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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.gui

File AnnotationColourChooser.java

 

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56% of files have more coverage

Code metrics

40
181
18
1
460
383
45
0.25
10.06
18
2.5

Classes

Class Line # Actions
AnnotationColourChooser 54 181 45 239
0.00%
 

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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 jalview.bin.Cache;
24    import jalview.datamodel.AlignmentAnnotation;
25    import jalview.datamodel.GraphLine;
26    import jalview.datamodel.SequenceGroup;
27    import jalview.gui.JalviewColourChooser.ColourChooserListener;
28    import jalview.schemes.AnnotationColourGradient;
29    import jalview.schemes.ColourSchemeI;
30    import jalview.util.MessageManager;
31   
32    import java.awt.BorderLayout;
33    import java.awt.Color;
34    import java.awt.Dimension;
35    import java.awt.FlowLayout;
36    import java.awt.event.ActionEvent;
37    import java.awt.event.ActionListener;
38    import java.awt.event.MouseAdapter;
39    import java.awt.event.MouseEvent;
40    import java.util.Hashtable;
41    import java.util.Vector;
42   
43    import javax.swing.BorderFactory;
44    import javax.swing.JButton;
45    import javax.swing.JCheckBox;
46    import javax.swing.JComboBox;
47    import javax.swing.JInternalFrame;
48    import javax.swing.JLayeredPane;
49    import javax.swing.JPanel;
50   
51    import net.miginfocom.swing.MigLayout;
52   
53    @SuppressWarnings("serial")
 
54    public class AnnotationColourChooser extends AnnotationRowFilter
55    {
56    private static final int ONETHOUSAND = 1000;
57   
58    private ColourSchemeI oldcs;
59   
60    private JButton defColours;
61   
62    private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
63   
64    private JCheckBox useOriginalColours = new JCheckBox();
65   
66    JPanel minColour = new JPanel();
67   
68    JPanel maxColour = new JPanel();
69   
70    private JCheckBox thresholdIsMin = new JCheckBox();
71   
72    protected static final int MIN_WIDTH = 500;
73   
74    protected static final int MIN_HEIGHT = 240;
75   
 
76  0 toggle public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
77    {
78  0 super(av, ap);
79  0 oldcs = av.getGlobalColourScheme();
80  0 if (av.getAlignment().getGroups() != null)
81    {
82  0 oldgroupColours = new Hashtable<>();
83  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
84    {
85  0 if (sg.getColourScheme() != null)
86    {
87  0 oldgroupColours.put(sg, sg.getColourScheme());
88    }
89    }
90    }
91  0 frame = new JInternalFrame();
92  0 frame.setContentPane(this);
93  0 frame.setLayer(JLayeredPane.PALETTE_LAYER);
94  0 Desktop.addInternalFrame(frame,
95    MessageManager.getString("label.colour_by_annotation"), 520,
96    215);
97  0 frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
98  0 addSliderChangeListener();
99  0 addSliderMouseListeners();
100   
101  0 if (av.getAlignment().getAlignmentAnnotation() == null)
102    {
103  0 return;
104    }
105   
106    // Always get default shading from preferences.
107  0 setDefaultMinMax();
108   
109  0 adjusting = true;
110  0 if (oldcs instanceof AnnotationColourGradient)
111    {
112  0 AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
113  0 useOriginalColours.setSelected(
114    acg.isPredefinedColours() || acg.getBaseColour() != null);
115  0 if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
116    {
117  0 minColour.setBackground(acg.getMinColour());
118  0 maxColour.setBackground(acg.getMaxColour());
119    }
120  0 seqAssociated.setSelected(acg.isSeqAssociated());
121   
122    }
123  0 Vector<String> annotItems = getAnnotationItems(
124    seqAssociated.isSelected());
125  0 annotations = new JComboBox<>(annotItems);
126   
127  0 populateThresholdComboBox(threshold);
128   
129  0 if (oldcs instanceof AnnotationColourGradient)
130    {
131  0 AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
132  0 String label = getAnnotationMenuLabel(acg.getAnnotation());
133  0 annotations.setSelectedItem(label);
134  0 switch (acg.getAboveThreshold())
135    {
136  0 case AnnotationColourGradient.NO_THRESHOLD:
137  0 getThreshold().setSelectedIndex(0);
138  0 break;
139  0 case AnnotationColourGradient.ABOVE_THRESHOLD:
140  0 getThreshold().setSelectedIndex(1);
141  0 break;
142  0 case AnnotationColourGradient.BELOW_THRESHOLD:
143  0 getThreshold().setSelectedIndex(2);
144  0 break;
145  0 default:
146  0 throw new Error(MessageManager.getString(
147    "error.implementation_error_dont_know_about_threshold_setting"));
148    }
149  0 thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
150  0 thresholdValue.setText("" + acg.getAnnotationThreshold());
151    }
152   
153  0 jbInit();
154  0 adjusting = false;
155   
156  0 updateView();
157  0 frame.invalidate();
158  0 frame.pack();
159    }
160   
 
161  0 toggle @Override
162    protected void jbInit()
163    {
164  0 super.jbInit();
165   
166  0 minColour.setFont(JvSwingUtils.getLabelFont());
167  0 minColour.setBorder(BorderFactory.createEtchedBorder());
168  0 minColour.setPreferredSize(new Dimension(40, 20));
169  0 minColour.setToolTipText(MessageManager.getString("label.min_colour"));
170  0 minColour.addMouseListener(new MouseAdapter()
171    {
 
172  0 toggle @Override
173    public void mousePressed(MouseEvent e)
174    {
175  0 if (minColour.isEnabled())
176    {
177  0 showColourChooser(minColour, "label.select_colour_minimum_value");
178    }
179    }
180    });
181  0 maxColour.setFont(JvSwingUtils.getLabelFont());
182  0 maxColour.setBorder(BorderFactory.createEtchedBorder());
183  0 maxColour.setPreferredSize(new Dimension(40, 20));
184  0 maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
185  0 maxColour.addMouseListener(new MouseAdapter()
186    {
 
187  0 toggle @Override
188    public void mousePressed(MouseEvent e)
189    {
190  0 if (maxColour.isEnabled())
191    {
192  0 showColourChooser(maxColour, "label.select_colour_maximum_value");
193    }
194    }
195    });
196   
197  0 defColours = new JButton();
198  0 defColours.setOpaque(false);
199  0 defColours.setText(MessageManager.getString("action.set_defaults"));
200  0 defColours.setToolTipText(MessageManager
201    .getString("label.reset_min_max_colours_to_defaults"));
202  0 defColours.addActionListener(new ActionListener()
203    {
204   
 
205  0 toggle @Override
206    public void actionPerformed(ActionEvent arg0)
207    {
208  0 resetColours_actionPerformed();
209    }
210    });
211   
212  0 useOriginalColours.setFont(JvSwingUtils.getLabelFont());
213  0 useOriginalColours.setOpaque(false);
214  0 useOriginalColours.setText(
215    MessageManager.getString("label.use_original_colours"));
216  0 useOriginalColours.addActionListener(new ActionListener()
217    {
 
218  0 toggle @Override
219    public void actionPerformed(ActionEvent e)
220    {
221  0 originalColours_actionPerformed();
222    }
223    });
224  0 thresholdIsMin.setBackground(Color.white);
225  0 thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
226  0 thresholdIsMin
227    .setText(MessageManager.getString("label.threshold_minmax"));
228  0 thresholdIsMin.addActionListener(new ActionListener()
229    {
 
230  0 toggle @Override
231    public void actionPerformed(ActionEvent actionEvent)
232    {
233  0 thresholdIsMin_actionPerformed();
234    }
235    });
236  0 seqAssociated.setBackground(Color.white);
237  0 seqAssociated.setFont(JvSwingUtils.getLabelFont());
238  0 seqAssociated
239    .setText(MessageManager.getString("label.per_sequence_only"));
240  0 seqAssociated.addActionListener(new ActionListener()
241    {
242   
 
243  0 toggle @Override
244    public void actionPerformed(ActionEvent arg0)
245    {
246  0 seqAssociated_actionPerformed(annotations);
247    }
248    });
249   
250  0 this.setLayout(new BorderLayout());
251  0 JPanel jPanel1 = new JPanel();
252  0 JPanel jPanel2 = new JPanel();
253  0 jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
254  0 jPanel1.setBackground(Color.white);
255  0 jPanel2.setBackground(Color.white);
256   
257  0 jPanel1.add(ok);
258  0 jPanel1.add(cancel);
259  0 jPanel2.add(annotations, "grow, wrap");
260  0 jPanel2.add(seqAssociated);
261  0 jPanel2.add(useOriginalColours);
262  0 JPanel colpanel = new JPanel(new FlowLayout());
263  0 colpanel.setBackground(Color.white);
264  0 colpanel.add(minColour);
265  0 colpanel.add(maxColour);
266  0 jPanel2.add(colpanel, "wrap");
267  0 jPanel2.add(getThreshold());
268  0 jPanel2.add(defColours, "skip 1, wrap");
269  0 jPanel2.add(thresholdIsMin);
270  0 jPanel2.add(slider, "grow");
271  0 jPanel2.add(thresholdValue, "grow");
272  0 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
273  0 this.add(jPanel2, java.awt.BorderLayout.CENTER);
274  0 this.validate();
275    }
276   
 
277  0 toggle protected void resetColours_actionPerformed()
278    {
279  0 setDefaultMinMax();
280  0 updateView();
281    }
282   
 
283  0 toggle private void setDefaultMinMax()
284    {
285  0 minColour.setBackground(
286    Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
287  0 maxColour.setBackground(
288    Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
289    }
290   
 
291  0 toggle protected void showColourChooser(JPanel colourPanel, String titleKey)
292    {
293  0 String ttl = MessageManager.getString(titleKey);
294  0 ColourChooserListener listener = new ColourChooserListener()
295    {
 
296  0 toggle @Override
297    public void colourSelected(Color c)
298    {
299  0 colourPanel.setBackground(c);
300  0 colourPanel.repaint();
301  0 updateView();
302    }
303    };
304  0 JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
305    colourPanel.getBackground(), listener);
306    }
307   
 
308  0 toggle @Override
309    public void reset()
310    {
311  0 av.setGlobalColourScheme(oldcs);
312  0 if (av.getAlignment().getGroups() != null)
313    {
314   
315  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
316    {
317  0 sg.setColourScheme(oldgroupColours.get(sg));
318    }
319    }
320    }
321   
 
322  0 toggle @Override
323    public void valueChanged(boolean updateAllAnnotation)
324    {
325  0 if (slider.isEnabled())
326    {
327  0 if (useOriginalColours.isSelected() && !(av
328    .getGlobalColourScheme() instanceof AnnotationColourGradient))
329    {
330  0 updateView();
331    }
332  0 getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
333  0 propagateSeqAssociatedThreshold(updateAllAnnotation,
334    getCurrentAnnotation());
335  0 ap.paintAlignment(false, false);
336    }
337    }
338   
 
339  0 toggle public void originalColours_actionPerformed()
340    {
341  0 boolean selected = useOriginalColours.isSelected();
342  0 if (selected)
343    {
344  0 reset();
345    }
346  0 maxColour.setEnabled(!selected);
347  0 minColour.setEnabled(!selected);
348  0 thresholdIsMin.setEnabled(!selected);
349  0 updateView();
350    }
351   
 
352  0 toggle @Override
353    public void updateView()
354    {
355    // Check if combobox is still adjusting
356  0 if (adjusting)
357    {
358  0 return;
359    }
360   
361  0 setCurrentAnnotation(
362    av.getAlignment().getAlignmentAnnotation()[annmap[annotations
363    .getSelectedIndex()]]);
364   
365  0 int selectedThresholdItem = getSelectedThresholdItem(
366    getThreshold().getSelectedIndex());
367   
368  0 slider.setEnabled(true);
369  0 thresholdValue.setEnabled(true);
370  0 thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
371   
372  0 if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
373    {
374  0 slider.setEnabled(false);
375  0 thresholdValue.setEnabled(false);
376  0 thresholdValue.setText("");
377  0 thresholdIsMin.setEnabled(false);
378    }
379  0 else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
380    && getCurrentAnnotation().threshold == null)
381    {
382  0 getCurrentAnnotation().setThreshold(new GraphLine(
383    (getCurrentAnnotation().graphMax
384    - getCurrentAnnotation().graphMin) / 2f,
385    "Threshold", Color.black));
386    }
387   
388  0 if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
389    {
390  0 adjusting = true;
391  0 float range = getCurrentAnnotation().graphMax * ONETHOUSAND
392    - getCurrentAnnotation().graphMin * ONETHOUSAND;
393   
394  0 slider.setMinimum(
395    (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
396  0 slider.setMaximum(
397    (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
398  0 slider.setValue(
399    (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
400  0 thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
401  0 slider.setMajorTickSpacing((int) (range / 10f));
402  0 slider.setEnabled(true);
403  0 thresholdValue.setEnabled(true);
404  0 adjusting = false;
405    }
406  0 colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
407   
408  0 ap.alignmentChanged();
409    }
410   
 
411  0 toggle protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
412    int selectedThresholdOption)
413    {
414   
415  0 AnnotationColourGradient acg = null;
416  0 if (useOriginalColours.isSelected())
417    {
418  0 acg = new AnnotationColourGradient(currentAnn,
419    av.getGlobalColourScheme(), selectedThresholdOption);
420    }
421    else
422    {
423  0 acg = new AnnotationColourGradient(currentAnn,
424    minColour.getBackground(), maxColour.getBackground(),
425    selectedThresholdOption);
426    }
427  0 acg.setSeqAssociated(seqAssociated.isSelected());
428   
429  0 if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
430    {
431  0 acg.setPredefinedColours(true);
432    }
433   
434  0 acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
435   
436  0 av.setGlobalColourScheme(acg);
437   
438  0 if (av.getAlignment().getGroups() != null)
439    {
440   
441  0 for (SequenceGroup sg : ap.av.getAlignment().getGroups())
442    {
443  0 if (sg.cs == null)
444    {
445  0 continue;
446    }
447  0 sg.setColourScheme(
448    acg.getInstance(sg, ap.av.getHiddenRepSequences()));
449    }
450    }
451    }
452   
 
453  0 toggle @Override
454    protected void sliderDragReleased()
455    {
456  0 super.sliderDragReleased();
457  0 ap.paintAlignment(true, true);
458    }
459   
460    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.