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Coverage Report

  1. Project Clover database Mon Dec 1 2025 15:35:32 GMT
  2. Package jalview.appletgui

File SliderPanel.java

 

Coverage histogram

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

Code metrics

38
140
25
1
461
367
49
0.35
5.6
25
1.96

Classes

Class Line # Actions
SliderPanel 50 140 49
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.Conservation;
24    import jalview.datamodel.SequenceGroup;
25    import jalview.renderer.ResidueShaderI;
26    import jalview.util.MessageManager;
27   
28    import java.awt.BorderLayout;
29    import java.awt.Button;
30    import java.awt.Checkbox;
31    import java.awt.Color;
32    import java.awt.FlowLayout;
33    import java.awt.Frame;
34    import java.awt.Label;
35    import java.awt.Panel;
36    import java.awt.Scrollbar;
37    import java.awt.TextField;
38    import java.awt.event.ActionEvent;
39    import java.awt.event.ActionListener;
40    import java.awt.event.AdjustmentEvent;
41    import java.awt.event.AdjustmentListener;
42    import java.awt.event.FocusAdapter;
43    import java.awt.event.FocusEvent;
44    import java.awt.event.MouseEvent;
45    import java.awt.event.MouseListener;
46    import java.awt.event.WindowAdapter;
47    import java.awt.event.WindowEvent;
48    import java.util.List;
49   
 
50    public class SliderPanel extends Panel
51    implements ActionListener, AdjustmentListener, MouseListener
52    {
53    private static final String BACKGROUND = "Background";
54   
55    AlignmentPanel ap;
56   
57    boolean forConservation = true;
58   
59    ResidueShaderI cs;
60   
61    static Frame conservationSlider;
62   
63    static Frame PIDSlider;
64   
 
65  0 toggle public static int setConservationSlider(AlignmentPanel ap,
66    ResidueShaderI ccs, String source)
67    {
68  0 SliderPanel sp = null;
69   
70  0 if (conservationSlider == null)
71    {
72  0 sp = new SliderPanel(ap, ccs.getConservationInc(), true, ccs);
73  0 conservationSlider = new Frame();
74  0 conservationSlider.add(sp);
75    }
76    else
77    {
78  0 sp = (SliderPanel) conservationSlider.getComponent(0);
79  0 sp.cs = ccs;
80  0 sp.valueField.setText(String.valueOf(ccs.getConservationInc()));
81    }
82   
83  0 conservationSlider.setTitle(MessageManager.formatMessage(
84    "label.conservation_colour_increment", new String[]
85  0 { source == null ? BACKGROUND : source }));
86  0 List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
87  0 if (groups != null && !groups.isEmpty())
88    {
89  0 sp.setAllGroupsCheckEnabled(true);
90    }
91    else
92    {
93  0 sp.setAllGroupsCheckEnabled(false);
94    }
95   
96  0 return sp.getValue();
97    }
98   
 
99  0 toggle public static void showConservationSlider()
100    {
101  0 try
102    {
103  0 PIDSlider.setVisible(false);
104  0 PIDSlider = null;
105    } catch (Exception ex)
106    {
107    }
108   
109  0 if (!conservationSlider.isVisible())
110    {
111  0 jalview.bin.JalviewLite.addFrame(conservationSlider,
112    conservationSlider.getTitle(), 420, 100);
113  0 conservationSlider.addWindowListener(new WindowAdapter()
114    {
 
115  0 toggle @Override
116    public void windowClosing(WindowEvent e)
117    {
118  0 conservationSlider = null;
119    }
120    });
121   
122    }
123   
124    }
125   
 
126  0 toggle public static int setPIDSliderSource(AlignmentPanel ap,
127    ResidueShaderI ccs, String source)
128    {
129  0 SliderPanel pid = null;
130  0 if (PIDSlider == null)
131    {
132  0 pid = new SliderPanel(ap, ccs.getThreshold(), false, ccs);
133  0 PIDSlider = new Frame();
134  0 PIDSlider.add(pid);
135    }
136    else
137    {
138  0 pid = (SliderPanel) PIDSlider.getComponent(0);
139  0 pid.cs = ccs;
140  0 pid.valueField.setText(String.valueOf(ccs.getThreshold()));
141    }
142  0 PIDSlider.setTitle(MessageManager.formatMessage(
143    "label.percentage_identity_threshold", new String[]
144  0 { source == null ? BACKGROUND : source }));
145   
146  0 if (ap.av.getAlignment().getGroups() != null)
147    {
148  0 pid.setAllGroupsCheckEnabled(true);
149    }
150    else
151    {
152  0 pid.setAllGroupsCheckEnabled(false);
153    }
154   
155  0 return pid.getValue();
156   
157    }
158   
 
159  0 toggle public static void showPIDSlider()
160    {
161  0 try
162    {
163  0 conservationSlider.setVisible(false);
164  0 conservationSlider = null;
165    } catch (Exception ex)
166    {
167    }
168   
169  0 if (!PIDSlider.isVisible())
170    {
171  0 jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,
172    100);
173  0 PIDSlider.addWindowListener(new WindowAdapter()
174    {
 
175  0 toggle @Override
176    public void windowClosing(WindowEvent e)
177    {
178  0 PIDSlider = null;
179    }
180    });
181    }
182   
183    }
184   
185    /**
186    * Hides the PID slider panel if it is shown
187    */
 
188  0 toggle public static void hidePIDSlider()
189    {
190  0 if (PIDSlider != null)
191    {
192  0 PIDSlider.setVisible(false);
193  0 PIDSlider = null;
194    }
195    }
196   
197    /**
198    * Hides the Conservation slider panel if it is shown
199    */
 
200  0 toggle public static void hideConservationSlider()
201    {
202  0 if (conservationSlider != null)
203    {
204  0 conservationSlider.setVisible(false);
205  0 conservationSlider = null;
206    }
207    }
208   
 
209  0 toggle public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
210    ResidueShaderI shader)
211    {
212  0 try
213    {
214  0 jbInit();
215    } catch (Exception e)
216    {
217  0 e.printStackTrace();
218    }
219  0 this.ap = ap;
220  0 this.cs = shader;
221  0 forConservation = forConserve;
222  0 undoButton.setVisible(false);
223  0 applyButton.setVisible(false);
224  0 if (forConservation)
225    {
226  0 label.setText(MessageManager
227    .getString("label.modify_conservation_visibility"));
228  0 slider.setMinimum(0);
229  0 slider.setMaximum(50 + slider.getVisibleAmount());
230  0 slider.setUnitIncrement(1);
231    }
232    else
233    {
234  0 label.setText(MessageManager
235    .getString("label.colour_residues_above_occurrence"));
236  0 slider.setMinimum(0);
237  0 slider.setMaximum(100 + slider.getVisibleAmount());
238  0 slider.setBlockIncrement(1);
239    }
240   
241  0 slider.addAdjustmentListener(this);
242  0 slider.addMouseListener(this);
243   
244  0 slider.setValue(value);
245  0 valueField.setText(value + "");
246    }
247   
 
248  0 toggle public void valueChanged(int i)
249    {
250  0 if (cs == null)
251    {
252  0 return;
253    }
254  0 if (forConservation)
255    {
256  0 cs.setConservationApplied(true);
257  0 cs.setConservationInc(i);
258    }
259    else
260    {
261  0 cs.setThreshold(i, ap.av.isIgnoreGapsConsensus());
262    }
263   
264  0 if (allGroupsCheck.getState())
265    {
266  0 for (SequenceGroup group : ap.av.getAlignment().getGroups())
267    {
268  0 ResidueShaderI groupColourScheme = group.getGroupColourScheme();
269  0 if (forConservation)
270    {
271  0 if (!groupColourScheme.conservationApplied())
272    {
273    /*
274    * first time the colour scheme has had Conservation shading applied
275    * - compute conservation
276    */
277  0 Conservation c = new Conservation("Group",
278    group.getSequences(null), group.getStartRes(),
279    group.getEndRes());
280  0 c.calculate();
281  0 c.verdict(false, ap.av.getConsPercGaps());
282  0 group.cs.setConservation(c);
283   
284    }
285  0 groupColourScheme.setConservationApplied(true);
286  0 groupColourScheme.setConservationInc(i);
287    }
288    else
289    {
290  0 groupColourScheme.setThreshold(i, ap.av.isIgnoreGapsConsensus());
291    }
292    }
293    }
294   
295  0 ap.seqPanel.seqCanvas.repaint();
296    }
297   
 
298  0 toggle public void setAllGroupsCheckEnabled(boolean b)
299    {
300  0 allGroupsCheck.setState(ap.av.getColourAppliesToAllGroups());
301  0 allGroupsCheck.setEnabled(b);
302    }
303   
 
304  0 toggle @Override
305    public void actionPerformed(ActionEvent evt)
306    {
307  0 if (evt.getSource() == applyButton)
308    {
309  0 applyButton_actionPerformed();
310    }
311  0 else if (evt.getSource() == undoButton)
312    {
313  0 undoButton_actionPerformed();
314    }
315  0 else if (evt.getSource() == valueField)
316    {
317  0 valueField_actionPerformed();
318    }
319    }
320   
 
321  0 toggle @Override
322    public void adjustmentValueChanged(AdjustmentEvent evt)
323    {
324  0 valueField.setText(slider.getValue() + "");
325  0 valueChanged(slider.getValue());
326    }
327   
 
328  0 toggle public void valueField_actionPerformed()
329    {
330  0 try
331    {
332  0 int i = Integer.valueOf(valueField.getText());
333  0 slider.setValue(i);
334    } catch (NumberFormatException ex)
335    {
336  0 valueField.setText(String.valueOf(slider.getValue()));
337    }
338    }
339   
 
340  0 toggle public void setValue(int value)
341    {
342  0 slider.setValue(value);
343    }
344   
 
345  0 toggle public int getValue()
346    {
347  0 return Integer.parseInt(valueField.getText());
348    }
349   
350    // this is used for conservation colours, PID colours and redundancy threshold
351    protected Scrollbar slider = new Scrollbar();
352   
353    protected TextField valueField = new TextField();
354   
355    protected Label label = new Label();
356   
357    Panel jPanel1 = new Panel();
358   
359    Panel jPanel2 = new Panel();
360   
361    protected Button applyButton = new Button();
362   
363    protected Button undoButton = new Button();
364   
365    FlowLayout flowLayout1 = new FlowLayout();
366   
367    protected Checkbox allGroupsCheck = new Checkbox();
368   
369    BorderLayout borderLayout1 = new BorderLayout();
370   
371    BorderLayout borderLayout2 = new BorderLayout();
372   
373    FlowLayout flowLayout2 = new FlowLayout();
374   
 
375  0 toggle private void jbInit() throws Exception
376    {
377  0 this.setLayout(borderLayout2);
378   
379    // slider.setMajorTickSpacing(10);
380    // slider.setMinorTickSpacing(1);
381    // slider.setPaintTicks(true);
382  0 slider.setBackground(Color.white);
383  0 slider.setFont(new java.awt.Font("Verdana", 0, 11));
384  0 slider.setOrientation(0);
385  0 valueField.setFont(new java.awt.Font("Verdana", 0, 11));
386  0 valueField.setText(" ");
387  0 valueField.addActionListener(this);
388  0 valueField.setColumns(3);
389  0 valueField.addFocusListener(new FocusAdapter()
390    {
 
391  0 toggle @Override
392    public void focusLost(FocusEvent e)
393    {
394  0 valueField_actionPerformed();
395  0 valueChanged(slider.getValue());
396    }
397    });
398   
399  0 label.setFont(new java.awt.Font("Verdana", 0, 11));
400  0 label.setText(MessageManager.getString("label.set_this_label_text"));
401  0 jPanel1.setLayout(borderLayout1);
402  0 jPanel2.setLayout(flowLayout1);
403  0 applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
404  0 applyButton.setLabel(MessageManager.getString("action.apply"));
405  0 applyButton.addActionListener(this);
406  0 undoButton.setEnabled(false);
407  0 undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
408  0 undoButton.setLabel(MessageManager.getString("action.undo"));
409  0 undoButton.addActionListener(this);
410  0 allGroupsCheck.setEnabled(false);
411  0 allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
412  0 allGroupsCheck.setLabel(
413    MessageManager.getString("action.apply_threshold_all_groups"));
414  0 allGroupsCheck
415    .setName(MessageManager.getString("action.apply_all_groups"));
416  0 this.setBackground(Color.white);
417  0 this.setForeground(Color.black);
418  0 jPanel2.add(label, null);
419  0 jPanel2.add(applyButton, null);
420  0 jPanel2.add(undoButton, null);
421  0 jPanel2.add(allGroupsCheck);
422  0 jPanel1.add(valueField, java.awt.BorderLayout.EAST);
423  0 jPanel1.add(slider, java.awt.BorderLayout.CENTER);
424  0 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
425  0 this.add(jPanel2, java.awt.BorderLayout.CENTER);
426    }
427   
 
428  0 toggle protected void applyButton_actionPerformed()
429    {
430    }
431   
 
432  0 toggle protected void undoButton_actionPerformed()
433    {
434    }
435   
 
436  0 toggle @Override
437    public void mousePressed(MouseEvent evt)
438    {
439    }
440   
 
441  0 toggle @Override
442    public void mouseReleased(MouseEvent evt)
443    {
444  0 ap.paintAlignment(true, true);
445    }
446   
 
447  0 toggle @Override
448    public void mouseClicked(MouseEvent evt)
449    {
450    }
451   
 
452  0 toggle @Override
453    public void mouseEntered(MouseEvent evt)
454    {
455    }
456   
 
457  0 toggle @Override
458    public void mouseExited(MouseEvent evt)
459    {
460    }
461    }
  • Report generated by OpenClover v 4.4.1 on Mon Dec 1 2025 15:44:56 GMT using coverage data from Mon Dec 1 2025 15:44:42 GMT.
  • OpenClover is free and open-source software.