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Coverage Report

  1. Project Clover database Mon Dec 1 2025 13:17:41 GMT
  2. Package jalview.appletgui

File AnnotationColourChooser.java

 

Coverage histogram

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

Code metrics

68
222
18
1
604
470
62
0.28
12.33
18
3.44

Classes

Class Line # Actions
AnnotationColourChooser 53 222 62
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.datamodel.AlignmentAnnotation;
24    import jalview.datamodel.SequenceGroup;
25    import jalview.schemes.AnnotationColourGradient;
26    import jalview.schemes.ColourSchemeI;
27    import jalview.util.MessageManager;
28   
29    import java.awt.BorderLayout;
30    import java.awt.Button;
31    import java.awt.Checkbox;
32    import java.awt.Choice;
33    import java.awt.Color;
34    import java.awt.Dimension;
35    import java.awt.FlowLayout;
36    import java.awt.Font;
37    import java.awt.Frame;
38    import java.awt.Panel;
39    import java.awt.Scrollbar;
40    import java.awt.TextField;
41    import java.awt.event.ActionEvent;
42    import java.awt.event.ActionListener;
43    import java.awt.event.AdjustmentEvent;
44    import java.awt.event.AdjustmentListener;
45    import java.awt.event.ItemEvent;
46    import java.awt.event.ItemListener;
47    import java.awt.event.MouseEvent;
48    import java.awt.event.MouseListener;
49    import java.util.HashMap;
50    import java.util.Map;
51    import java.util.Vector;
52   
 
53    public class AnnotationColourChooser extends Panel implements
54    ActionListener, AdjustmentListener, ItemListener, MouseListener
55    {
56    Frame frame;
57   
58    AlignViewport av;
59   
60    AlignmentPanel ap;
61   
62    ColourSchemeI oldcs;
63   
64    Map<SequenceGroup, ColourSchemeI> oldgroupColours;
65   
66    /*
67    * map from annotation to its menu item display label
68    * - so we know which item to pre-select on restore
69    */
70    private Map<AlignmentAnnotation, String> annotationLabels;
71   
72    AlignmentAnnotation currentAnnotation;
73   
74    boolean adjusting = false;
75   
 
76  0 toggle public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
77    {
78  0 try
79    {
80  0 jbInit();
81    } catch (Exception ex)
82    {
83    }
84   
85  0 oldcs = av.getGlobalColourScheme();
86  0 if (av.getAlignment().getGroups() != null)
87    {
88  0 oldgroupColours = new HashMap<>();
89  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
90    {
91  0 oldgroupColours.put(sg, sg.getColourScheme());
92    }
93    }
94  0 this.av = av;
95  0 this.ap = ap;
96   
97  0 slider.addAdjustmentListener(this);
98  0 slider.addMouseListener(this);
99   
100  0 AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
101  0 if (anns == null)
102    {
103  0 return;
104    }
105   
106  0 setDefaultMinMax();
107   
108  0 adjusting = true;
109  0 if (oldcs instanceof AnnotationColourGradient)
110    {
111  0 AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
112  0 currentColours.setState(
113    acg.isPredefinedColours() || acg.getBaseColour() != null);
114  0 if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
115    {
116  0 minColour.setBackground(acg.getMinColour());
117  0 maxColour.setBackground(acg.getMaxColour());
118    }
119    // seqAssociated.setState(acg.isSeqAssociated());
120    }
121   
122  0 Vector<String> list = getAnnotationItems();
123   
124  0 for (int i = 0; i < list.size(); i++)
125    {
126  0 annotations.addItem(list.elementAt(i).toString());
127    }
128   
129  0 threshold.addItem(MessageManager
130    .getString("label.threshold_feature_no_threshold"));
131  0 threshold.addItem(MessageManager
132    .getString("label.threshold_feature_above_threshold"));
133  0 threshold.addItem(MessageManager
134    .getString("label.threshold_feature_below_threshold"));
135   
136  0 if (oldcs instanceof AnnotationColourGradient)
137    {
138  0 AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
139  0 String label = annotationLabels.get(acg.getAnnotation());
140  0 annotations.select(label);
141  0 switch (acg.getAboveThreshold())
142    {
143  0 case AnnotationColourGradient.NO_THRESHOLD:
144  0 threshold.select(0);
145  0 break;
146  0 case AnnotationColourGradient.ABOVE_THRESHOLD:
147  0 threshold.select(1);
148  0 break;
149  0 case AnnotationColourGradient.BELOW_THRESHOLD:
150  0 threshold.select(1);
151  0 break;
152  0 default:
153  0 throw new Error(MessageManager.getString(
154    "error.implementation_error_dont_know_threshold_annotationcolourgradient"));
155    }
156  0 thresholdIsMin.setState(acg.isThresholdIsMinMax());
157  0 thresholdValue.setText("" + acg.getAnnotationThreshold());
158    }
159   
160  0 adjusting = false;
161   
162  0 changeColour();
163   
164  0 frame = new Frame();
165  0 frame.add(this);
166  0 jalview.bin.JalviewLite.addFrame(frame,
167    MessageManager.getString("label.colour_by_annotation"), 560,
168    175);
169  0 validate();
170    }
171   
172    /**
173    * Builds and returns a list of menu items (display text) for choice of
174    * annotation. Also builds a map between annotations and their display labels.
175    *
176    * @return
177    */
 
178  0 toggle protected Vector<String> getAnnotationItems()
179    {
180    // TODO remove duplication with gui.AnnotationRowFilter
181    // TODO add 'per sequence only' option / parameter
182   
183  0 annotationLabels = new HashMap<>();
184  0 Vector<String> list = new Vector<>();
185  0 AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
186  0 if (anns == null)
187    {
188  0 return list;
189    }
190  0 int index = 1;
191  0 for (int i = 0; i < anns.length; i++)
192    {
193  0 String label = anns[i].label;
194  0 if (anns[i].sequenceRef != null)
195    {
196    /*
197    * be helpful and include sequence id in label for
198    * sequence-associated annotation (JAL-2236)
199    */
200  0 label = label + "_" + anns[i].sequenceRef.getName();
201    }
202  0 if (!list.contains(label))
203    {
204  0 list.addElement(label);
205  0 annotationLabels.put(anns[i], label);
206    }
207    else
208    {
209  0 label = label + "_" + (index++);
210  0 list.addElement(label);
211  0 annotationLabels.put(anns[i], label);
212    }
213    }
214  0 return list;
215    }
216   
 
217  0 toggle private void setDefaultMinMax()
218    {
219  0 minColour.setBackground(av.applet.getDefaultColourParameter(
220    "ANNOTATIONCOLOUR_MIN", Color.orange));
221  0 maxColour.setBackground(av.applet
222    .getDefaultColourParameter("ANNOTATIONCOLOUR_MAX", Color.red));
223   
224    }
225   
 
226  0 toggle public AnnotationColourChooser()
227    {
228  0 try
229    {
230  0 jbInit();
231    } catch (Exception ex)
232    {
233  0 ex.printStackTrace();
234    }
235    }
236   
 
237  0 toggle private void jbInit() throws Exception
238    {
239  0 minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
240  0 minColour.setLabel(MessageManager.getString("label.min_colour"));
241  0 minColour.addActionListener(this);
242   
243  0 maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
244  0 maxColour.setLabel(MessageManager.getString("label.max_colour"));
245  0 maxColour.addActionListener(this);
246   
247  0 thresholdIsMin.addItemListener(this);
248  0 ok.setLabel(MessageManager.getString("action.ok"));
249  0 ok.addActionListener(this);
250   
251  0 cancel.setLabel(MessageManager.getString("action.cancel"));
252  0 cancel.addActionListener(this);
253   
254  0 defColours.setLabel(MessageManager.getString("action.set_defaults"));
255  0 defColours.addActionListener(this);
256   
257  0 annotations.addItemListener(this);
258   
259  0 thresholdValue.addActionListener(this);
260  0 slider.setBackground(Color.white);
261  0 slider.setPreferredSize(new Dimension(193, 21));
262  0 slider.setEnabled(false);
263  0 thresholdValue.setPreferredSize(new Dimension(79, 22));
264  0 thresholdValue.setEnabled(false);
265  0 thresholdValue.setColumns(5);
266  0 currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
267  0 currentColours.setLabel(
268    MessageManager.getString("label.use_original_colours"));
269  0 currentColours.addItemListener(this);
270   
271  0 thresholdIsMin.setBackground(Color.white);
272  0 thresholdIsMin
273    .setLabel(MessageManager.getString("label.threshold_minmax"));
274   
275  0 this.setLayout(borderLayout1);
276   
277  0 jPanel1.setBackground(Color.white);
278   
279  0 jPanel2.setLayout(new FlowLayout());
280  0 jPanel2.setBackground(Color.white);
281  0 threshold.addItemListener(this);
282  0 jPanel3.setLayout(new FlowLayout());
283  0 jPanel3.setBackground(Color.white);
284  0 Panel jPanel4 = new Panel();
285  0 jPanel4.setLayout(new BorderLayout());
286  0 jPanel4.setBackground(Color.white);
287   
288  0 jPanel1.add(ok);
289  0 jPanel1.add(cancel);
290   
291  0 jPanel2.add(annotations);
292  0 jPanel2.add(currentColours);
293  0 jPanel2.add(minColour);
294  0 jPanel2.add(maxColour);
295   
296  0 jPanel4.add(thresholdIsMin, BorderLayout.WEST);
297  0 jPanel4.add(slider, BorderLayout.CENTER);
298  0 jPanel4.add(thresholdValue, BorderLayout.EAST);
299   
300  0 Panel jPanel34 = new Panel();
301  0 jPanel34.setLayout(new BorderLayout());
302  0 jPanel34.setBackground(Color.white);
303  0 jPanel34.add(jPanel2, BorderLayout.NORTH);
304  0 jPanel34.add(threshold, BorderLayout.WEST);
305  0 jPanel3.add(defColours);
306  0 jPanel34.add(jPanel3, BorderLayout.EAST);
307  0 jPanel34.add(jPanel4, BorderLayout.SOUTH);
308   
309  0 this.add(jPanel34, java.awt.BorderLayout.CENTER);
310  0 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
311   
312    }
313   
314    Choice annotations = new Choice();
315   
316    Button minColour = new Button();
317   
318    Button maxColour = new Button();
319   
320    Button ok = new Button();
321   
322    Button cancel = new Button();
323   
324    Button defColours = new Button();
325   
326    Panel jPanel1 = new Panel();
327   
328    Panel jPanel2 = new Panel();
329   
330    Choice threshold = new Choice();
331   
332    FlowLayout flowLayout1 = new FlowLayout();
333   
334    Panel jPanel3 = new Panel();
335   
336    Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
337   
338    TextField thresholdValue = new TextField(20);
339   
340    Checkbox currentColours = new Checkbox();
341   
342    BorderLayout borderLayout1 = new BorderLayout();
343   
344    Checkbox thresholdIsMin = new Checkbox();
345   
 
346  0 toggle @Override
347    public void actionPerformed(ActionEvent evt)
348    {
349  0 if (evt.getSource() == thresholdValue)
350    {
351  0 try
352    {
353  0 float f = Float.valueOf(thresholdValue.getText()).floatValue();
354  0 slider.setValue((int) (f * 1000));
355  0 adjustmentValueChanged(null);
356    } catch (NumberFormatException ex)
357    {
358    }
359    }
360  0 else if (evt.getSource() == minColour)
361    {
362  0 minColour_actionPerformed(null);
363    }
364  0 else if (evt.getSource() == maxColour)
365    {
366  0 maxColour_actionPerformed(null);
367    }
368  0 else if (evt.getSource() == defColours)
369    {
370  0 defColour_actionPerformed();
371    }
372  0 else if (evt.getSource() == ok)
373    {
374  0 frame.setVisible(false);
375    }
376  0 else if (evt.getSource() == cancel)
377    {
378  0 reset();
379  0 ap.paintAlignment(true, true);
380  0 frame.setVisible(false);
381    }
382   
383    else
384    {
385  0 changeColour();
386    }
387    }
388   
 
389  0 toggle @Override
390    public void itemStateChanged(ItemEvent evt)
391    {
392  0 if (evt.getSource() == currentColours)
393    {
394  0 if (currentColours.getState())
395    {
396  0 reset();
397    }
398   
399  0 maxColour.setEnabled(!currentColours.getState());
400  0 minColour.setEnabled(!currentColours.getState());
401   
402    }
403   
404  0 changeColour();
405    }
406   
 
407  0 toggle @Override
408    public void adjustmentValueChanged(AdjustmentEvent evt)
409    {
410  0 if (!adjusting)
411    {
412  0 thresholdValue.setText((slider.getValue() / 1000f) + "");
413  0 if (currentColours.getState() && !(av
414    .getGlobalColourScheme() instanceof AnnotationColourGradient))
415    {
416  0 changeColour();
417    }
418   
419  0 currentAnnotation.threshold.value = slider.getValue() / 1000f;
420  0 ap.paintAlignment(false, false);
421    }
422    }
423   
 
424  0 toggle public void minColour_actionPerformed(Color newCol)
425    {
426  0 if (newCol != null)
427    {
428  0 minColour.setBackground(newCol);
429  0 minColour.repaint();
430  0 changeColour();
431    }
432    else
433    {
434  0 new UserDefinedColours(this, "Min Colour", minColour.getBackground());
435    }
436   
437    }
438   
 
439  0 toggle public void maxColour_actionPerformed(Color newCol)
440    {
441  0 if (newCol != null)
442    {
443  0 maxColour.setBackground(newCol);
444  0 maxColour.repaint();
445  0 changeColour();
446    }
447    else
448    {
449  0 new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
450    }
451    }
452   
 
453  0 toggle public void defColour_actionPerformed()
454    {
455  0 setDefaultMinMax();
456  0 minColour.repaint();
457  0 maxColour.repaint();
458  0 changeColour();
459    }
460   
 
461  0 toggle void changeColour()
462    {
463    // Check if combobox is still adjusting
464  0 if (adjusting)
465    {
466  0 return;
467    }
468   
469  0 currentAnnotation = av.getAlignment()
470    .getAlignmentAnnotation()[annotations.getSelectedIndex()];
471   
472  0 int aboveThreshold = -1;
473  0 if (threshold.getSelectedIndex() == 1)
474    {
475  0 aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
476    }
477  0 else if (threshold.getSelectedIndex() == 2)
478    {
479  0 aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
480    }
481   
482  0 slider.setEnabled(true);
483  0 thresholdValue.setEnabled(true);
484  0 thresholdIsMin.setEnabled(true);
485   
486  0 if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
487    {
488  0 slider.setEnabled(false);
489  0 thresholdValue.setEnabled(false);
490  0 thresholdIsMin.setEnabled(false);
491  0 thresholdValue.setText("");
492    }
493  0 else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
494    && currentAnnotation.threshold == null)
495    {
496  0 currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
497    (currentAnnotation.graphMax - currentAnnotation.graphMin)
498    / 2f,
499    "Threshold", Color.black));
500    }
501   
502  0 if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
503    {
504  0 adjusting = true;
505   
506  0 slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
507  0 slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
508  0 slider.setValue((int) (currentAnnotation.threshold.value * 1000));
509  0 thresholdValue.setText(currentAnnotation.threshold.value + "");
510  0 slider.setEnabled(true);
511  0 thresholdValue.setEnabled(true);
512  0 adjusting = false;
513    }
514   
515  0 AnnotationColourGradient acg = null;
516  0 if (currentColours.getState())
517    {
518    }
519    else
520    {
521  0 acg = new AnnotationColourGradient(currentAnnotation,
522    minColour.getBackground(), maxColour.getBackground(),
523    aboveThreshold);
524    }
525   
526  0 if (currentAnnotation.graphMin == 0f
527    && currentAnnotation.graphMax == 0f)
528    {
529  0 acg.setPredefinedColours(true);
530    }
531   
532  0 acg.setThresholdIsMinMax(thresholdIsMin.getState());
533   
534  0 av.setGlobalColourScheme(acg);
535   
536    // TODO: per group colour propagation not always desired
537  0 if (av.getAlignment().getGroups() != null)
538    {
539  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
540    {
541  0 if (sg.getColourScheme() == null)
542    {
543  0 continue;
544    }
545   
546  0 if (currentColours.getState())
547    {
548  0 sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
549    sg.getColourScheme(), aboveThreshold));
550    }
551    else
552    {
553  0 sg.setColourScheme(new AnnotationColourGradient(currentAnnotation,
554    minColour.getBackground(), maxColour.getBackground(),
555    aboveThreshold));
556    }
557    }
558    }
559   
560    // update colours in linked windows
561  0 ap.alignmentChanged();
562  0 ap.paintAlignment(true, true);
563    }
564   
 
565  0 toggle void reset()
566    {
567  0 av.setGlobalColourScheme(oldcs);
568  0 if (av.getAlignment().getGroups() != null)
569    {
570  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
571    {
572  0 sg.setColourScheme(oldgroupColours.get(sg));
573    }
574    }
575  0 ap.paintAlignment(true, true);
576    }
577   
 
578  0 toggle @Override
579    public void mouseClicked(MouseEvent evt)
580    {
581    }
582   
 
583  0 toggle @Override
584    public void mousePressed(MouseEvent evt)
585    {
586    }
587   
 
588  0 toggle @Override
589    public void mouseReleased(MouseEvent evt)
590    {
591  0 ap.paintAlignment(true, true);
592    }
593   
 
594  0 toggle @Override
595    public void mouseEntered(MouseEvent evt)
596    {
597    }
598   
 
599  0 toggle @Override
600    public void mouseExited(MouseEvent evt)
601    {
602    }
603   
604    }
  • Report generated by OpenClover v 4.4.1 on Mon Dec 1 2025 13:27:33 GMT using coverage data from Mon Dec 1 2025 13:27:18 GMT.
  • OpenClover is free and open-source software.