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Coverage Report

  1. Project Clover database Thu Nov 27 2025 16:51:35 GMT
  2. Package jalview.gui

File AnnotationColourChooser.java

 

Coverage histogram

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

Code metrics

52
195
21
1
513
422
57
0.29
9.29
21
2.71

Classes

Class Line # Actions
AnnotationColourChooser 54 195 57
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.gui;
22   
23    import java.awt.BorderLayout;
24    import java.awt.Color;
25    import java.awt.Dimension;
26    import java.awt.FlowLayout;
27    import java.awt.event.ActionEvent;
28    import java.awt.event.ActionListener;
29    import java.awt.event.MouseAdapter;
30    import java.awt.event.MouseEvent;
31    import java.util.Hashtable;
32    import java.util.Vector;
33   
34    import javax.swing.BorderFactory;
35    import javax.swing.JButton;
36    import javax.swing.JCheckBox;
37    import javax.swing.JComboBox;
38    import javax.swing.JInternalFrame;
39    import javax.swing.JLayeredPane;
40    import javax.swing.JPanel;
41   
42    import jalview.bin.Cache;
43    import jalview.datamodel.AlignmentAnnotation;
44    import jalview.datamodel.Annotation;
45    import jalview.datamodel.GraphLine;
46    import jalview.datamodel.SequenceGroup;
47    import jalview.gui.JalviewColourChooser.ColourChooserListener;
48    import jalview.schemes.AnnotationColourGradient;
49    import jalview.schemes.ColourSchemeI;
50    import jalview.util.MessageManager;
51    import net.miginfocom.swing.MigLayout;
52   
53    @SuppressWarnings("serial")
 
54    public class AnnotationColourChooser extends AnnotationRowFilter
55    {
56    private ColourSchemeI oldcs;
57   
58    private JButton defColours;
59   
60    private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
61   
62    private JCheckBox useOriginalColours = new JCheckBox();
63   
64    JPanel minColour = new JPanel();
65   
66    JPanel maxColour = new JPanel();
67   
68    private JCheckBox thresholdIsMin = new JCheckBox();
69   
70    protected static final int MIN_WIDTH = 500;
71   
72    protected static final int MIN_HEIGHT = 240;
73   
 
74  0 toggle public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
75    {
76  0 this(av, ap, null);
77    }
78   
 
79  0 toggle public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,
80    AnnotationColourGradient initSettings)
81    {
82  0 super(av, ap);
83  0 oldcs = av.getGlobalColourScheme();
84  0 if (av.getAlignment().getGroups() != null)
85    {
86  0 oldgroupColours = new Hashtable<>();
87  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
88    {
89  0 if (sg.getColourScheme() != null)
90    {
91  0 oldgroupColours.put(sg, sg.getColourScheme());
92    }
93    }
94    }
95  0 frame = new JInternalFrame();
96  0 frame.setFrameIcon(null);
97  0 frame.setContentPane(this);
98  0 frame.setLayer(JLayeredPane.PALETTE_LAYER);
99  0 Desktop.addInternalFrame(frame,
100    MessageManager.getString("label.colour_by_annotation"), 520,
101    215);
102  0 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
103  0 addSliderChangeListener();
104  0 addSliderMouseListeners();
105   
106  0 if (av.getAlignment().getAlignmentAnnotation() == null)
107    {
108  0 return;
109    }
110   
111    // Always get default shading from preferences.
112  0 setDefaultMinMax();
113   
114  0 adjusting = true;
115  0 if (oldcs instanceof AnnotationColourGradient && initSettings == null)
116    {
117    // init from oldcs
118  0 initialiseFrom((AnnotationColourGradient) oldcs);
119    }
120    else
121    {
122    // use initial colour gradient - if any..
123  0 initialiseFrom(initSettings);
124    }
125   
126  0 jbInit();
127  0 adjusting = false;
128   
129  0 updateView();
130  0 frame.invalidate();
131  0 frame.pack();
132    }
133   
 
134  0 toggle private void initialiseFrom(AnnotationColourGradient acg)
135    {
136  0 if (acg != null)
137    {
138  0 useOriginalColours.setSelected(
139    acg.isPredefinedColours() || acg.getBaseColour() != null);
140  0 if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
141    {
142  0 minColour.setBackground(acg.getMinColour());
143  0 maxColour.setBackground(acg.getMaxColour());
144    }
145  0 seqAssociated.setSelected(acg.isSeqAssociated());
146   
147    }
148  0 Vector<String> annotItems = getAnnotationItems(
149    seqAssociated.isSelected());
150  0 annotations = new JComboBox<>(annotItems);
151   
152  0 populateThresholdComboBox(threshold);
153   
154  0 if (acg != null)
155    {
156  0 String label = getAnnotationMenuLabel(acg.getAnnotation());
157    // TODO: workaround below shouldn't be necessary - there's a bug in
158    // getAnnotationMenuLabel!
159  0 if (acg.isSeqAssociated())
160    {
161  0 label = acg.getAnnotation().label;
162    }
163  0 annotations.setSelectedItem(label);
164  0 switch (acg.getAboveThreshold())
165    {
166  0 case AnnotationColourGradient.NO_THRESHOLD:
167  0 getThreshold().setSelectedIndex(0);
168  0 break;
169  0 case AnnotationColourGradient.ABOVE_THRESHOLD:
170  0 getThreshold().setSelectedIndex(1);
171  0 break;
172  0 case AnnotationColourGradient.BELOW_THRESHOLD:
173  0 getThreshold().setSelectedIndex(2);
174  0 break;
175  0 default:
176  0 throw new Error(MessageManager.getString(
177    "error.implementation_error_dont_know_about_threshold_setting"));
178    }
179  0 thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
180  0 thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
181    }
182    }
183   
 
184  0 toggle @Override
185    protected void jbInit()
186    {
187  0 super.jbInit();
188   
189  0 minColour.setFont(JvSwingUtils.getLabelFont());
190  0 minColour.setBorder(BorderFactory.createEtchedBorder());
191  0 minColour.setPreferredSize(new Dimension(40, 20));
192  0 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
193  0 minColour.addMouseListener(new MouseAdapter()
194    {
 
195  0 toggle @Override
196    public void mousePressed(MouseEvent e)
197    {
198  0 if (minColour.isEnabled())
199    {
200  0 showColourChooser(minColour, "label.select_colour_minimum_value");
201    }
202    }
203    });
204  0 maxColour.setFont(JvSwingUtils.getLabelFont());
205  0 maxColour.setBorder(BorderFactory.createEtchedBorder());
206  0 maxColour.setPreferredSize(new Dimension(40, 20));
207  0 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
208  0 maxColour.addMouseListener(new MouseAdapter()
209    {
 
210  0 toggle @Override
211    public void mousePressed(MouseEvent e)
212    {
213  0 if (maxColour.isEnabled())
214    {
215  0 showColourChooser(maxColour, "label.select_colour_maximum_value");
216    }
217    }
218    });
219   
220  0 defColours = new JButton();
221  0 defColours.setOpaque(false);
222  0 defColours.setText(MessageManager.getString("action.set_defaults"));
223  0 defColours.setToolTipText(MessageManager
224    .getString("label.reset_min_max_colours_to_defaults"));
225  0 defColours.addActionListener(new ActionListener()
226    {
227   
 
228  0 toggle @Override
229    public void actionPerformed(ActionEvent arg0)
230    {
231  0 resetColours_actionPerformed();
232    }
233    });
234   
235  0 useOriginalColours.setFont(JvSwingUtils.getLabelFont());
236  0 useOriginalColours.setOpaque(false);
237  0 useOriginalColours.setText(
238    MessageManager.getString("label.use_original_colours"));
239  0 useOriginalColours.addActionListener(new ActionListener()
240    {
 
241  0 toggle @Override
242    public void actionPerformed(ActionEvent e)
243    {
244  0 originalColours_actionPerformed();
245    }
246    });
247  0 thresholdIsMin.setBackground(Color.white);
248  0 thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
249  0 thresholdIsMin
250    .setText(MessageManager.getString("label.threshold_minmax"));
251  0 thresholdIsMin.addActionListener(new ActionListener()
252    {
 
253  0 toggle @Override
254    public void actionPerformed(ActionEvent actionEvent)
255    {
256  0 thresholdIsMin_actionPerformed();
257    }
258    });
259  0 seqAssociated.setBackground(Color.white);
260  0 seqAssociated.setFont(JvSwingUtils.getLabelFont());
261  0 seqAssociated
262    .setText(MessageManager.getString("label.per_sequence_only"));
263  0 seqAssociated.addActionListener(new ActionListener()
264    {
265   
 
266  0 toggle @Override
267    public void actionPerformed(ActionEvent arg0)
268    {
269  0 seqAssociated_actionPerformed(annotations);
270    }
271    });
272   
273  0 this.setLayout(new BorderLayout());
274  0 JPanel jPanel1 = new JPanel();
275  0 JPanel jPanel2 = new JPanel();
276  0 jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
277  0 jPanel1.setBackground(Color.white);
278  0 jPanel2.setBackground(Color.white);
279   
280  0 jPanel1.add(ok);
281  0 jPanel1.add(cancel);
282  0 jPanel2.add(annotations, "grow, wrap");
283  0 jPanel2.add(seqAssociated);
284  0 jPanel2.add(useOriginalColours);
285  0 JPanel colpanel = new JPanel(new FlowLayout());
286  0 colpanel.setBackground(Color.white);
287  0 colpanel.add(minColour);
288  0 colpanel.add(maxColour);
289  0 jPanel2.add(colpanel, "wrap");
290  0 jPanel2.add(getThreshold());
291  0 jPanel2.add(defColours, "skip 1, wrap");
292  0 jPanel2.add(thresholdIsMin);
293  0 jPanel2.add(slider, "grow");
294  0 jPanel2.add(thresholdValue, "grow");
295  0 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
296  0 this.add(jPanel2, java.awt.BorderLayout.CENTER);
297  0 this.validate();
298    }
299   
 
300  0 toggle protected void resetColours_actionPerformed()
301    {
302  0 setDefaultMinMax();
303  0 updateView();
304    }
305   
 
306  0 toggle private void setDefaultMinMax()
307    {
308  0 minColour.setBackground(
309    Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
310  0 maxColour.setBackground(
311    Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
312    }
313   
 
314  0 toggle protected void showColourChooser(JPanel colourPanel, String titleKey)
315    {
316  0 String ttl = MessageManager.getString(titleKey);
317  0 ColourChooserListener listener = new ColourChooserListener()
318    {
 
319  0 toggle @Override
320    public void colourSelected(Color c)
321    {
322  0 colourPanel.setBackground(c);
323  0 colourPanel.repaint();
324  0 updateView();
325    }
326    };
327  0 JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
328    colourPanel.getBackground(), listener);
329    }
330   
 
331  0 toggle @Override
332    public void reset()
333    {
334  0 this.ap.alignFrame.changeColour(oldcs);
335  0 if (av.getAlignment().getGroups() != null)
336    {
337   
338  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
339    {
340  0 sg.setColourScheme(oldgroupColours.get(sg));
341    }
342    }
343    }
344   
 
345  0 toggle @Override
346    public void valueChanged(boolean updateAllAnnotation)
347    {
348  0 if (slider.isEnabled())
349    {
350  0 if (useOriginalColours.isSelected() && !(av
351    .getGlobalColourScheme() instanceof AnnotationColourGradient))
352    {
353  0 updateView();
354    }
355  0 getCurrentAnnotation().threshold.value = getSliderValue();
356  0 propagateSeqAssociatedThreshold(updateAllAnnotation,
357    getCurrentAnnotation());
358  0 ap.paintAlignment(false, false);
359    }
360    }
361   
 
362  0 toggle public void originalColours_actionPerformed()
363    {
364  0 boolean selected = useOriginalColours.isSelected();
365  0 if (selected)
366    {
367  0 reset();
368    }
369  0 maxColour.setEnabled(!selected);
370  0 minColour.setEnabled(!selected);
371  0 thresholdIsMin.setEnabled(!selected);
372  0 updateView();
373    }
374   
 
375  0 toggle @Override
376    public void updateView()
377    {
378    // Check if combobox is still adjusting
379  0 if (adjusting)
380    {
381  0 return;
382    }
383   
384  0 int selIndex = annotations.getSelectedIndex();
385  0 int annIndex = annmap[selIndex];
386  0 setCurrentAnnotation(
387    av.getAlignment().getAlignmentAnnotation()[annIndex]);
388   
389  0 int selectedThresholdItem = getSelectedThresholdItem(
390    getThreshold().getSelectedIndex());
391   
392  0 slider.setEnabled(true);
393  0 thresholdValue.setEnabled(true);
394  0 thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
395   
396  0 final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
397  0 if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
398    {
399  0 slider.setEnabled(false);
400  0 thresholdValue.setEnabled(false);
401  0 thresholdValue.setText("");
402  0 thresholdIsMin.setEnabled(false);
403    }
404  0 else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
405    && currentAnnotation.threshold == null)
406    {
407  0 currentAnnotation.setThreshold(new GraphLine(
408    (currentAnnotation.graphMax - currentAnnotation.graphMin)
409    / 2f,
410    "Threshold", Color.black));
411    }
412   
413  0 if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
414    {
415  0 adjusting = true;
416  0 setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
417    currentAnnotation.threshold.value);
418  0 slider.setEnabled(true);
419   
420  0 setThresholdValueText();
421  0 thresholdValue.setEnabled(true);
422  0 adjusting = false;
423    }
424  0 colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
425   
426  0 ap.alignmentChanged();
427    }
428   
 
429  0 toggle protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
430    int selectedThresholdOption)
431    {
432   
433  0 AnnotationColourGradient acg = null;
434  0 if (useOriginalColours.isSelected())
435    {
436  0 acg = new AnnotationColourGradient(currentAnn,
437    av.getGlobalColourScheme(), selectedThresholdOption);
438    }
439    else
440    {
441  0 acg = new AnnotationColourGradient(currentAnn,
442    minColour.getBackground(), maxColour.getBackground(),
443    selectedThresholdOption);
444    }
445  0 acg.setSeqAssociated(seqAssociated.isSelected());
446   
447  0 if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
448    {
449  0 acg.setPredefinedColours(true);
450    }
451   
452  0 acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
453   
454  0 this.ap.alignFrame.changeColour(acg);
455   
456  0 if (av.getAlignment().getGroups() != null)
457    {
458   
459  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
460    {
461  0 if (sg.cs == null)
462    {
463  0 continue;
464    }
465  0 sg.setColourScheme(acg.getInstance(av, sg));
466    }
467    }
468    }
469   
 
470  0 toggle @Override
471    protected void sliderDragReleased()
472    {
473  0 super.sliderDragReleased();
474  0 ap.paintAlignment(true, true);
475    }
476   
477    /**
478    * construct and display a colourchooser for a given annotation row
479    *
480    * @param av
481    * @param ap
482    * @param alignmentAnnotation
483    * @param perseq
484    * - when true, enable per-sequence if alignment annotation is per
485    * sequence
486    */
 
487  0 toggle public static void displayFor(AlignViewport av, AlignmentPanel ap,
488    AlignmentAnnotation alignmentAnnotation, boolean perSeq)
489    {
490  0 ColourSchemeI global = av.getGlobalColourScheme();
491  0 AnnotationColourGradient newCS = new AnnotationColourGradient(
492    alignmentAnnotation, global,
493  0 alignmentAnnotation.threshold != null
494    ? AnnotationColourGradient.ABOVE_THRESHOLD
495    : AnnotationColourGradient.NO_THRESHOLD);
496  0 if (alignmentAnnotation.sequenceRef != null)
497    {
498  0 newCS.setSeqAssociated(perSeq);
499    }
500  0 for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
501    {
502  0 Annotation ann = alignmentAnnotation.annotations[i];
503  0 if (ann != null && ann.colour != null
504    && !ann.colour.equals(Color.white))
505    {
506  0 newCS.setPredefinedColours(true);
507  0 break;
508    }
509    }
510  0 AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
511    newCS);
512    }
513    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:01:26 GMT using coverage data from Thu Nov 27 2025 17:01:12 GMT.
  • OpenClover is free and open-source software.