2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import java.awt.Color;
25 import java.awt.Insets;
26 import java.awt.event.MouseAdapter;
27 import java.awt.event.MouseEvent;
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;
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;
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;
61 * This panel allows the user to assign colours to Amino Acid residue codes, and
62 * save the colour scheme.
64 * @author Andrew Waterhouse
65 * @author Mungo Carstairs
67 public class UserDefinedColours extends GUserDefinedColours
68 implements ChangeListener
70 private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD,
73 public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
75 private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
77 private static final int MY_FRAME_HEIGHT = 440;
79 private static final int MY_FRAME_WIDTH = 810;
81 private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
86 * the colour scheme when the dialog was opened, or
87 * the scheme last saved to file
89 ColourSchemeI oldColourScheme;
92 * flag is true if the colour scheme has been changed since the
93 * dialog was opened, or the changes last saved to file
95 boolean changedButNotSaved;
99 List<JButton> upperCaseButtons;
101 List<JButton> lowerCaseButtons;
104 * Creates and displays a new UserDefinedColours panel
108 public UserDefinedColours(AlignmentPanel alignPanel)
112 lcaseColour.setEnabled(false);
114 this.ap = alignPanel;
116 oldColourScheme = alignPanel.av.getGlobalColourScheme();
118 if (oldColourScheme instanceof UserColourScheme)
120 schemeName.setText(oldColourScheme.getSchemeName());
121 if (((UserColourScheme) oldColourScheme)
122 .getLowerCaseColours() != null)
124 caseSensitive.setSelected(true);
125 lcaseColour.setEnabled(true);
126 resetButtonPanel(true);
130 resetButtonPanel(false);
135 resetButtonPanel(false);
144 selectedButtons = new ArrayList<>();
149 colorChooser.getSelectionModel().addChangeListener(this);
150 frame = new JInternalFrame();
151 frame.setContentPane(this);
152 Desktop.addInternalFrame(frame,
153 MessageManager.getString("label.user_defined_colours"),
154 MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
158 * Rebuilds the panel with coloured buttons for residues. If not case
159 * sensitive colours, show 3-letter amino acid code as button text. If case
160 * sensitive, just show the single letter code, in order to make space for the
161 * additional buttons.
163 * @param isCaseSensitive
165 void resetButtonPanel(boolean isCaseSensitive)
167 buttonPanel.removeAll();
169 if (upperCaseButtons == null)
171 upperCaseButtons = new ArrayList<>();
174 for (int i = 0; i < 20; i++)
176 String label = isCaseSensitive ? ResidueProperties.aa[i]
177 : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
179 JButton button = makeButton(label, ResidueProperties.aa[i],
180 upperCaseButtons, i);
181 buttonPanel.add(button);
184 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
185 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
186 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
187 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
189 if (!isCaseSensitive)
191 gridLayout.setRows(6);
192 gridLayout.setColumns(4);
196 gridLayout.setRows(7);
198 gridLayout.setColumns(cols + 1);
200 if (lowerCaseButtons == null)
202 lowerCaseButtons = new ArrayList<>();
205 for (int i = 0; i < 20; i++)
207 int row = i / cols + 1;
208 int index = (row * cols) + i;
209 JButton button = makeButton(
210 ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
211 ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
212 lowerCaseButtons, i);
214 buttonPanel.add(button, index);
220 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
221 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
222 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
225 // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
227 if (this.frame != null)
229 int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
231 this.frame.setSize(newWidth, this.frame.getHeight());
234 buttonPanel.validate();
239 * ChangeListener handler for when a colour is picked in the colour chooser.
240 * The action is to apply the colour to all selected buttons as their
241 * background colour. Foreground colour (text) is set to a lighter shade in
242 * order to highlight which buttons are selected. If 'Lower Case Colour' is
243 * active, then the colour is applied to all lower case buttons (as well as
244 * the Lower Case Colour button itself).
249 public void stateChanged(ChangeEvent evt)
251 JButton button = null;
252 final Color newColour = colorChooser.getColor();
253 if (lcaseColour.isSelected())
255 selectedButtons.clear();
256 for (int i = 0; i < lowerCaseButtons.size(); i++)
258 button = lowerCaseButtons.get(i);
259 button.setBackground(newColour);
260 button.setForeground(
261 ColorUtils.brighterThan(button.getBackground()));
264 for (int i = 0; i < selectedButtons.size(); i++)
266 button = selectedButtons.get(i);
267 button.setBackground(newColour);
268 button.setForeground(ColorUtils.brighterThan(newColour));
271 changedButNotSaved = true;
275 * Performs actions when a residue button is clicked. This manages the button
276 * selection set (highlighted by brighter foreground text).
278 * On select button(s) with Ctrl/click or Shift/click: set button foreground
279 * text to brighter than background.
281 * On unselect button(s) with Ctrl/click on selected, or click to release
282 * current selection: reset foreground text to darker than background.
284 * Simple click: clear selection (resetting foreground to darker); set clicked
285 * button foreground to brighter
287 * Finally, synchronize the colour chooser to the colour of the first button
288 * in the selected set.
292 public void colourButtonPressed(MouseEvent e)
294 JButton pressed = (JButton) e.getSource();
298 JButton start, end = (JButton) e.getSource();
299 if (selectedButtons.size() > 0)
301 start = selectedButtons.get(selectedButtons.size() - 1);
305 start = (JButton) e.getSource();
308 int startIndex = 0, endIndex = 0;
309 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
311 if (buttonPanel.getComponent(b) == start)
315 if (buttonPanel.getComponent(b) == end)
321 if (startIndex > endIndex)
323 int temp = startIndex;
324 startIndex = endIndex;
328 for (int b = startIndex; b <= endIndex; b++)
330 JButton button = (JButton) buttonPanel.getComponent(b);
331 if (!selectedButtons.contains(button))
333 button.setForeground(
334 ColorUtils.brighterThan(button.getBackground()));
335 selectedButtons.add(button);
339 else if (!e.isControlDown())
341 for (int b = 0; b < selectedButtons.size(); b++)
343 JButton button = selectedButtons.get(b);
344 button.setForeground(ColorUtils.darkerThan(button.getBackground()));
346 selectedButtons.clear();
347 pressed.setForeground(
348 ColorUtils.brighterThan(pressed.getBackground()));
349 selectedButtons.add(pressed);
352 else if (e.isControlDown())
354 if (selectedButtons.contains(pressed))
356 pressed.setForeground(
357 ColorUtils.darkerThan(pressed.getBackground()));
358 selectedButtons.remove(pressed);
362 pressed.setForeground(
363 ColorUtils.brighterThan(pressed.getBackground()));
364 selectedButtons.add(pressed);
368 if (selectedButtons.size() > 0)
370 colorChooser.setColor((selectedButtons.get(0)).getBackground());
375 * A helper method to update or make a colour button, whose background colour
376 * is the associated colour, and text colour a darker shade of the same. If
377 * the button is already in the list, then its text and margins are updated,
378 * if not then it is created and added. This method supports toggling between
379 * case-sensitive and case-insensitive button panels. The case-sensitive
380 * version has abbreviated button text in order to fit in more buttons.
387 * the button's position in the list
389 JButton makeButton(String label, String residue, List<JButton> buttons,
392 final JButton button;
395 if (buttonIndex < buttons.size())
397 button = buttons.get(buttonIndex);
398 col = button.getBackground();
402 button = new JButton();
403 button.addMouseListener(new MouseAdapter()
406 public void mouseClicked(MouseEvent e)
408 colourButtonPressed(e);
415 * make initial button colour that of the current colour scheme,
416 * if it is a simple per-residue colouring, else white
419 if (oldColourScheme != null && oldColourScheme.isSimple())
421 col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
426 if (caseSensitive.isSelected())
428 button.setMargin(new Insets(2, 2, 2, 2));
432 button.setMargin(new Insets(2, 14, 2, 14));
435 button.setOpaque(true); // required for the next line to have effect
436 button.setBackground(col);
437 button.setText(label);
438 button.setForeground(ColorUtils.darkerThan(col));
439 button.setFont(VERDANA_BOLD_10);
445 * On 'OK', check that at least one colour has been assigned to a residue (and
446 * if not issue a warning), and apply the chosen colour scheme and close the
450 protected void okButton_actionPerformed()
452 if (isNoSelectionMade())
454 JvOptionPane.showMessageDialog(Desktop.desktop,
456 .getString("label.no_colour_selection_in_scheme"),
457 MessageManager.getString("label.no_colour_selection_warn"),
458 JvOptionPane.WARNING_MESSAGE);
463 * OK is treated as 'apply colours and close'
465 applyButton_actionPerformed();
468 * If editing a named colour scheme, warn if changes
469 * have not been saved
471 warnIfUnsavedChanges();
475 frame.setClosed(true);
476 } catch (Exception ex)
483 * If we have made changes to an existing user defined colour scheme but not
484 * saved them, show a dialog with the option to save. If the user chooses to
485 * save, do so, else clear the colour scheme name to indicate a new colour
488 protected void warnIfUnsavedChanges()
490 // BH 2018 no warning in JavaScript TODO
492 if (!Platform.isJS() && changedButNotSaved)
499 String name = schemeName.getText().trim();
500 if (oldColourScheme != null && !"".equals(name)
501 && name.equals(oldColourScheme.getSchemeName()))
503 String message = MessageManager
504 .formatMessage("label.scheme_changed", name);
505 String title = MessageManager.getString("label.save_changes");
506 String[] options = new String[] { title,
507 MessageManager.getString("label.dont_save_changes"), };
508 final String question = JvSwingUtils.wrapTooltip(true, message);
509 int response = JvOptionPane.showOptionDialog(Desktop.desktop,
510 question, title, JvOptionPane.DEFAULT_OPTION,
511 JvOptionPane.PLAIN_MESSAGE, null, options, options[0]);
516 * prompt to save changes to file; if done,
517 * resets 'changed' flag to false
519 savebutton_actionPerformed();
523 * if user chooses not to save (either in this dialog or in the
524 * save as dialogs), treat this as a new user defined colour scheme
526 if (changedButNotSaved)
529 * clear scheme name and re-apply as an anonymous scheme
531 schemeName.setText("");
532 applyButton_actionPerformed();
539 * Returns true if the user has not made any colour selection (including if
540 * 'case-sensitive' selected and no lower-case colour chosen).
544 protected boolean isNoSelectionMade()
546 final boolean noUpperCaseSelected = upperCaseButtons == null
547 || upperCaseButtons.isEmpty();
548 final boolean noLowerCaseSelected = caseSensitive.isSelected()
549 && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
550 final boolean noSelectionMade = noUpperCaseSelected
551 || noLowerCaseSelected;
552 return noSelectionMade;
556 * Applies the current colour scheme to the alignment or sequence group
559 protected void applyButton_actionPerformed()
561 if (isNoSelectionMade())
563 JvOptionPane.showMessageDialog(Desktop.desktop,
565 .getString("label.no_colour_selection_in_scheme"),
566 MessageManager.getString("label.no_colour_selection_warn"),
567 JvOptionPane.WARNING_MESSAGE);
570 UserColourScheme ucs = getSchemeFromButtons();
572 ap.alignFrame.changeColour(ucs);
576 * Constructs an instance of UserColourScheme with the residue colours
577 * currently set on the buttons on the panel
581 UserColourScheme getSchemeFromButtons()
584 Color[] newColours = new Color[24];
586 int length = upperCaseButtons.size();
590 for (JButton btn : upperCaseButtons)
592 newColours[i] = btn.getBackground();
598 for (int i = 0; i < 24; i++)
600 JButton button = upperCaseButtons.get(i);
601 newColours[i] = button.getBackground();
605 UserColourScheme ucs = new UserColourScheme(newColours);
606 ucs.setName(schemeName.getText());
608 if (caseSensitive.isSelected())
610 newColours = new Color[23];
611 length = lowerCaseButtons.size();
615 for (JButton btn : lowerCaseButtons)
617 newColours[i] = btn.getBackground();
623 for (int i = 0; i < 23; i++)
625 JButton button = lowerCaseButtons.get(i);
626 newColours[i] = button.getBackground();
629 ucs.setLowerCaseColours(newColours);
636 * Action on clicking Load scheme button.
638 * <li>Open a file chooser to browse for files with extension .jc</li>
639 * <li>Load in the colour scheme and transfer it to this panel's buttons</li>
640 * <li>Register the loaded colour scheme</li>
644 protected void loadbutton_actionPerformed()
646 upperCaseButtons = new ArrayList<>();
647 lowerCaseButtons = new ArrayList<>();
648 JalviewFileChooser chooser = new JalviewFileChooser("jc",
649 "Jalview User Colours");
650 chooser.setFileView(new JalviewFileView());
651 chooser.setDialogTitle(
652 MessageManager.getString("label.load_colour_scheme"));
653 chooser.setToolTipText(MessageManager.getString("action.load"));
654 chooser.setResponseHandler(0, () -> {
655 File choice = chooser.getSelectedFile();
656 Cache.setProperty(LAST_DIRECTORY, choice.getParent());
658 UserColourScheme ucs = ColourSchemeLoader
659 .loadColourScheme(choice.getAbsolutePath());
660 Color[] colors = ucs.getColours();
661 schemeName.setText(ucs.getSchemeName());
663 if (ucs.getLowerCaseColours() != null)
665 caseSensitive.setSelected(true);
666 lcaseColour.setEnabled(true);
667 resetButtonPanel(true);
668 for (int i = 0; i < lowerCaseButtons.size(); i++)
670 JButton button = lowerCaseButtons.get(i);
671 button.setBackground(ucs.getLowerCaseColours()[i]);
676 caseSensitive.setSelected(false);
677 lcaseColour.setEnabled(false);
678 resetButtonPanel(false);
681 for (int i = 0; i < upperCaseButtons.size(); i++)
683 JButton button = upperCaseButtons.get(i);
684 button.setBackground(colors[i]);
687 addNewColourScheme(choice.getPath());
691 chooser.showOpenDialog(this);
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.
700 public static UserColourScheme loadDefaultColours()
702 UserColourScheme ret = null;
704 String colours = Cache.getProperty(USER_DEFINED_COLOURS);
707 if (colours.indexOf("|") > -1)
709 colours = colours.substring(0, colours.indexOf("|"));
711 ret = ColourSchemeLoader.loadColourScheme(colours);
716 ret = new UserColourScheme("white");
723 * Action on pressing the Save button.
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
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>
735 * If the scheme is saved to file, the 'changed' flag field is reset to false.
738 protected void savebutton_actionPerformed()
740 String name = schemeName.getText().trim();
741 if (name.length() < 1)
743 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
745 .getString("label.user_colour_scheme_must_have_name"),
746 MessageManager.getString("label.no_name_colour_scheme"),
747 JvOptionPane.WARNING_MESSAGE);
750 if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name))
758 int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
759 MessageManager.formatMessage(
760 "label.colour_scheme_exists_overwrite", new Object[]
762 MessageManager.getString("label.duplicate_scheme_name"),
763 JvOptionPane.YES_NO_OPTION);
764 if (reply != JvOptionPane.YES_OPTION)
771 JalviewFileChooser chooser = new JalviewFileChooser("jc",
772 "Jalview User Colours");
774 JalviewFileView fileView = new JalviewFileView();
775 chooser.setFileView(fileView);
776 chooser.setDialogTitle(
777 MessageManager.getString("label.save_colour_scheme"));
778 chooser.setToolTipText(MessageManager.getString("action.save"));
779 int option = chooser.showSaveDialog(this);
780 if (option == JalviewFileChooser.APPROVE_OPTION)
782 File file = chooser.getSelectedFile();
783 UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
785 changedButNotSaved = false;
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
792 if (oldColourScheme != null
793 && name.equals(oldColourScheme.getSchemeName()))
795 oldColourScheme = updatedScheme;
796 applyButton_actionPerformed();
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
810 protected UserColourScheme addNewColourScheme(String filePath)
813 * update the delimited list of user defined colour files in
814 * Jalview property USER_DEFINED_COLOURS
816 String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS,
818 if (defaultColours.indexOf(filePath) == -1)
820 if (defaultColours.length() > 0)
822 defaultColours = defaultColours.concat("|");
824 defaultColours = defaultColours.concat(filePath);
826 Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
829 * construct and register the colour scheme
831 UserColourScheme ucs = getSchemeFromButtons();
832 ColourSchemes.getInstance().registerColourScheme(ucs);
835 * update the Colour menu items
839 ap.alignFrame.buildColourMenu();
846 * Saves the colour scheme to file in XML format
850 protected void saveToFile(File toFile)
853 * build a Java model of colour scheme as XML, and
856 JalviewUserColours ucs = new JalviewUserColours();
857 String name = schemeName.getText();
858 ucs.setSchemeName(name);
861 PrintWriter out = new PrintWriter(new OutputStreamWriter(
862 new FileOutputStream(toFile), "UTF-8"));
864 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
866 JButton button = (JButton) buttonPanel.getComponent(i);
867 Colour col = new Colour();
868 col.setName(button.getText());
869 col.setRGB(Format.getHexString(button.getBackground()));
870 ucs.getColour().add(col);
872 JAXBContext jaxbContext = JAXBContext
873 .newInstance(JalviewUserColours.class);
874 Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
875 jaxbMarshaller.marshal(
876 new ObjectFactory().createJalviewUserColours(ucs), out);
879 } catch (Exception ex)
881 ex.printStackTrace();
886 * On cancel, restores the colour scheme that was selected before the dialogue
890 protected void cancelButton_actionPerformed()
892 ap.alignFrame.changeColour(oldColourScheme);
893 ap.paintAlignment(true, true);
897 frame.setClosed(true);
898 } catch (Exception ex)
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.
910 public void caseSensitive_actionPerformed()
912 boolean selected = caseSensitive.isSelected();
913 resetButtonPanel(selected);
914 lcaseColour.setEnabled(selected);