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 jalview.api.structures.JalviewStructureDisplayI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.io.JalviewFileChooser;
27 import jalview.io.JalviewFileView;
28 import jalview.jbgui.GUserDefinedColours;
29 import jalview.schemabinding.version2.Colour;
30 import jalview.schemabinding.version2.JalviewUserColours;
31 import jalview.schemes.ColourSchemeI;
32 import jalview.schemes.ColourSchemeLoader;
33 import jalview.schemes.ColourSchemes;
34 import jalview.schemes.ResidueProperties;
35 import jalview.schemes.UserColourScheme;
36 import jalview.util.ColorUtils;
37 import jalview.util.Format;
38 import jalview.util.MessageManager;
40 import java.awt.Color;
42 import java.awt.Insets;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.MouseAdapter;
45 import java.awt.event.MouseEvent;
47 import java.io.FileOutputStream;
48 import java.io.OutputStreamWriter;
49 import java.io.PrintWriter;
50 import java.util.ArrayList;
51 import java.util.List;
53 import javax.swing.JButton;
54 import javax.swing.JInternalFrame;
55 import javax.swing.event.ChangeEvent;
56 import javax.swing.event.ChangeListener;
59 * This panel allows the user to assign colours to Amino Acid residue codes, and
60 * save the colour scheme.
62 * @author Andrew Waterhouse
63 * @author Mungo Carstairs
65 public class UserDefinedColours extends GUserDefinedColours implements
68 private static final Font VERDANA_BOLD_10 = new Font("Verdana",
71 public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
73 private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
75 private static final int MY_FRAME_HEIGHT = 440;
77 private static final int MY_FRAME_WIDTH = 810;
79 private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
83 SequenceGroup seqGroup;
85 List<JButton> selectedButtons;
87 ColourSchemeI oldColourScheme;
91 JalviewStructureDisplayI structureViewer;
93 List<JButton> upperCaseButtons;
95 List<JButton> lowerCaseButtons;
98 * Creates a new UserDefinedColours object.
103 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
107 lcaseColour.setEnabled(false);
112 if (seqGroup != null)
114 oldColourScheme = seqGroup.getColourScheme();
118 oldColourScheme = ap.av.getGlobalColourScheme();
121 if (oldColourScheme instanceof UserColourScheme)
123 schemeName.setText(oldColourScheme.getSchemeName());
124 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
126 caseSensitive.setSelected(true);
127 lcaseColour.setEnabled(true);
128 resetButtonPanel(true);
132 resetButtonPanel(false);
137 resetButtonPanel(false);
143 public UserDefinedColours(JalviewStructureDisplayI viewer,
147 this.structureViewer = viewer;
149 colorChooser.getSelectionModel().addChangeListener(this);
151 oldColourScheme = oldcs;
153 if (oldColourScheme instanceof UserColourScheme)
155 schemeName.setText(((UserColourScheme) oldColourScheme)
159 resetButtonPanel(false);
165 public UserDefinedColours()
168 selectedButtons = new ArrayList<JButton>();
173 colorChooser.getSelectionModel().addChangeListener(this);
174 frame = new JInternalFrame();
175 frame.setContentPane(this);
176 Desktop.addInternalFrame(frame,
177 MessageManager.getString("label.user_defined_colours"),
178 MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
180 if (seqGroup != null)
182 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
187 * Rebuilds the panel with coloured buttons for residues. If not case
188 * sensitive colours, show 3-letter amino acid code as button text. If case
189 * sensitive, just show the single letter code, in order to make space for the
190 * additional buttons.
192 * @param isCaseSensitive
194 void resetButtonPanel(boolean isCaseSensitive)
196 buttonPanel.removeAll();
198 if (upperCaseButtons == null)
200 upperCaseButtons = new ArrayList<JButton>();
203 for (int i = 0; i < 20; i++)
205 String label = isCaseSensitive ? ResidueProperties.aa[i]
206 : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
208 JButton button = makeButton(label, ResidueProperties.aa[i],
209 upperCaseButtons, i);
210 buttonPanel.add(button);
213 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
214 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
215 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
216 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
218 if (!isCaseSensitive)
220 gridLayout.setRows(6);
221 gridLayout.setColumns(4);
225 gridLayout.setRows(7);
227 gridLayout.setColumns(cols + 1);
229 if (lowerCaseButtons == null)
231 lowerCaseButtons = new ArrayList<JButton>();
234 for (int i = 0; i < 20; i++)
236 int row = i / cols + 1;
237 int index = (row * cols) + i;
238 JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
239 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
241 buttonPanel.add(button, index);
247 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
248 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
249 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
252 // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
254 if (this.frame != null)
256 int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
258 this.frame.setSize(newWidth, this.frame.getHeight());
261 buttonPanel.validate();
266 * ChangeListener handler for when a colour is picked in the colour chooser.
267 * The action is to apply the colour to all selected buttons as their
268 * background colour. Foreground colour (text) is set to a lighter shade in
269 * order to highlight which buttons are selected. If 'Lower Case Colour' is
270 * active, then the colour is applied to all lower case buttons (as well as
271 * the Lower Case Colour button itself).
276 public void stateChanged(ChangeEvent evt)
278 JButton button = null;
279 final Color newColour = colorChooser.getColor();
280 if (lcaseColour.isSelected())
282 selectedButtons.clear();
283 for (int i = 0; i < lowerCaseButtons.size(); i++)
285 button = lowerCaseButtons.get(i);
286 button.setBackground(newColour);
287 button.setForeground(ColorUtils.brighterThan(button.getBackground()));
290 for (int i = 0; i < selectedButtons.size(); i++)
292 button = selectedButtons.get(i);
293 button.setBackground(newColour);
294 button.setForeground(ColorUtils.brighterThan(newColour));
299 * Performs actions when a residue button is clicked. This manages the button
300 * selection set (highlighted by brighter foreground text).
302 * On select button(s) with Ctrl/click or Shift/click: set button foreground
303 * text to brighter than background.
305 * On unselect button(s) with Ctrl/click on selected, or click to release
306 * current selection: reset foreground text to darker than background.
308 * Simple click: clear selection (resetting foreground to darker); set clicked
309 * button foreground to brighter
311 * Finally, synchronize the colour chooser to the colour of the first button
312 * in the selected set.
316 public void colourButtonPressed(MouseEvent e)
318 JButton pressed = (JButton) e.getSource();
322 JButton start, end = (JButton) e.getSource();
323 if (selectedButtons.size() > 0)
325 start = selectedButtons.get(selectedButtons.size() - 1);
329 start = (JButton) e.getSource();
332 int startIndex = 0, endIndex = 0;
333 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
335 if (buttonPanel.getComponent(b) == start)
339 if (buttonPanel.getComponent(b) == end)
345 if (startIndex > endIndex)
347 int temp = startIndex;
348 startIndex = endIndex;
352 for (int b = startIndex; b <= endIndex; b++)
354 JButton button = (JButton) buttonPanel.getComponent(b);
355 if (!selectedButtons.contains(button))
357 button.setForeground(ColorUtils.brighterThan(button
359 selectedButtons.add(button);
363 else if (!e.isControlDown())
365 for (int b = 0; b < selectedButtons.size(); b++)
367 JButton button = selectedButtons.get(b);
368 button.setForeground(ColorUtils.darkerThan(button.getBackground()));
370 selectedButtons.clear();
371 pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
372 selectedButtons.add(pressed);
375 else if (e.isControlDown())
377 if (selectedButtons.contains(pressed))
379 pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
380 selectedButtons.remove(pressed);
384 pressed.setForeground(ColorUtils.brighterThan(pressed
386 selectedButtons.add(pressed);
390 if (selectedButtons.size() > 0)
392 colorChooser.setColor((selectedButtons.get(0)).getBackground());
397 * A helper method to update or make a colour button, whose background colour
398 * is the associated colour, and text colour a darker shade of the same. If
399 * the button is already in the list, then its text and margins are updated,
400 * if not then it is created and added. This method supports toggling between
401 * case-sensitive and case-insensitive button panels. The case-sensitive
402 * version has abbreviated button text in order to fit in more buttons.
409 * the button's position in the list
411 JButton makeButton(String label, String residue, List<JButton> buttons,
414 final JButton button;
417 if (buttonIndex < buttons.size())
419 button = buttons.get(buttonIndex);
420 col = button.getBackground();
424 button = new JButton();
425 button.addMouseListener(new MouseAdapter()
428 public void mouseClicked(MouseEvent e)
430 colourButtonPressed(e);
437 * make initial button colour that of the current colour scheme,
438 * if it is a simple per-residue colouring, else white
441 if (oldColourScheme != null && oldColourScheme.isSimple())
443 col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
448 if (caseSensitive.isSelected())
450 button.setMargin(new Insets(2, 2, 2, 2));
454 button.setMargin(new Insets(2, 14, 2, 14));
457 button.setOpaque(true); // required for the next line to have effect
458 button.setBackground(col);
459 button.setText(label);
460 button.setForeground(ColorUtils.darkerThan(col));
461 button.setFont(VERDANA_BOLD_10);
467 * On 'OK', check that at least one colour has been assigned to a residue (and
468 * if not issue a warning), and apply the chosen colour scheme and close the
472 protected void okButton_actionPerformed()
474 if (isNoSelectionMade())
476 JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
477 .getString("label.no_colour_selection_in_scheme"),
478 MessageManager.getString("label.no_colour_selection_warn"),
479 JvOptionPane.WARNING_MESSAGE);
483 applyButton_actionPerformed();
487 frame.setClosed(true);
488 } catch (Exception ex)
495 * Returns true if the user has not made any colour selection (including if
496 * 'case-sensitive' selected and no lower-case colour chosen).
500 protected boolean isNoSelectionMade()
502 final boolean noUpperCaseSelected = upperCaseButtons == null
503 || upperCaseButtons.isEmpty();
504 final boolean noLowerCaseSelected = caseSensitive.isSelected()
505 && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
506 final boolean noSelectionMade = noUpperCaseSelected
507 || noLowerCaseSelected;
508 return noSelectionMade;
512 * Applies the current colour scheme to the alignment, sequence group or
516 protected void applyButton_actionPerformed()
518 if (isNoSelectionMade())
520 JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
521 .getString("label.no_colour_selection_in_scheme"),
522 MessageManager.getString("label.no_colour_selection_warn"),
523 JvOptionPane.WARNING_MESSAGE);
526 UserColourScheme ucs = getSchemeFromButtons();
528 if (seqGroup != null)
530 seqGroup.setColourScheme(ucs);
531 ap.paintAlignment(true);
535 ap.alignFrame.changeColour(ucs);
537 else if (structureViewer != null)
539 structureViewer.setJalviewColourScheme(ucs);
543 UserColourScheme getSchemeFromButtons()
546 Color[] newColours = new Color[24];
548 int length = upperCaseButtons.size();
552 for (JButton btn : upperCaseButtons)
554 newColours[i] = btn.getBackground();
560 for (int i = 0; i < 24; i++)
562 JButton button = upperCaseButtons.get(i);
563 newColours[i] = button.getBackground();
567 UserColourScheme ucs = new UserColourScheme(newColours);
568 ucs.setName(schemeName.getText());
570 if (caseSensitive.isSelected())
572 newColours = new Color[23];
573 length = lowerCaseButtons.size();
577 for (JButton btn : lowerCaseButtons)
579 newColours[i] = btn.getBackground();
585 for (int i = 0; i < 23; i++)
587 JButton button = lowerCaseButtons.get(i);
588 newColours[i] = button.getBackground();
591 ucs.setLowerCaseColours(newColours);
604 protected void loadbutton_actionPerformed(ActionEvent e)
606 upperCaseButtons = new ArrayList<JButton>();
607 lowerCaseButtons = new ArrayList<JButton>();
609 JalviewFileChooser chooser = new JalviewFileChooser("jc",
610 "Jalview User Colours");
611 chooser.setFileView(new JalviewFileView());
612 chooser.setDialogTitle(MessageManager
613 .getString("label.load_colour_scheme"));
614 chooser.setToolTipText(MessageManager.getString("action.load"));
616 int value = chooser.showOpenDialog(this);
618 if (value != JalviewFileChooser.APPROVE_OPTION)
622 File choice = chooser.getSelectedFile();
623 Cache.setProperty(LAST_DIRECTORY, choice.getParent());
625 UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
627 Color[] colors = ucs.getColours();
628 schemeName.setText(ucs.getSchemeName());
630 if (ucs.getLowerCaseColours() != null)
632 caseSensitive.setSelected(true);
633 lcaseColour.setEnabled(true);
634 resetButtonPanel(true);
635 for (int i = 0; i < lowerCaseButtons.size(); i++)
637 JButton button = lowerCaseButtons.get(i);
638 button.setBackground(ucs.getLowerCaseColours()[i]);
643 caseSensitive.setSelected(false);
644 lcaseColour.setEnabled(false);
645 resetButtonPanel(false);
648 for (int i = 0; i < upperCaseButtons.size(); i++)
650 JButton button = upperCaseButtons.get(i);
651 button.setBackground(colors[i]);
654 addNewColourScheme(choice.getPath());
658 * Loads the user-defined colour scheme from the first file listed in property
659 * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
663 public static UserColourScheme loadDefaultColours()
665 UserColourScheme ret = null;
667 String colours = Cache.getProperty(USER_DEFINED_COLOURS);
670 if (colours.indexOf("|") > -1)
672 colours = colours.substring(0, colours.indexOf("|"));
674 ret = ColourSchemeLoader.loadColourScheme(colours);
679 ret = new UserColourScheme("white");
692 protected void savebutton_actionPerformed(ActionEvent e)
694 String name = schemeName.getText().trim();
695 if (name.length() < 1)
697 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
698 .getString("label.user_colour_scheme_must_have_name"),
699 MessageManager.getString("label.no_name_colour_scheme"),
700 JvOptionPane.WARNING_MESSAGE);
704 if (ColourSchemes.getInstance().nameExists(name))
706 int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
707 MessageManager.formatMessage(
708 "label.colour_scheme_exists_overwrite", new Object[] {
710 MessageManager.getString("label.duplicate_scheme_name"),
711 JvOptionPane.YES_NO_OPTION);
712 if (reply != JvOptionPane.YES_OPTION)
716 ColourSchemes.getInstance().removeColourScheme(name);
718 JalviewFileChooser chooser = new JalviewFileChooser("jc",
719 "Jalview User Colours");
721 JalviewFileView fileView = new JalviewFileView();
722 chooser.setFileView(fileView);
723 chooser.setDialogTitle(MessageManager
724 .getString("label.save_colour_scheme"));
725 chooser.setToolTipText(MessageManager.getString("action.save"));
727 int value = chooser.showSaveDialog(this);
729 if (value == JalviewFileChooser.APPROVE_OPTION)
731 File file = chooser.getSelectedFile();
732 addNewColourScheme(file.getPath());
738 * Adds the current colour scheme to the Jalview properties file so it is
739 * loaded on next startup, and updates the Colour menu in the parent
740 * AlignFrame (if there is one). Note this action does not including applying
745 protected void addNewColourScheme(String filePath)
748 * update the delimited list of user defined colour files in
749 * Jalview property USER_DEFINED_COLOURS
751 String defaultColours = Cache
752 .getDefault(USER_DEFINED_COLOURS, filePath);
753 if (defaultColours.indexOf(filePath) == -1)
755 if (defaultColours.length() > 0)
757 defaultColours = defaultColours.concat("|");
759 defaultColours = defaultColours.concat(filePath);
761 Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
764 * construct and register the colour scheme
766 UserColourScheme ucs = getSchemeFromButtons();
767 ColourSchemes.getInstance().registerColourScheme(ucs);
770 * update the Colour menu items
774 ap.alignFrame.buildColourMenu();
779 * Saves the colour scheme to file in XML format
783 protected void saveToFile(File toFile)
786 * build a Java model of colour scheme as XML, and
789 JalviewUserColours ucs = new JalviewUserColours();
790 ucs.setSchemeName(schemeName.getText());
793 PrintWriter out = new PrintWriter(new OutputStreamWriter(
794 new FileOutputStream(toFile), "UTF-8"));
796 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
798 JButton button = (JButton) buttonPanel.getComponent(i);
799 Colour col = new Colour();
800 col.setName(button.getText());
801 col.setRGB(Format.getHexString(button.getBackground()));
806 } catch (Exception ex)
808 ex.printStackTrace();
813 * On cancel, restores the colour scheme before the dialogue was opened
818 protected void cancelButton_actionPerformed(ActionEvent e)
822 if (seqGroup != null)
824 seqGroup.setColourScheme(oldColourScheme);
828 ap.alignFrame.changeColour(oldColourScheme);
830 ap.paintAlignment(true);
833 if (structureViewer != null)
835 structureViewer.setJalviewColourScheme(oldColourScheme);
840 frame.setClosed(true);
841 } catch (Exception ex)
847 public void caseSensitive_actionPerformed(ActionEvent e)
849 boolean selected = caseSensitive.isSelected();
850 resetButtonPanel(selected);
851 lcaseColour.setEnabled(selected);