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Coverage Report

  1. Project Clover database Wed Nov 12 2025 13:01:44 GMT
  2. Package jalview.appletgui

File FeatureColourChooser.java

 

Coverage histogram

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

Code metrics

42
178
20
1
515
393
45
0.25
8.9
20
2.25

Classes

Class Line # Actions
FeatureColourChooser 52 178 45
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.api.FeatureColourI;
24    import jalview.datamodel.GraphLine;
25    import jalview.schemes.AnnotationColourGradient;
26    import jalview.schemes.FeatureColour;
27    import jalview.util.MessageManager;
28   
29    import java.awt.Checkbox;
30    import java.awt.Choice;
31    import java.awt.Color;
32    import java.awt.Dimension;
33    import java.awt.FlowLayout;
34    import java.awt.Font;
35    import java.awt.Frame;
36    import java.awt.GridLayout;
37    import java.awt.Label;
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.FocusAdapter;
46    import java.awt.event.FocusEvent;
47    import java.awt.event.ItemEvent;
48    import java.awt.event.ItemListener;
49    import java.awt.event.MouseEvent;
50    import java.awt.event.MouseListener;
51   
 
52    public class FeatureColourChooser extends Panel implements ActionListener,
53    AdjustmentListener, ItemListener, MouseListener
54    {
55    /*
56    * the absolute min-max range of a feature score is scaled to
57    * 1000 positions on the colour threshold slider
58    */
59    private static final int SCALE_FACTOR_1K = 1000;
60   
61    private static final String COLON = ":";
62   
63    private JVDialog frame;
64   
65    private Frame owner;
66   
67    private FeatureRenderer fr;
68   
69    private FeatureSettings fs = null;
70   
71    private FeatureColourI cs;
72   
73    private FeatureColourI oldcs;
74   
75    private boolean adjusting = false;
76   
77    private float min, max;
78   
79    private String type = null;
80   
81    private AlignFrame af = null;
82   
83    private Panel minColour = new Panel();
84   
85    private Panel maxColour = new Panel();
86   
87    private Choice threshold = new Choice();
88   
89    private Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
90   
91    private TextField thresholdValue = new TextField(20);
92   
93    private Checkbox thresholdIsMin = new Checkbox();
94   
95    private Checkbox colourFromLabel = new Checkbox();
96   
97    private GraphLine threshline;
98   
99    /**
100    * Constructor given a context AlignFrame and a feature type. This is used
101    * when opening the graduated colour dialog from the Amend Feature dialog.
102    *
103    * @param alignFrame
104    * @param featureType
105    */
 
106  0 toggle public FeatureColourChooser(AlignFrame alignFrame, String featureType)
107    {
108  0 this.af = alignFrame;
109  0 init(alignFrame.getSeqcanvas().getFeatureRenderer(), featureType);
110    }
111   
112    /**
113    * Constructor given a context FeatureSettings and a feature type. This is
114    * used when opening the graduated colour dialog from Feature Settings.
115    *
116    * @param fsettings
117    * @param featureType
118    */
 
119  0 toggle public FeatureColourChooser(FeatureSettings fsettings, String featureType)
120    {
121  0 this.fs = fsettings;
122  0 init(fsettings.fr, featureType);
123    }
124   
 
125  0 toggle private void init(FeatureRenderer frenderer, String featureType)
126    {
127  0 this.type = featureType;
128  0 fr = frenderer;
129  0 float mm[] = fr.getMinMax().get(type)[0];
130  0 min = mm[0];
131  0 max = mm[1];
132  0 threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
133  0 oldcs = fr.getFeatureColours().get(type);
134  0 if (oldcs.isGraduatedColour())
135    {
136  0 threshline.value = oldcs.getThreshold();
137  0 cs = new FeatureColour(oldcs.getColour(), oldcs.getMinColour(),
138    oldcs.getMaxColour(), oldcs.getNoColour(), min, max);
139    }
140    else
141    {
142    // promote original color to a graduated color
143  0 Color bl = Color.black;
144  0 if (oldcs.isSimpleColour())
145    {
146  0 bl = oldcs.getColour();
147    }
148    // original colour becomes the maximum colour
149  0 cs = new FeatureColour(bl, Color.white, bl, Color.white, mm[0],
150    mm[1]);
151    }
152  0 minColour.setBackground(cs.getMinColour());
153  0 maxColour.setBackground(cs.getMaxColour());
154  0 minColour.setForeground(cs.getMinColour());
155  0 maxColour.setForeground(cs.getMaxColour());
156  0 colourFromLabel.setState(cs.isColourByLabel());
157  0 adjusting = true;
158   
159  0 try
160    {
161  0 jbInit();
162    } catch (Exception ex)
163    {
164    }
165  0 threshold.select(
166  0 cs.isAboveThreshold() ? 1 : (cs.isBelowThreshold() ? 2 : 0));
167   
168  0 adjusting = false;
169  0 changeColour(true);
170  0 colourFromLabel.addItemListener(this);
171  0 slider.addAdjustmentListener(this);
172  0 slider.addMouseListener(this);
173  0 owner = (af != null) ? af : fs.frame;
174  0 frame = new JVDialog(owner, MessageManager
175    .formatMessage("label.variable_color_for", new String[]
176    { type }), true, 480, 248);
177  0 frame.setMainPanel(this);
178  0 validate();
179  0 frame.setVisible(true);
180  0 if (frame.accept)
181    {
182  0 changeColour(true);
183    }
184    else
185    {
186    // cancel
187  0 reset();
188  0 frame.setVisible(false);
189    }
190    }
191   
 
192  0 toggle public FeatureColourChooser()
193    {
194  0 try
195    {
196  0 jbInit();
197    } catch (Exception ex)
198    {
199  0 ex.printStackTrace();
200    }
201    }
202   
 
203  0 toggle private void jbInit() throws Exception
204    {
205  0 Label minLabel = new Label(
206    MessageManager.getString("label.min_value") + COLON);
207  0 Label maxLabel = new Label(
208    MessageManager.getString("label.max_value") + COLON);
209  0 minLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
210  0 maxLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
211    // minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
212    // minColour.setLabel("Min Colour");
213   
214  0 minColour.setBounds(0, 0, 40, 27);
215  0 maxColour.setBounds(0, 0, 40, 27);
216  0 minColour.addMouseListener(this);
217   
218  0 maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
219  0 maxColour.addMouseListener(this);
220   
221  0 thresholdIsMin.addItemListener(this);
222   
223  0 this.setLayout(new GridLayout(4, 1));
224  0 Panel jPanel1 = new Panel();
225  0 jPanel1.setLayout(new FlowLayout());
226  0 Panel jPanel2 = new Panel();
227  0 jPanel2.setLayout(new FlowLayout());
228  0 Panel jPanel3 = new Panel();
229  0 jPanel3.setLayout(new GridLayout(1, 1));
230  0 Panel jPanel4 = new Panel();
231  0 jPanel4.setLayout(new FlowLayout());
232  0 jPanel1.setBackground(Color.white);
233  0 jPanel2.setBackground(Color.white);
234  0 jPanel4.setBackground(Color.white);
235  0 threshold.addItemListener(this);
236  0 threshold.addItem(MessageManager
237    .getString("label.threshold_feature_no_threshold"));
238  0 threshold.addItem(MessageManager
239    .getString("label.threshold_feature_above_threshold"));
240  0 threshold.addItem(MessageManager
241    .getString("label.threshold_feature_below_threshold"));
242  0 thresholdValue.addActionListener(this);
243  0 thresholdValue.addFocusListener(new FocusAdapter()
244    {
 
245  0 toggle @Override
246    public void focusLost(FocusEvent e)
247    {
248  0 thresholdValue_actionPerformed();
249    }
250    });
251  0 slider.setBackground(Color.white);
252  0 slider.setEnabled(false);
253  0 slider.setSize(new Dimension(93, 21));
254  0 thresholdValue.setEnabled(false);
255  0 thresholdValue.setSize(new Dimension(79, 22)); // setBounds(new
256    // Rectangle(248, 2, 79,
257    // 22));
258  0 thresholdValue.setColumns(5);
259  0 jPanel3.setBackground(Color.white);
260   
261  0 colourFromLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
262  0 colourFromLabel
263    .setLabel(MessageManager.getString("label.colour_by_label"));
264  0 colourFromLabel.setSize(new Dimension(139, 22));
265    // threshold.setBounds(new Rectangle(11, 3, 139, 22));
266  0 thresholdIsMin.setBackground(Color.white);
267  0 thresholdIsMin
268    .setLabel(MessageManager.getString("label.threshold_minmax"));
269  0 thresholdIsMin.setSize(new Dimension(135, 23));
270    // thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
271  0 jPanel1.add(minLabel);
272  0 jPanel1.add(minColour);
273  0 jPanel1.add(maxLabel);
274  0 jPanel1.add(maxColour);
275  0 jPanel1.add(colourFromLabel);
276  0 jPanel2.add(threshold);
277  0 jPanel3.add(slider);
278  0 jPanel4.add(thresholdValue);
279  0 jPanel4.add(thresholdIsMin);
280  0 this.add(jPanel1);// , java.awt.BorderLayout.NORTH);
281  0 this.add(jPanel2);// , java.awt.BorderLayout.NORTH);
282  0 this.add(jPanel3);// , java.awt.BorderLayout.CENTER);
283  0 this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
284    }
285   
 
286  0 toggle @Override
287    public void actionPerformed(ActionEvent evt)
288    {
289  0 if (evt.getSource() == thresholdValue)
290    {
291  0 thresholdValue_actionPerformed();
292    }
293  0 else if (evt.getSource() == minColour)
294    {
295  0 minColour_actionPerformed(null);
296    }
297  0 else if (evt.getSource() == maxColour)
298    {
299  0 maxColour_actionPerformed(null);
300    }
301    else
302    {
303  0 changeColour(true);
304    }
305    }
306   
307    /**
308    * Action on input of a value for colour score threshold
309    */
 
310  0 toggle protected void thresholdValue_actionPerformed()
311    {
312  0 try
313    {
314  0 float f = Float.valueOf(thresholdValue.getText()).floatValue();
315  0 slider.setValue((int) (f * SCALE_FACTOR_1K));
316  0 adjustmentValueChanged(null);
317   
318    /*
319    * force repaint of any Overview window or structure
320    */
321  0 changeColour(true);
322    } catch (NumberFormatException ex)
323    {
324    }
325    }
326   
 
327  0 toggle @Override
328    public void itemStateChanged(ItemEvent evt)
329    {
330  0 maxColour.setEnabled(!colourFromLabel.getState());
331  0 minColour.setEnabled(!colourFromLabel.getState());
332  0 changeColour(true);
333    }
334   
335    /**
336    * Handler called when the value of the threshold slider changes, either by
337    * user action or programmatically
338    */
 
339  0 toggle @Override
340    public void adjustmentValueChanged(AdjustmentEvent evt)
341    {
342  0 if (!adjusting)
343    {
344  0 thresholdValue.setText((slider.getValue() / 1000f) + "");
345  0 valueChanged();
346    }
347    }
348   
349    /**
350    * Responds to a change of colour threshold by computing the absolute value
351    * and refreshing the alignment.
352    */
 
353  0 toggle protected void valueChanged()
354    {
355  0 threshline.value = slider.getValue() / 1000f;
356  0 cs.setThreshold(threshline.value);
357  0 changeColour(false);
358  0 PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
359    }
360   
 
361  0 toggle public void minColour_actionPerformed(Color newCol)
362    {
363  0 if (newCol == null)
364    {
365  0 new UserDefinedColours(this, minColour.getBackground(), owner,
366    MessageManager
367    .getString("label.select_colour_minimum_value"));
368    }
369    else
370    {
371  0 minColour.setBackground(newCol);
372  0 minColour.setForeground(newCol);
373  0 minColour.repaint();
374  0 changeColour(true);
375    }
376   
377    }
378   
 
379  0 toggle public void maxColour_actionPerformed(Color newCol)
380    {
381  0 if (newCol == null)
382    {
383  0 new UserDefinedColours(this, maxColour.getBackground(), owner,
384    MessageManager
385    .getString("label.select_colour_maximum_value"));
386    }
387    else
388    {
389  0 maxColour.setBackground(newCol);
390  0 maxColour.setForeground(newCol);
391  0 maxColour.repaint();
392  0 changeColour(true);
393    }
394    }
395   
 
396  0 toggle void changeColour(boolean updateOverview)
397    {
398    // Check if combobox is still adjusting
399  0 if (adjusting)
400    {
401  0 return;
402    }
403   
404  0 int thresholdOption = AnnotationColourGradient.NO_THRESHOLD;
405  0 if (threshold.getSelectedIndex() == 1)
406    {
407  0 thresholdOption = AnnotationColourGradient.ABOVE_THRESHOLD;
408    }
409  0 else if (threshold.getSelectedIndex() == 2)
410    {
411  0 thresholdOption = AnnotationColourGradient.BELOW_THRESHOLD;
412    }
413   
414  0 slider.setEnabled(true);
415  0 thresholdValue.setEnabled(true);
416  0 Color minc = minColour.getBackground();
417  0 Color maxc = maxColour.getBackground();
418  0 FeatureColour acg = new FeatureColour(maxc, minc, maxc, minc, min, max);
419   
420  0 acg.setColourByLabel(colourFromLabel.getState());
421  0 maxColour.setEnabled(!colourFromLabel.getState());
422  0 minColour.setEnabled(!colourFromLabel.getState());
423  0 if (thresholdOption == AnnotationColourGradient.NO_THRESHOLD)
424    {
425  0 slider.setEnabled(false);
426  0 thresholdValue.setEnabled(false);
427  0 thresholdValue.setText("");
428    }
429   
430  0 if (thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
431    {
432  0 adjusting = true;
433  0 acg.setThreshold(threshline.value);
434   
435  0 slider.setMinimum((int) (min * SCALE_FACTOR_1K));
436  0 slider.setMaximum((int) (max * SCALE_FACTOR_1K));
437  0 slider.setValue((int) (threshline.value * SCALE_FACTOR_1K));
438  0 thresholdValue.setText(threshline.value + "");
439  0 slider.setEnabled(true);
440  0 thresholdValue.setEnabled(true);
441  0 adjusting = false;
442    }
443   
444  0 acg.setAboveThreshold(
445    thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD);
446  0 acg.setBelowThreshold(
447    thresholdOption == AnnotationColourGradient.BELOW_THRESHOLD);
448   
449  0 if (thresholdIsMin.getState()
450    && thresholdOption != AnnotationColourGradient.NO_THRESHOLD)
451    {
452  0 if (thresholdOption == AnnotationColourGradient.ABOVE_THRESHOLD)
453    {
454  0 acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
455    acg.getMaxColour(), acg.getNoColour(), threshline.value,
456    max);
457    }
458    else
459    {
460  0 acg = new FeatureColour(acg.getColour(), acg.getMinColour(),
461    acg.getMaxColour(), acg.getNoColour(), min,
462    threshline.value);
463    }
464    }
465   
466  0 fr.setColour(type, acg);
467  0 cs = acg;
468  0 fs.selectionChanged(updateOverview);
469    }
470   
 
471  0 toggle void reset()
472    {
473  0 fr.setColour(type, oldcs);
474  0 fs.selectionChanged(true);
475    }
476   
 
477  0 toggle @Override
478    public void mouseClicked(MouseEvent evt)
479    {
480    }
481   
 
482  0 toggle @Override
483    public void mousePressed(MouseEvent evt)
484    {
485    }
486   
 
487  0 toggle @Override
488    public void mouseReleased(MouseEvent evt)
489    {
490  0 if (evt.getSource() == minColour)
491    {
492  0 minColour_actionPerformed(null);
493    }
494  0 else if (evt.getSource() == maxColour)
495    {
496  0 maxColour_actionPerformed(null);
497    }
498    else
499    {
500  0 changeColour(true);
501    // PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
502    }
503    }
504   
 
505  0 toggle @Override
506    public void mouseEntered(MouseEvent evt)
507    {
508    }
509   
 
510  0 toggle @Override
511    public void mouseExited(MouseEvent evt)
512    {
513    }
514   
515    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 12 2025 13:12:42 GMT using coverage data from Wed Nov 12 2025 13:12:28 GMT.
  • OpenClover is free and open-source software.