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  1. Project Clover database Thu Nov 27 2025 17:21:41 GMT
  2. Package jalview.gui

File UserDefinedColours.java

 

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

Code metrics

112
266
20
1
916
600
85
0.32
13.3
20
4.25

Classes

Class Line # Actions
UserDefinedColours 67 266 85
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 java.awt.Color;
24    import java.awt.Font;
25    import java.awt.Insets;
26    import java.awt.event.MouseAdapter;
27    import java.awt.event.MouseEvent;
28    import java.io.File;
29    import java.io.FileOutputStream;
30    import java.io.OutputStreamWriter;
31    import java.io.PrintWriter;
32    import java.util.ArrayList;
33    import java.util.List;
34    import java.util.Locale;
35   
36    import javax.swing.JButton;
37    import javax.swing.JInternalFrame;
38    import javax.swing.event.ChangeEvent;
39    import javax.swing.event.ChangeListener;
40    import javax.xml.bind.JAXBContext;
41    import javax.xml.bind.Marshaller;
42   
43    import jalview.bin.Cache;
44    import jalview.io.JalviewFileChooser;
45    import jalview.io.JalviewFileView;
46    import jalview.jbgui.GUserDefinedColours;
47    import jalview.schemes.ColourSchemeI;
48    import jalview.schemes.ColourSchemeLoader;
49    import jalview.schemes.ColourSchemes;
50    import jalview.schemes.ResidueProperties;
51    import jalview.schemes.UserColourScheme;
52    import jalview.util.ColorUtils;
53    import jalview.util.Format;
54    import jalview.util.MessageManager;
55    import jalview.util.Platform;
56    import jalview.xml.binding.jalview.JalviewUserColours;
57    import jalview.xml.binding.jalview.JalviewUserColours.Colour;
58    import jalview.xml.binding.jalview.ObjectFactory;
59   
60    /**
61    * This panel allows the user to assign colours to Amino Acid residue codes, and
62    * save the colour scheme.
63    *
64    * @author Andrew Waterhouse
65    * @author Mungo Carstairs
66    */
 
67    public class UserDefinedColours extends GUserDefinedColours
68    implements ChangeListener
69    {
70    private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD,
71    10);
72   
73    public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
74   
75    private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
76   
77    private static final int MY_FRAME_HEIGHT = 440;
78   
79    private static final int MY_FRAME_WIDTH = 810;
80   
81    private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
82   
83    AlignmentPanel ap;
84   
85    /*
86    * the colour scheme when the dialog was opened, or
87    * the scheme last saved to file
88    */
89    ColourSchemeI oldColourScheme;
90   
91    /*
92    * flag is true if the colour scheme has been changed since the
93    * dialog was opened, or the changes last saved to file
94    */
95    boolean changedButNotSaved;
96   
97    JInternalFrame frame;
98   
99    List<JButton> upperCaseButtons;
100   
101    List<JButton> lowerCaseButtons;
102   
103    /**
104    * Creates and displays a new UserDefinedColours panel
105    *
106    * @param alignPanel
107    */
 
108  0 toggle public UserDefinedColours(AlignmentPanel alignPanel)
109    {
110  0 this();
111   
112  0 lcaseColour.setEnabled(false);
113   
114  0 this.ap = alignPanel;
115   
116  0 oldColourScheme = alignPanel.av.getGlobalColourScheme();
117   
118  0 if (oldColourScheme instanceof UserColourScheme)
119    {
120  0 schemeName.setText(oldColourScheme.getSchemeName());
121  0 if (((UserColourScheme) oldColourScheme)
122    .getLowerCaseColours() != null)
123    {
124  0 caseSensitive.setSelected(true);
125  0 lcaseColour.setEnabled(true);
126  0 resetButtonPanel(true);
127    }
128    else
129    {
130  0 resetButtonPanel(false);
131    }
132    }
133    else
134    {
135  0 resetButtonPanel(false);
136    }
137   
138  0 showFrame();
139    }
140   
 
141  0 toggle UserDefinedColours()
142    {
143  0 super();
144  0 selectedButtons = new ArrayList<>();
145    }
146   
 
147  0 toggle void showFrame()
148    {
149  0 colorChooser.getSelectionModel().addChangeListener(this);
150  0 frame = new JInternalFrame();
151  0 frame.setFrameIcon(null);
152  0 frame.setContentPane(this);
153  0 Desktop.addInternalFrame(frame,
154    MessageManager.getString("label.user_defined_colours"),
155    MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
156    }
157   
158    /**
159    * Rebuilds the panel with coloured buttons for residues. If not case
160    * sensitive colours, show 3-letter amino acid code as button text. If case
161    * sensitive, just show the single letter code, in order to make space for the
162    * additional buttons.
163    *
164    * @param isCaseSensitive
165    */
 
166  0 toggle void resetButtonPanel(boolean isCaseSensitive)
167    {
168  0 buttonPanel.removeAll();
169   
170  0 if (upperCaseButtons == null)
171    {
172  0 upperCaseButtons = new ArrayList<>();
173    }
174   
175  0 for (int i = 0; i < 20; i++)
176    {
177  0 String label = isCaseSensitive ? ResidueProperties.aa[i]
178    : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
179    .toString();
180  0 JButton button = makeButton(label, ResidueProperties.aa[i],
181    upperCaseButtons, i);
182  0 buttonPanel.add(button);
183    }
184   
185  0 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
186  0 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
187  0 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
188  0 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
189   
190  0 if (!isCaseSensitive)
191    {
192  0 gridLayout.setRows(6);
193  0 gridLayout.setColumns(4);
194    }
195    else
196    {
197  0 gridLayout.setRows(7);
198  0 int cols = 7;
199  0 gridLayout.setColumns(cols + 1);
200   
201  0 if (lowerCaseButtons == null)
202    {
203  0 lowerCaseButtons = new ArrayList<>();
204    }
205   
206  0 for (int i = 0; i < 20; i++)
207    {
208  0 int row = i / cols + 1;
209  0 int index = (row * cols) + i;
210  0 JButton button = makeButton(
211    ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
212    ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
213    lowerCaseButtons, i);
214   
215  0 buttonPanel.add(button, index);
216    }
217    }
218   
219  0 if (isCaseSensitive)
220    {
221  0 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
222  0 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
223  0 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
224    }
225   
226    // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
227    // codes
228  0 if (this.frame != null)
229    {
230  0 int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
231    : MY_FRAME_WIDTH;
232  0 this.frame.setSize(newWidth, this.frame.getHeight());
233    }
234   
235  0 buttonPanel.validate();
236  0 validate();
237    }
238   
239    /**
240    * ChangeListener handler for when a colour is picked in the colour chooser.
241    * The action is to apply the colour to all selected buttons as their
242    * background colour. Foreground colour (text) is set to a lighter shade in
243    * order to highlight which buttons are selected. If 'Lower Case Colour' is
244    * active, then the colour is applied to all lower case buttons (as well as
245    * the Lower Case Colour button itself).
246    *
247    * @param evt
248    */
 
249  0 toggle @Override
250    public void stateChanged(ChangeEvent evt)
251    {
252  0 JButton button = null;
253  0 final Color newColour = colorChooser.getColor();
254  0 if (lcaseColour.isSelected())
255    {
256  0 selectedButtons.clear();
257  0 for (int i = 0; i < lowerCaseButtons.size(); i++)
258    {
259  0 button = lowerCaseButtons.get(i);
260  0 button.setBackground(newColour);
261  0 button.setForeground(
262    ColorUtils.brighterThan(button.getBackground()));
263    }
264    }
265  0 for (int i = 0; i < selectedButtons.size(); i++)
266    {
267  0 button = selectedButtons.get(i);
268  0 button.setBackground(newColour);
269  0 button.setForeground(ColorUtils.brighterThan(newColour));
270    }
271   
272  0 changedButNotSaved = true;
273    }
274   
275    /**
276    * Performs actions when a residue button is clicked. This manages the button
277    * selection set (highlighted by brighter foreground text).
278    * <p>
279    * On select button(s) with Ctrl/click or Shift/click: set button foreground
280    * text to brighter than background.
281    * <p>
282    * On unselect button(s) with Ctrl/click on selected, or click to release
283    * current selection: reset foreground text to darker than background.
284    * <p>
285    * Simple click: clear selection (resetting foreground to darker); set clicked
286    * button foreground to brighter
287    * <p>
288    * Finally, synchronize the colour chooser to the colour of the first button
289    * in the selected set.
290    *
291    * @param e
292    */
 
293  0 toggle public void colourButtonPressed(MouseEvent e)
294    {
295  0 JButton pressed = (JButton) e.getSource();
296   
297  0 if (e.isShiftDown())
298    {
299  0 JButton start, end = (JButton) e.getSource();
300  0 if (selectedButtons.size() > 0)
301    {
302  0 start = selectedButtons.get(selectedButtons.size() - 1);
303    }
304    else
305    {
306  0 start = (JButton) e.getSource();
307    }
308   
309  0 int startIndex = 0, endIndex = 0;
310  0 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
311    {
312  0 if (buttonPanel.getComponent(b) == start)
313    {
314  0 startIndex = b;
315    }
316  0 if (buttonPanel.getComponent(b) == end)
317    {
318  0 endIndex = b;
319    }
320    }
321   
322  0 if (startIndex > endIndex)
323    {
324  0 int temp = startIndex;
325  0 startIndex = endIndex;
326  0 endIndex = temp;
327    }
328   
329  0 for (int b = startIndex; b <= endIndex; b++)
330    {
331  0 JButton button = (JButton) buttonPanel.getComponent(b);
332  0 if (!selectedButtons.contains(button))
333    {
334  0 button.setForeground(
335    ColorUtils.brighterThan(button.getBackground()));
336  0 selectedButtons.add(button);
337    }
338    }
339    }
340  0 else if (!e.isControlDown())
341    {
342  0 for (int b = 0; b < selectedButtons.size(); b++)
343    {
344  0 JButton button = selectedButtons.get(b);
345  0 button.setForeground(ColorUtils.darkerThan(button.getBackground()));
346    }
347  0 selectedButtons.clear();
348  0 pressed.setForeground(
349    ColorUtils.brighterThan(pressed.getBackground()));
350  0 selectedButtons.add(pressed);
351   
352    }
353  0 else if (e.isControlDown())
354    {
355  0 if (selectedButtons.contains(pressed))
356    {
357  0 pressed.setForeground(
358    ColorUtils.darkerThan(pressed.getBackground()));
359  0 selectedButtons.remove(pressed);
360    }
361    else
362    {
363  0 pressed.setForeground(
364    ColorUtils.brighterThan(pressed.getBackground()));
365  0 selectedButtons.add(pressed);
366    }
367    }
368   
369  0 if (selectedButtons.size() > 0)
370    {
371  0 colorChooser.setColor((selectedButtons.get(0)).getBackground());
372    }
373    }
374   
375    /**
376    * A helper method to update or make a colour button, whose background colour
377    * is the associated colour, and text colour a darker shade of the same. If
378    * the button is already in the list, then its text and margins are updated,
379    * if not then it is created and added. This method supports toggling between
380    * case-sensitive and case-insensitive button panels. The case-sensitive
381    * version has abbreviated button text in order to fit in more buttons.
382    *
383    * @param label
384    * @param residue
385    * @param the
386    * list of buttons
387    * @param buttonIndex
388    * the button's position in the list
389    */
 
390  0 toggle JButton makeButton(String label, String residue, List<JButton> buttons,
391    int buttonIndex)
392    {
393  0 final JButton button;
394  0 Color col;
395   
396  0 if (buttonIndex < buttons.size())
397    {
398  0 button = buttons.get(buttonIndex);
399  0 col = button.getBackground();
400    }
401    else
402    {
403  0 button = new JButton();
404  0 button.addMouseListener(new MouseAdapter()
405    {
 
406  0 toggle @Override
407    public void mouseClicked(MouseEvent e)
408    {
409  0 colourButtonPressed(e);
410    }
411    });
412   
413  0 buttons.add(button);
414   
415    /*
416    * make initial button colour that of the current colour scheme,
417    * if it is a simple per-residue colouring, else white
418    */
419  0 col = Color.white;
420  0 if (oldColourScheme != null && oldColourScheme.isSimple())
421    {
422  0 col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
423    0f);
424    }
425    }
426   
427  0 if (caseSensitive.isSelected())
428    {
429  0 button.setMargin(new Insets(2, 2, 2, 2));
430    }
431    else
432    {
433  0 button.setMargin(new Insets(2, 14, 2, 14));
434    }
435   
436  0 button.setOpaque(true); // required for the next line to have effect
437  0 button.setBackground(col);
438  0 button.setText(label);
439  0 button.setForeground(ColorUtils.darkerThan(col));
440  0 button.setFont(VERDANA_BOLD_10);
441   
442  0 return button;
443    }
444   
445    /**
446    * On 'OK', check that at least one colour has been assigned to a residue (and
447    * if not issue a warning), and apply the chosen colour scheme and close the
448    * panel.
449    */
 
450  0 toggle @Override
451    protected void okButton_actionPerformed()
452    {
453  0 if (isNoSelectionMade())
454    {
455  0 JvOptionPane.showMessageDialog(Desktop.desktop,
456    MessageManager
457    .getString("label.no_colour_selection_in_scheme"),
458    MessageManager.getString("label.no_colour_selection_warn"),
459    JvOptionPane.WARNING_MESSAGE);
460    }
461    else
462    {
463    /*
464    * OK is treated as 'apply colours and close'
465    */
466  0 applyButton_actionPerformed();
467   
468    /*
469    * If editing a named colour scheme, warn if changes
470    * have not been saved
471    */
472  0 warnIfUnsavedChanges();
473   
474  0 try
475    {
476  0 frame.setClosed(true);
477    } catch (Exception ex)
478    {
479    }
480    }
481    }
482   
483    /**
484    * If we have made changes to an existing user defined colour scheme but not
485    * saved them, show a dialog with the option to save. If the user chooses to
486    * save, do so, else clear the colour scheme name to indicate a new colour
487    * scheme.
488    */
 
489  0 toggle protected void warnIfUnsavedChanges()
490    {
491    // BH 2018 no warning in JavaScript TODO
492   
493  0 if (!Platform.isJS() && changedButNotSaved)
494    /**
495    * Java only
496    *
497    * @j2sIgnore
498    */
499    {
500  0 String name = schemeName.getText().trim();
501  0 if (oldColourScheme != null && !"".equals(name)
502    && name.equals(oldColourScheme.getSchemeName()))
503    {
504  0 String message = MessageManager
505    .formatMessage("label.scheme_changed", name);
506  0 String title = MessageManager.getString("label.save_changes");
507  0 String[] options = new String[] { title,
508    MessageManager.getString("label.dont_save_changes"), };
509  0 final String question = JvSwingUtils.wrapTooltip(true, message);
510  0 int response = JvOptionPane.showOptionDialog(Desktop.desktop,
511    question, title, JvOptionPane.DEFAULT_OPTION,
512    JvOptionPane.PLAIN_MESSAGE, null, options, options[0]);
513   
514  0 if (response == 0)
515    {
516    /*
517    * prompt to save changes to file; if done,
518    * resets 'changed' flag to false
519    */
520  0 savebutton_actionPerformed();
521    }
522   
523    /*
524    * if user chooses not to save (either in this dialog or in the
525    * save as dialogs), treat this as a new user defined colour scheme
526    */
527  0 if (changedButNotSaved)
528    {
529    /*
530    * clear scheme name and re-apply as an anonymous scheme
531    */
532  0 schemeName.setText("");
533  0 applyButton_actionPerformed();
534    }
535    }
536    }
537    }
538   
539    /**
540    * Returns true if the user has not made any colour selection (including if
541    * 'case-sensitive' selected and no lower-case colour chosen).
542    *
543    * @return
544    */
 
545  0 toggle protected boolean isNoSelectionMade()
546    {
547  0 final boolean noUpperCaseSelected = upperCaseButtons == null
548    || upperCaseButtons.isEmpty();
549  0 final boolean noLowerCaseSelected = caseSensitive.isSelected()
550    && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
551  0 final boolean noSelectionMade = noUpperCaseSelected
552    || noLowerCaseSelected;
553  0 return noSelectionMade;
554    }
555   
556    /**
557    * Applies the current colour scheme to the alignment or sequence group
558    */
 
559  0 toggle @Override
560    protected void applyButton_actionPerformed()
561    {
562  0 if (isNoSelectionMade())
563    {
564  0 JvOptionPane.showMessageDialog(Desktop.desktop,
565    MessageManager
566    .getString("label.no_colour_selection_in_scheme"),
567    MessageManager.getString("label.no_colour_selection_warn"),
568    JvOptionPane.WARNING_MESSAGE);
569   
570    }
571  0 UserColourScheme ucs = getSchemeFromButtons();
572   
573  0 ap.alignFrame.changeColour(ucs);
574    }
575   
576    /**
577    * Constructs an instance of UserColourScheme with the residue colours
578    * currently set on the buttons on the panel
579    *
580    * @return
581    */
 
582  0 toggle UserColourScheme getSchemeFromButtons()
583    {
584   
585  0 Color[] newColours = new Color[24];
586   
587  0 int length = upperCaseButtons.size();
588  0 if (length < 24)
589    {
590  0 int i = 0;
591  0 for (JButton btn : upperCaseButtons)
592    {
593  0 newColours[i] = btn.getBackground();
594  0 i++;
595    }
596    }
597    else
598    {
599  0 for (int i = 0; i < 24; i++)
600    {
601  0 JButton button = upperCaseButtons.get(i);
602  0 newColours[i] = button.getBackground();
603    }
604    }
605   
606  0 UserColourScheme ucs = new UserColourScheme(newColours);
607  0 ucs.setName(schemeName.getText());
608   
609  0 if (caseSensitive.isSelected())
610    {
611  0 newColours = new Color[23];
612  0 length = lowerCaseButtons.size();
613  0 if (length < 23)
614    {
615  0 int i = 0;
616  0 for (JButton btn : lowerCaseButtons)
617    {
618  0 newColours[i] = btn.getBackground();
619  0 i++;
620    }
621    }
622    else
623    {
624  0 for (int i = 0; i < 23; i++)
625    {
626  0 JButton button = lowerCaseButtons.get(i);
627  0 newColours[i] = button.getBackground();
628    }
629    }
630  0 ucs.setLowerCaseColours(newColours);
631    }
632   
633  0 return ucs;
634    }
635   
636    /**
637    * Action on clicking Load scheme button.
638    * <ul>
639    * <li>Open a file chooser to browse for files with extension .jc</li>
640    * <li>Load in the colour scheme and transfer it to this panel's buttons</li>
641    * <li>Register the loaded colour scheme</li>
642    * </ul>
643    */
 
644  0 toggle @Override
645    protected void loadbutton_actionPerformed()
646    {
647  0 upperCaseButtons = new ArrayList<>();
648  0 lowerCaseButtons = new ArrayList<>();
649  0 JalviewFileChooser chooser = new JalviewFileChooser("jc",
650    "Jalview User Colours");
651  0 chooser.setFileView(new JalviewFileView());
652  0 chooser.setDialogTitle(
653    MessageManager.getString("label.load_colour_scheme"));
654  0 chooser.setToolTipText(MessageManager.getString("action.load"));
655  0 chooser.setResponseHandler(0, () -> {
656  0 File choice = chooser.getSelectedFile();
657  0 Cache.setProperty(LAST_DIRECTORY, choice.getParent());
658   
659  0 UserColourScheme ucs = ColourSchemeLoader
660    .loadColourScheme(choice.getAbsolutePath());
661  0 Color[] colors = ucs.getColours();
662  0 schemeName.setText(ucs.getSchemeName());
663   
664  0 if (ucs.getLowerCaseColours() != null)
665    {
666  0 caseSensitive.setSelected(true);
667  0 lcaseColour.setEnabled(true);
668  0 resetButtonPanel(true);
669  0 for (int i = 0; i < lowerCaseButtons.size(); i++)
670    {
671  0 JButton button = lowerCaseButtons.get(i);
672  0 button.setBackground(ucs.getLowerCaseColours()[i]);
673    }
674    }
675    else
676    {
677  0 caseSensitive.setSelected(false);
678  0 lcaseColour.setEnabled(false);
679  0 resetButtonPanel(false);
680    }
681   
682  0 for (int i = 0; i < upperCaseButtons.size(); i++)
683    {
684  0 JButton button = upperCaseButtons.get(i);
685  0 button.setBackground(colors[i]);
686    }
687   
688  0 addNewColourScheme(choice.getPath());
689    });
690   
691  0 chooser.showOpenDialog(this);
692    }
693   
694    /**
695    * Loads the user-defined colour scheme from the first file listed in property
696    * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
697    *
698    * @return
699    */
 
700  0 toggle public static UserColourScheme loadDefaultColours()
701    {
702  0 UserColourScheme ret = null;
703   
704  0 String colours = Cache.getProperty(USER_DEFINED_COLOURS);
705  0 if (colours != null)
706    {
707  0 if (colours.indexOf("|") > -1)
708    {
709  0 colours = colours.substring(0, colours.indexOf("|"));
710    }
711  0 ret = ColourSchemeLoader.loadColourScheme(colours);
712    }
713   
714  0 if (ret == null)
715    {
716  0 ret = new UserColourScheme("white");
717    }
718   
719  0 return ret;
720    }
721   
722    /**
723    * Action on pressing the Save button.
724    * <ul>
725    * <li>Check a name has been entered</li>
726    * <li>Warn if the name already exists, remove any existing scheme of the same
727    * name if overwriting</li>
728    * <li>Do the standard file chooser thing to write with extension .jc</li>
729    * <li>If saving changes (possibly not yet applied) to the currently selected
730    * colour scheme, then apply the changes, as it is too late to back out
731    * now</li>
732    * <li>Don't apply the changes if the currently selected scheme is different,
733    * to allow a new scheme to be configured and saved but not applied</li>
734    * </ul>
735    * If the scheme is saved to file, the 'changed' flag field is reset to false.
736    */
 
737  0 toggle @Override
738    protected void savebutton_actionPerformed()
739    {
740  0 String name = schemeName.getText().trim();
741  0 if (name.length() < 1)
742    {
743  0 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
744    MessageManager
745    .getString("label.user_colour_scheme_must_have_name"),
746    MessageManager.getString("label.no_name_colour_scheme"),
747    JvOptionPane.WARNING_MESSAGE);
748    }
749   
750  0 if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name))
751    {
752    /**
753    * java only
754    *
755    * @j2sIgnore
756    */
757    {
758  0 int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
759    MessageManager.formatMessage(
760    "label.colour_scheme_exists_overwrite", new Object[]
761    { name, name }),
762    MessageManager.getString("label.duplicate_scheme_name"),
763    JvOptionPane.YES_NO_OPTION);
764  0 if (reply != JvOptionPane.YES_OPTION)
765    {
766  0 return;
767    }
768    }
769    }
770   
771  0 JalviewFileChooser chooser = new JalviewFileChooser("jc",
772    "Jalview User Colours");
773   
774  0 JalviewFileView fileView = new JalviewFileView();
775  0 chooser.setFileView(fileView);
776  0 chooser.setDialogTitle(
777    MessageManager.getString("label.save_colour_scheme"));
778  0 chooser.setToolTipText(MessageManager.getString("action.save"));
779  0 int option = chooser.showSaveDialog(this);
780  0 if (option == JalviewFileChooser.APPROVE_OPTION)
781    {
782  0 File file = chooser.getSelectedFile();
783  0 UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
784  0 saveToFile(file);
785  0 changedButNotSaved = false;
786   
787    /*
788    * changes saved - apply to alignment if we are changing
789    * the currently selected colour scheme; also make the updated
790    * colours the 'backout' scheme on Cancel
791    */
792  0 if (oldColourScheme != null
793    && name.equals(oldColourScheme.getSchemeName()))
794    {
795  0 oldColourScheme = updatedScheme;
796  0 applyButton_actionPerformed();
797    }
798    }
799    }
800   
801    /**
802    * Adds the current colour scheme to the Jalview properties file so it is
803    * loaded on next startup, and updates the Colour menu in the parent
804    * AlignFrame (if there is one). Note this action does not including applying
805    * the colour scheme.
806    *
807    * @param filePath
808    * @return
809    */
 
810  0 toggle protected UserColourScheme addNewColourScheme(String filePath)
811    {
812    /*
813    * update the delimited list of user defined colour files in
814    * Jalview property USER_DEFINED_COLOURS
815    */
816  0 String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS,
817    filePath);
818  0 if (defaultColours.indexOf(filePath) == -1)
819    {
820  0 if (defaultColours.length() > 0)
821    {
822  0 defaultColours = defaultColours.concat("|");
823    }
824  0 defaultColours = defaultColours.concat(filePath);
825    }
826  0 Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
827   
828    /*
829    * construct and register the colour scheme
830    */
831  0 UserColourScheme ucs = getSchemeFromButtons();
832  0 ColourSchemes.getInstance().registerColourScheme(ucs);
833   
834    /*
835    * update the Colour menu items
836    */
837  0 if (ap != null)
838    {
839  0 ap.alignFrame.buildColourMenu();
840    }
841   
842  0 return ucs;
843    }
844   
845    /**
846    * Saves the colour scheme to file in XML format
847    *
848    * @param path
849    */
 
850  0 toggle protected void saveToFile(File toFile)
851    {
852    /*
853    * build a Java model of colour scheme as XML, and
854    * marshal to file
855    */
856  0 JalviewUserColours ucs = new JalviewUserColours();
857  0 String name = schemeName.getText();
858  0 ucs.setSchemeName(name);
859  0 try
860    {
861  0 PrintWriter out = new PrintWriter(new OutputStreamWriter(
862    new FileOutputStream(toFile), "UTF-8"));
863   
864  0 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
865    {
866  0 JButton button = (JButton) buttonPanel.getComponent(i);
867  0 Colour col = new Colour();
868  0 col.setName(button.getText());
869  0 col.setRGB(Format.getHexString(button.getBackground()));
870  0 ucs.getColour().add(col);
871    }
872  0 JAXBContext jaxbContext = JAXBContext
873    .newInstance(JalviewUserColours.class);
874  0 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
875  0 jaxbMarshaller.marshal(
876    new ObjectFactory().createJalviewUserColours(ucs), out);
877    // ucs.marshal(out);
878  0 out.close();
879    } catch (Exception ex)
880    {
881  0 ex.printStackTrace();
882    }
883    }
884   
885    /**
886    * On cancel, restores the colour scheme that was selected before the dialogue
887    * was opened
888    */
 
889  0 toggle @Override
890    protected void cancelButton_actionPerformed()
891    {
892  0 ap.alignFrame.changeColour(oldColourScheme);
893  0 ap.paintAlignment(true, true);
894   
895  0 try
896    {
897  0 frame.setClosed(true);
898    } catch (Exception ex)
899    {
900    }
901    }
902   
903    /**
904    * Action on selecting or deselecting the Case Sensitive option. When
905    * selected, separate buttons are shown for lower case residues, and the panel
906    * is resized to accommodate them. Also, the checkbox for 'apply colour to all
907    * lower case' is enabled.
908    */
 
909  0 toggle @Override
910    public void caseSensitive_actionPerformed()
911    {
912  0 boolean selected = caseSensitive.isSelected();
913  0 resetButtonPanel(selected);
914  0 lcaseColour.setEnabled(selected);
915    }
916    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:31:18 GMT using coverage data from Thu Nov 27 2025 17:31:04 GMT.
  • OpenClover is free and open-source software.