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Coverage Report

  1. Project Clover database Mon Nov 11 2024 20:42:03 GMT
  2. Package jalview.gui

File SliderPanel.java

 

Coverage histogram

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

Code metrics

64
165
29
1
625
430
72
0.44
5.69
29
2.48

Classes

Class Line # Actions
SliderPanel 47 165 72
0.635658963.6%
 

Contributing tests

This file is covered by 20 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.gui;
22   
23    import java.awt.event.MouseAdapter;
24    import java.awt.event.MouseEvent;
25    import java.beans.PropertyVetoException;
26    import java.util.List;
27   
28    import javax.swing.JInternalFrame;
29    import javax.swing.JLayeredPane;
30    import javax.swing.event.ChangeEvent;
31    import javax.swing.event.ChangeListener;
32    import javax.swing.event.InternalFrameAdapter;
33    import javax.swing.event.InternalFrameEvent;
34   
35    import jalview.analysis.Conservation;
36    import jalview.datamodel.SequenceGroup;
37    import jalview.jbgui.GSliderPanel;
38    import jalview.renderer.ResidueShaderI;
39    import jalview.util.MessageManager;
40   
41    /**
42    * DOCUMENT ME!
43    *
44    * @author $author$
45    * @version $Revision$
46    */
 
47    public class SliderPanel extends GSliderPanel
48    {
49    private static final String BACKGROUND = "Background";
50   
51    static JInternalFrame conservationSlider;
52   
53    static JInternalFrame consensusSecondaryStructureSlider;
54   
55    static JInternalFrame PIDSlider;
56   
57    AlignmentPanel ap;
58   
59    boolean forConservation = true;
60   
61    boolean forConsensusSecondaryStructure = false;
62   
63    ResidueShaderI cs;
64   
65    /**
66    * Returns the currently displayed slider panel (or null if none).
67    *
68    * @return
69    */
 
70  19 toggle public static SliderPanel getSliderPanel()
71    {
72  19 if (conservationSlider != null && conservationSlider.isVisible())
73    {
74  10 return (SliderPanel) conservationSlider.getContentPane();
75    }
76  9 if (PIDSlider != null && PIDSlider.isVisible())
77    {
78  9 return (SliderPanel) PIDSlider.getContentPane();
79    }
80  0 if (consensusSecondaryStructureSlider != null
81    && consensusSecondaryStructureSlider.isVisible())
82    {
83  0 return (SliderPanel) consensusSecondaryStructureSlider
84    .getContentPane();
85    }
86  0 return null;
87    }
88   
89    /**
90    * Creates a new SliderPanel object.
91    *
92    * @param ap
93    * DOCUMENT ME!
94    * @param value
95    * DOCUMENT ME!
96    * @param forConserve
97    * DOCUMENT ME!
98    * @param scheme
99    * DOCUMENT ME!
100    */
 
101  17 toggle public SliderPanel(final AlignmentPanel ap, int value,
102    boolean forConserve, boolean forConsensusSS,
103    ResidueShaderI scheme)
104    {
105  17 this.ap = ap;
106  17 this.cs = scheme;
107  17 forConservation = forConserve;
108  17 forConsensusSecondaryStructure = forConsensusSS;
109   
110  17 undoButton.setVisible(false);
111  17 applyButton.setVisible(false);
112   
113  17 if (forConservation)
114    {
115  7 label.setText(MessageManager.getString(
116    "label.enter_value_increase_conservation_visibility"));
117  7 slider.setMinimum(0);
118  7 slider.setMaximum(100);
119    }
120  17 if (forConsensusSS)
121    {
122  0 label.setText(MessageManager.getString(
123    "label.enter_value_increase_conservation_visibility"));
124  0 slider.setMinimum(0);
125  0 slider.setMaximum(100);
126    }
127    else
128    {
129  17 label.setText(MessageManager.getString(
130    "label.enter_percentage_identity_above_which_colour_residues"));
131  17 slider.setMinimum(0);
132  17 slider.setMaximum(100);
133    }
134   
135  17 slider.addChangeListener(new ChangeListener()
136    {
 
137  17 toggle @Override
138    public void stateChanged(ChangeEvent evt)
139    {
140  17 valueField.setText(String.valueOf(slider.getValue()));
141  17 valueChanged(slider.getValue());
142    }
143    });
144   
145  17 slider.addMouseListener(new MouseAdapter()
146    {
 
147  0 toggle @Override
148    public void mouseReleased(MouseEvent evt)
149    {
150  0 ap.paintAlignment(true, true);
151    }
152    });
153   
154  17 slider.setValue(value);
155  17 valueField.setText(String.valueOf(value));
156    }
157   
158    /**
159    * Method to 'set focus' of the Conservation slider panel
160    *
161    * @param ap
162    * the panel to repaint on change of slider
163    * @param rs
164    * the colour scheme to update on change of slider
165    * @param source
166    * a text description for the panel's title
167    *
168    * @return
169    */
 
170  11 toggle public static int setConservationSlider(AlignmentPanel ap,
171    ResidueShaderI rs, String source)
172    {
173  11 SliderPanel sliderPanel = null;
174   
175  11 if (conservationSlider == null)
176    {
177  7 sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true,
178    false, rs);
179  7 conservationSlider = new JInternalFrame();
180  7 conservationSlider.setFrameIcon(null);
181  7 conservationSlider.setContentPane(sliderPanel);
182  7 conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
183    }
184    else
185    {
186  4 sliderPanel = (SliderPanel) conservationSlider.getContentPane();
187  4 sliderPanel.valueField
188    .setText(String.valueOf(rs.getConservationInc()));
189  4 sliderPanel.cs = rs;
190  4 sliderPanel.ap = ap;
191  4 sliderPanel.slider.setValue(rs.getConservationInc());
192    }
193   
194  11 conservationSlider.setTitle(MessageManager.formatMessage(
195    "label.conservation_colour_increment", new String[]
196  11 { source == null ? BACKGROUND : source }));
197   
198  11 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
199  11 if (groups != null && !groups.isEmpty())
200    {
201  6 sliderPanel.setAllGroupsCheckEnabled(true);
202  6 sliderPanel.allGroupsCheck
203    .setSelected(ap.av.getColourAppliesToAllGroups());
204    }
205    else
206    {
207  5 sliderPanel.setAllGroupsCheckEnabled(false);
208    }
209   
210  11 return sliderPanel.getValue();
211    }
212   
213    /**
214    * Hides the PID slider panel if it is shown
215    */
 
216  170 toggle public static void hidePIDSlider()
217    {
218  170 if (PIDSlider != null)
219    {
220  8 try
221    {
222  8 PIDSlider.setClosed(true);
223  8 PIDSlider = null;
224    } catch (PropertyVetoException ex)
225    {
226    }
227    }
228    }
229   
230    /**
231    * Hides the conservation slider panel if it is shown
232    */
 
233  169 toggle public static void hideConservationSlider()
234    {
235  169 if (conservationSlider != null)
236    {
237  6 try
238    {
239  6 conservationSlider.setClosed(true);
240  6 conservationSlider = null;
241    } catch (PropertyVetoException ex)
242    {
243    }
244    }
245    }
246   
247    /**
248    * DOCUMENT ME!
249    */
 
250  9 toggle public static void showConservationSlider()
251    {
252  9 hidePIDSlider();
253   
254  9 if (!conservationSlider.isVisible())
255    {
256  7 Desktop.addInternalFrame(conservationSlider,
257    conservationSlider.getTitle(), true, FRAME_WIDTH,
258    FRAME_HEIGHT, false, true);
259  7 conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
260    {
 
261  7 toggle @Override
262    public void internalFrameClosed(InternalFrameEvent e)
263    {
264  7 conservationSlider = null;
265    }
266    });
267  7 conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
268    }
269    }
270   
 
271  0 toggle public static int setConsensusSecondaryStructureSlider(AlignmentPanel ap,
272    ResidueShaderI rs, String source)
273    {
274  0 SliderPanel sliderPanel = null;
275   
276  0 if (consensusSecondaryStructureSlider == null)
277    {
278  0 sliderPanel = new SliderPanel(ap,
279    rs.getConsensusSecondaryStructureThreshold(), false, true,
280    rs);
281  0 consensusSecondaryStructureSlider = new JInternalFrame();
282  0 consensusSecondaryStructureSlider.setFrameIcon(null);
283  0 consensusSecondaryStructureSlider.setContentPane(sliderPanel);
284  0 consensusSecondaryStructureSlider
285    .setLayer(JLayeredPane.PALETTE_LAYER);
286    }
287    else
288    {
289  0 sliderPanel = (SliderPanel) consensusSecondaryStructureSlider
290    .getContentPane();
291  0 sliderPanel.valueField.setText(
292    String.valueOf(rs.getConsensusSecondaryStructureThreshold()));
293  0 sliderPanel.cs = rs;
294  0 sliderPanel.ap = ap;
295  0 sliderPanel.slider
296    .setValue(rs.getConsensusSecondaryStructureThreshold());
297    }
298   
299  0 consensusSecondaryStructureSlider.setTitle(MessageManager.formatMessage(
300    "label.secondary_structure_conservation_threshold", new String[]
301  0 { source == null ? BACKGROUND : source }));
302   
303  0 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
304  0 if (groups != null && !groups.isEmpty())
305    {
306  0 sliderPanel.setAllGroupsCheckEnabled(true);
307  0 sliderPanel.allGroupsCheck
308    .setSelected(ap.av.getColourAppliesToAllGroups());
309    }
310    else
311    {
312  0 sliderPanel.setAllGroupsCheckEnabled(false);
313    }
314   
315  0 return sliderPanel.getValue();
316    }
317   
 
318  160 toggle public static void hideConsensusSecondaryStructureSlider()
319    {
320  160 if (consensusSecondaryStructureSlider != null)
321    {
322  0 try
323    {
324  0 consensusSecondaryStructureSlider.setClosed(true);
325  0 consensusSecondaryStructureSlider = null;
326    } catch (PropertyVetoException ex)
327    {
328    }
329    }
330    }
331   
 
332  0 toggle public static void showConsensusSecondaryStructureSlider()
333    {
334  0 hidePIDSlider();
335  0 hideConservationSlider();
336   
337  0 if (!consensusSecondaryStructureSlider.isVisible())
338    {
339  0 Desktop.addInternalFrame(consensusSecondaryStructureSlider,
340    consensusSecondaryStructureSlider.getTitle(), true,
341    FRAME_WIDTH, FRAME_HEIGHT, false, true);
342  0 consensusSecondaryStructureSlider
343    .addInternalFrameListener(new InternalFrameAdapter()
344    {
 
345  0 toggle @Override
346    public void internalFrameClosed(InternalFrameEvent e)
347    {
348  0 consensusSecondaryStructureSlider = null;
349    }
350    });
351  0 consensusSecondaryStructureSlider
352    .setLayer(JLayeredPane.PALETTE_LAYER);
353    }
354    }
355   
356    /**
357    * Method to 'set focus' of the PID slider panel
358    *
359    * @param ap
360    * the panel to repaint on change of slider
361    * @param rs
362    * the colour scheme to update on change of slider
363    * @param source
364    * a text description for the panel's title
365    *
366    * @return
367    */
 
368  11 toggle public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
369    String source)
370    {
371  11 int threshold = rs.getThreshold();
372   
373  11 SliderPanel sliderPanel = null;
374   
375  11 if (PIDSlider == null)
376    {
377  10 sliderPanel = new SliderPanel(ap, threshold, false, false, rs);
378  10 PIDSlider = new JInternalFrame();
379  10 PIDSlider.setFrameIcon(null);
380  10 PIDSlider.setContentPane(sliderPanel);
381  10 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
382    }
383    else
384    {
385  1 sliderPanel = (SliderPanel) PIDSlider.getContentPane();
386  1 sliderPanel.cs = rs;
387  1 sliderPanel.ap = ap;
388  1 sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
389  1 sliderPanel.slider.setValue(rs.getThreshold());
390    }
391   
392  11 PIDSlider.setTitle(MessageManager.formatMessage(
393    "label.percentage_identity_threshold", new String[]
394  11 { source == null ? BACKGROUND : source }));
395   
396  11 if (ap.av.getAlignment().getGroups() != null)
397    {
398  11 sliderPanel.setAllGroupsCheckEnabled(true);
399    }
400    else
401    {
402  0 sliderPanel.setAllGroupsCheckEnabled(false);
403    }
404   
405  11 return sliderPanel.getValue();
406    }
407   
408    /**
409    * DOCUMENT ME!
410    *
411    * @return
412    */
 
413  9 toggle public static JInternalFrame showPIDSlider()
414    {
415  9 hideConservationSlider();
416   
417  9 if (!PIDSlider.isVisible())
418    {
419  9 Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true,
420    FRAME_WIDTH, FRAME_HEIGHT, false, true);
421  9 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
422  9 PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
423    {
 
424  9 toggle @Override
425    public void internalFrameClosed(InternalFrameEvent e)
426    {
427  9 PIDSlider = null;
428    }
429    });
430  9 PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
431    }
432  9 return PIDSlider;
433    }
434   
435    /**
436    * Updates the colour scheme with the current (identity threshold or
437    * conservation) percentage value. Also updates all groups if 'apply to all
438    * groups' is selected.
439    *
440    * @param percent
441    */
 
442  37 toggle public void valueChanged(int percent)
443    {
444  37 if (!forConservation && !forConsensusSecondaryStructure)
445    {
446  21 ap.av.setThreshold(percent);
447    }
448  37 updateColourScheme(percent, cs, null);
449   
450  37 if (allGroupsCheck.isSelected())
451    {
452  2 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
453  2 for (SequenceGroup sg : groups)
454    {
455  2 updateColourScheme(percent, sg.getGroupColourScheme(), sg);
456    }
457    }
458   
459  37 ap.getSeqPanel().seqCanvas.repaint();
460    }
461   
462    /**
463    * Updates the colour scheme (if not null) with the current (identity
464    * threshold or conservation) percentage value
465    *
466    * @param percent
467    * @param scheme
468    * @param sg
469    */
 
470  39 toggle protected void updateColourScheme(int percent, ResidueShaderI scheme,
471    SequenceGroup sg)
472    {
473  39 if (scheme == null)
474    {
475  0 return;
476    }
477  39 if (forConservation)
478    {
479  18 if (!scheme.conservationApplied() && sg != null)
480    {
481    /*
482    * first time the colour scheme has had Conservation shading applied
483    * - compute conservation
484    */
485  0 Conservation c = new Conservation("Group", sg.getSequences(null),
486    sg.getStartRes(), sg.getEndRes());
487  0 c.calculate();
488  0 c.verdict(false, ap.av.getConsPercGaps());
489  0 sg.cs.setConservation(c);
490   
491    }
492  18 scheme.setConservationApplied(true);
493  18 scheme.setConservationInc(percent);
494    }
495  21 else if(forConsensusSecondaryStructure)
496    {
497  0 scheme.setConsensusSecondaryStructureColouring(true);
498  0 scheme.setConsensusSecondaryStructureThreshold(percent);
499    }
500    else
501    {
502  21 scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
503   
504    }
505    }
506   
507    /**
508    * DOCUMENT ME!
509    *
510    * @param b
511    * DOCUMENT ME!
512    */
 
513  22 toggle public void setAllGroupsCheckEnabled(boolean b)
514    {
515  22 allGroupsCheck.setEnabled(b);
516    }
517   
518    /**
519    * DOCUMENT ME!
520    *
521    * @param e
522    * DOCUMENT ME!
523    */
 
524  0 toggle @Override
525    public void valueField_actionPerformed()
526    {
527  0 try
528    {
529  0 int i = Integer.parseInt(valueField.getText());
530  0 slider.setValue(i);
531    } catch (NumberFormatException ex)
532    {
533  0 valueField.setText(slider.getValue() + "");
534    }
535    }
536   
537    /**
538    * DOCUMENT ME!
539    *
540    * @param value
541    * DOCUMENT ME!
542    */
 
543  0 toggle public void setValue(int value)
544    {
545  0 slider.setValue(value);
546    }
547   
548    /**
549    * DOCUMENT ME!
550    *
551    * @return DOCUMENT ME!
552    */
 
553  24 toggle public int getValue()
554    {
555  24 return Integer.parseInt(valueField.getText());
556    }
557   
 
558  0 toggle @Override
559    public void slider_mouseReleased(MouseEvent e)
560    {
561  0 if (ap.overviewPanel != null)
562    {
563  0 ap.overviewPanel.updateOverviewImage();
564    }
565    }
566   
 
567  0 toggle public static int getConservationValue()
568    {
569  0 return getValue(conservationSlider);
570    }
571   
 
572  0 toggle static int getValue(JInternalFrame slider)
573    {
574  0 return slider == null ? 0
575    : ((SliderPanel) slider.getContentPane()).getValue();
576    }
577   
 
578  0 toggle public static int getPIDValue()
579    {
580  0 return getValue(PIDSlider);
581    }
582   
 
583  0 toggle public static int getConsensusSecondaryStructureSliderValue()
584    {
585  0 return getValue(consensusSecondaryStructureSlider);
586    }
587   
588    /**
589    * Answers true if the SliderPanel is for Conservation, false if it is for PID
590    * threshold
591    *
592    * @return
593    */
 
594  24 toggle public boolean isForConservation()
595    {
596  24 return forConservation;
597    }
598   
599    /**
600    * Answers the title for the slider panel; this may include 'Background' if
601    * for the alignment, or the group id if for a group
602    *
603    * @return
604    */
 
605  6 toggle public String getTitle()
606    {
607  6 String title = null;
608  6 if (isForConservation())
609    {
610  4 if (conservationSlider != null)
611    {
612  4 title = conservationSlider.getTitle();
613    }
614    }
615  2 else if (PIDSlider != null)
616    {
617  2 title = PIDSlider.getTitle();
618    }
619  0 else if (consensusSecondaryStructureSlider != null)
620    {
621  0 title = consensusSecondaryStructureSlider.getTitle();
622    }
623  6 return title;
624    }
625    }
  • Report generated by OpenClover v 4.4.1 on Mon Nov 11 2024 20:49:40 GMT using coverage data from Mon Nov 11 2024 20:49:29 GMT.
  • OpenClover is free and open-source software.