void outputValues_actionPerformed()
328    {
329    }
330   
 
331  0 toggle protected void print_actionPerformed()
332    {
333    }
334   
 
335  0 toggle protected void showLabels_actionPerformed()
336    {
337    }
338   
 
339  0 toggle protected void bgcolour_actionPerformed()
340    {
341    }
342   
 
343  0 toggle protected void originalSeqData_actionPerformed()
344    {
345    }
346   
 
347  0 toggle protected void viewMenu_menuSelected()
348    {
349    }
350   
 
351  0 toggle protected void doDimensionChange()
352    {
353    }
354    }