2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.datamodel.SequenceGroup;
25 import jalview.io.JalviewFileChooser;
26 import jalview.jbgui.GUserDefinedColours;
27 import jalview.schemes.ColourSchemeI;
28 import jalview.schemes.ResidueProperties;
29 import jalview.schemes.UserColourScheme;
30 import jalview.util.ColorUtils;
31 import jalview.util.MessageManager;
33 import java.awt.Color;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.MouseEvent;
38 import java.io.FileInputStream;
39 import java.io.FileOutputStream;
40 import java.io.InputStreamReader;
41 import java.io.OutputStreamWriter;
42 import java.io.PrintWriter;
43 import java.util.ArrayList;
44 import java.util.Hashtable;
45 import java.util.StringTokenizer;
47 import javax.swing.JButton;
48 import javax.swing.JInternalFrame;
49 import javax.swing.JOptionPane;
50 import javax.swing.event.ChangeEvent;
51 import javax.swing.event.ChangeListener;
54 * This panel allows the user to assign colours to Amino Acid residue codes, and
55 * save the colour scheme.
57 * @author Andrew Waterhouse
58 * @author Mungo Carstairs
60 public class UserDefinedColours extends GUserDefinedColours implements
63 private static final int MY_FRAME_HEIGHT = 420;
65 private static final int MY_FRAME_WIDTH = 810;
67 private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
71 SequenceGroup seqGroup;
73 ArrayList<JButton> selectedButtons;
75 ColourSchemeI oldColourScheme;
79 JalviewStructureDisplayI jmol;
81 ArrayList<JButton> upperCaseButtons;
83 ArrayList<JButton> lowerCaseButtons;
86 * Creates a new UserDefinedColours object.
93 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
97 lcaseColour.setEnabled(false);
102 if (seqGroup != null)
104 oldColourScheme = seqGroup.cs;
108 oldColourScheme = ap.av.getGlobalColourScheme();
111 if (oldColourScheme instanceof UserColourScheme)
113 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
114 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
116 caseSensitive.setSelected(true);
117 lcaseColour.setEnabled(true);
118 resetButtonPanel(true);
122 resetButtonPanel(false);
127 resetButtonPanel(false);
133 public UserDefinedColours(JalviewStructureDisplayI jmol,
139 colorChooser.getSelectionModel().addChangeListener(this);
141 oldColourScheme = oldcs;
143 if (oldColourScheme instanceof UserColourScheme)
145 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
148 resetButtonPanel(false);
156 colorChooser.getSelectionModel().addChangeListener(this);
157 frame = new JInternalFrame();
158 frame.setContentPane(this);
159 Desktop.addInternalFrame(frame,
160 MessageManager.getString("label.user_defined_colours"),
161 MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
163 if (seqGroup != null)
165 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
169 void resetButtonPanel(boolean caseSensitive)
171 buttonPanel.removeAll();
173 if (upperCaseButtons == null)
175 upperCaseButtons = new ArrayList<JButton>();
180 for (int i = 0; i < 20; i++)
184 label = ResidueProperties.aa[i];
188 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
192 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
195 buttonPanel.add(button);
198 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
199 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
200 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
201 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
205 gridLayout.setRows(6);
206 gridLayout.setColumns(4);
210 gridLayout.setRows(7);
212 gridLayout.setColumns(cols + 1);
214 if (lowerCaseButtons == null)
216 lowerCaseButtons = new ArrayList<JButton>();
219 for (int i = 0; i < 20; i++)
221 int row = i / cols + 1;
222 int index = (row * cols) + i;
223 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
224 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
226 buttonPanel.add(button, index);
232 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
233 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
234 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
237 // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
239 if (this.frame != null)
241 int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
243 this.frame.setSize(newWidth, this.frame.getHeight());
246 buttonPanel.validate();
257 public void stateChanged(ChangeEvent evt)
259 if (selectedButtons != null)
261 JButton button = null;
262 final Color newColour = colorChooser.getColor();
263 for (int i = 0; i < selectedButtons.size(); i++)
265 button = selectedButtons.get(i);
266 button.setBackground(newColour);
267 button.setForeground(ColorUtils.brighterThan(newColour));
269 if (button == lcaseColour)
271 for (int i = 0; i < lowerCaseButtons.size(); i++)
273 button = lowerCaseButtons.get(i);
274 button.setBackground(newColour);
275 button.setForeground(ColorUtils.brighterThan(button
283 * Performs actions when a residue button is clicked. This manages the button
284 * selection set (highlighted by brighter foreground text).
286 * On select button(s) with Ctrl/click or Shift/click: set button foreground
287 * text to brighter than background.
289 * On unselect button(s) with Ctrl/click on selected, or click to release
290 * current selection: reset foreground text to darker than background.
292 * Simple click: clear selection (resetting foreground to darker); set clicked
293 * button foreground to brighter
295 * Finally, synchronize the colour chooser to the colour of the first button
296 * in the selected set.
300 public void colourButtonPressed(MouseEvent e)
302 if (selectedButtons == null)
304 selectedButtons = new ArrayList<JButton>();
307 JButton pressed = (JButton) e.getSource();
311 JButton start, end = (JButton) e.getSource();
312 if (selectedButtons.size() > 0)
314 start = selectedButtons.get(selectedButtons.size() - 1);
318 start = (JButton) e.getSource();
321 int startIndex = 0, endIndex = 0;
322 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
324 if (buttonPanel.getComponent(b) == start)
328 if (buttonPanel.getComponent(b) == end)
334 if (startIndex > endIndex)
336 int temp = startIndex;
337 startIndex = endIndex;
341 for (int b = startIndex; b <= endIndex; b++)
343 JButton button = (JButton) buttonPanel.getComponent(b);
344 if (!selectedButtons.contains(button))
346 button.setForeground(ColorUtils.brighterThan(button
348 selectedButtons.add(button);
352 else if (!e.isControlDown())
354 for (int b = 0; b < selectedButtons.size(); b++)
356 JButton button = selectedButtons.get(b);
357 button.setForeground(ColorUtils.darkerThan(button.getBackground()));
359 selectedButtons.clear();
360 pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
361 selectedButtons.add(pressed);
364 else if (e.isControlDown())
366 if (selectedButtons.contains(pressed))
368 pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
369 selectedButtons.remove(pressed);
373 pressed.setForeground(ColorUtils.brighterThan(pressed
375 selectedButtons.add(pressed);
379 if (selectedButtons.size() > 0)
381 colorChooser.setColor((selectedButtons.get(0)).getBackground());
393 JButton makeButton(String label, String aa,
394 ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
396 final JButton button;
399 if (buttonIndex < caseSensitiveButtons.size())
401 button = caseSensitiveButtons.get(buttonIndex);
402 col = button.getBackground();
406 button = new JButton();
407 button.addMouseListener(new java.awt.event.MouseAdapter()
410 public void mouseClicked(MouseEvent e)
412 colourButtonPressed(e);
416 caseSensitiveButtons.add(button);
419 if (oldColourScheme != null)
423 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
424 } catch (Exception ex)
430 if (caseSensitive.isSelected())
432 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
436 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
439 button.setOpaque(true); // required for the next line to have effect
440 button.setBackground(col);
441 button.setText(label);
442 button.setForeground(ColorUtils.darkerThan(col));
443 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
455 protected void okButton_actionPerformed(ActionEvent e)
457 applyButton_actionPerformed(null);
461 frame.setClosed(true);
462 } catch (Exception ex)
474 protected void applyButton_actionPerformed(ActionEvent e)
476 UserColourScheme ucs = getSchemeFromButtons();
477 ucs.setName(schemeName.getText());
479 if (seqGroup != null)
482 ap.paintAlignment(true);
486 ap.alignFrame.changeColour(ucs);
488 else if (jmol != null)
490 jmol.setJalviewColourScheme(ucs);
494 UserColourScheme getSchemeFromButtons()
497 Color[] newColours = new Color[24];
499 for (int i = 0; i < 24; i++)
501 JButton button = upperCaseButtons.get(i);
502 newColours[i] = button.getBackground();
505 UserColourScheme ucs = new UserColourScheme(newColours);
507 if (caseSensitive.isSelected())
509 newColours = new Color[23];
510 for (int i = 0; i < 23; i++)
512 JButton button = lowerCaseButtons.get(i);
513 newColours[i] = button.getBackground();
515 ucs.setLowerCaseColours(newColours);
520 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
533 protected void loadbutton_actionPerformed(ActionEvent e)
535 upperCaseButtons = new ArrayList<JButton>();
536 lowerCaseButtons = new ArrayList<JButton>();
538 JalviewFileChooser chooser = new JalviewFileChooser(
539 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
540 { "jc" }, new String[]
541 { "Jalview User Colours" }, "Jalview User Colours");
542 chooser.setFileView(new jalview.io.JalviewFileView());
543 chooser.setDialogTitle(MessageManager
544 .getString("label.load_colour_scheme"));
545 chooser.setToolTipText(MessageManager.getString("action.load"));
547 int value = chooser.showOpenDialog(this);
549 if (value == JalviewFileChooser.APPROVE_OPTION)
551 File choice = chooser.getSelectedFile();
552 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
553 String defaultColours = jalview.bin.Cache.getDefault(
554 "USER_DEFINED_COLOURS", choice.getPath());
555 if (defaultColours.indexOf(choice.getPath()) == -1)
557 defaultColours = defaultColours.concat("|")
558 .concat(choice.getPath());
561 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
563 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
564 Color[] colors = ucs.getColours();
565 schemeName.setText(ucs.getName());
567 if (ucs.getLowerCaseColours() != null)
569 caseSensitive.setSelected(true);
570 lcaseColour.setEnabled(true);
571 resetButtonPanel(true);
572 for (int i = 0; i < lowerCaseButtons.size(); i++)
574 JButton button = lowerCaseButtons.get(i);
575 button.setBackground(ucs.getLowerCaseColours()[i]);
581 caseSensitive.setSelected(false);
582 lcaseColour.setEnabled(false);
583 resetButtonPanel(false);
586 for (int i = 0; i < upperCaseButtons.size(); i++)
588 JButton button = upperCaseButtons.get(i);
589 button.setBackground(colors[i]);
598 * @return DOCUMENT ME!
600 public static UserColourScheme loadDefaultColours()
602 UserColourScheme ret = null;
604 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
607 if (colours.indexOf("|") > -1)
609 colours = colours.substring(0, colours.indexOf("|"));
612 ret = loadColours(colours);
617 Color[] newColours = new Color[24];
618 for (int i = 0; i < 24; i++)
620 newColours[i] = Color.white;
622 ret = new UserColourScheme(newColours);
634 * @return DOCUMENT ME!
636 static UserColourScheme loadColours(String file)
638 UserColourScheme ucs = null;
639 Color[] newColours = null;
642 InputStreamReader in = new InputStreamReader(
643 new FileInputStream(file), "UTF-8");
645 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
647 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
649 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
652 newColours = new Color[24];
654 Color[] lowerCase = null;
655 boolean caseSensitive = false;
659 for (int i = 0; i < jucs.getColourCount(); i++)
661 name = jucs.getColour(i).getName();
662 if (ResidueProperties.aa3Hash.containsKey(name))
664 index = ((Integer) ResidueProperties.aa3Hash.get(name))
669 index = ResidueProperties.aaIndex[name.charAt(0)];
676 if (name.toLowerCase().equals(name))
678 if (lowerCase == null)
680 lowerCase = new Color[23];
682 caseSensitive = true;
683 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
688 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
693 if (newColours != null)
695 ucs = new UserColourScheme(newColours);
696 ucs.setName(jucs.getSchemeName());
699 ucs.setLowerCaseColours(lowerCase);
703 } catch (Exception ex)
705 // Could be Archive Jalview format
708 InputStreamReader in = new InputStreamReader(new FileInputStream(
711 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
713 jucs = jucs.unmarshal(in);
715 newColours = new Color[jucs.getColourCount()];
717 for (int i = 0; i < 24; i++)
719 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
722 if (newColours != null)
724 ucs = new UserColourScheme(newColours);
725 ucs.setName(jucs.getSchemeName());
727 } catch (Exception ex2)
729 ex2.printStackTrace();
732 if (newColours == null)
734 System.out.println("Error loading User ColourFile\n" + ex);
748 protected void savebutton_actionPerformed(ActionEvent e)
750 if (schemeName.getText().trim().length() < 1)
752 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
753 .getString("label.user_colour_scheme_must_have_name"),
754 MessageManager.getString("label.no_name_colour_scheme"),
755 JOptionPane.WARNING_MESSAGE);
759 if (userColourSchemes != null
760 && userColourSchemes.containsKey(schemeName.getText()))
762 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
763 MessageManager.formatMessage(
764 "label.colour_scheme_exists_overwrite", new Object[]
765 { schemeName.getText(), schemeName.getText() }),
766 MessageManager.getString("label.duplicate_scheme_name"),
767 JOptionPane.YES_NO_OPTION);
768 if (reply != JOptionPane.YES_OPTION)
773 userColourSchemes.remove(schemeName.getText());
775 JalviewFileChooser chooser = new JalviewFileChooser(
776 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
777 { "jc" }, new String[]
778 { "Jalview User Colours" }, "Jalview User Colours");
780 chooser.setFileView(new jalview.io.JalviewFileView());
781 chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
782 chooser.setToolTipText(MessageManager.getString("action.save"));
784 int value = chooser.showSaveDialog(this);
786 if (value == JalviewFileChooser.APPROVE_OPTION)
788 String choice = chooser.getSelectedFile().getPath();
789 String defaultColours = jalview.bin.Cache.getDefault(
790 "USER_DEFINED_COLOURS", choice);
791 if (defaultColours.indexOf(choice) == -1)
793 if (defaultColours.length() > 0)
795 defaultColours = defaultColours.concat("|");
797 defaultColours = defaultColours.concat(choice);
800 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
802 ap.alignFrame.updateUserColourMenu();
804 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
806 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
808 ucs.setSchemeName(schemeName.getText());
811 PrintWriter out = new PrintWriter(new OutputStreamWriter(
812 new FileOutputStream(choice), "UTF-8"));
814 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
816 JButton button = (JButton) buttonPanel.getComponent(i);
817 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
818 col.setName(button.getText());
819 col.setRGB(jalview.util.Format.getHexString(button
826 } catch (Exception ex)
828 ex.printStackTrace();
840 protected void cancelButton_actionPerformed(ActionEvent e)
844 if (seqGroup != null)
846 seqGroup.cs = oldColourScheme;
850 ap.av.setGlobalColourScheme(oldColourScheme);
852 ap.paintAlignment(true);
857 jmol.setJalviewColourScheme(oldColourScheme);
862 frame.setClosed(true);
863 } catch (Exception ex)
868 static Hashtable userColourSchemes;
870 public static Hashtable getUserColourSchemes()
872 return userColourSchemes;
875 public static void initUserColourSchemes(String files)
877 userColourSchemes = new Hashtable();
879 if (files == null || files.length() == 0)
884 // In case colours can't be loaded, we'll remove them
885 // from the default list here.
886 StringBuffer coloursFound = new StringBuffer();
887 StringTokenizer st = new StringTokenizer(files, "|");
888 while (st.hasMoreElements())
890 String file = st.nextToken();
893 UserColourScheme ucs = loadColours(file);
896 if (coloursFound.length() > 0)
898 coloursFound.append("|");
900 coloursFound.append(file);
901 userColourSchemes.put(ucs.getName(), ucs);
903 } catch (Exception ex)
905 System.out.println("Error loading User ColourFile\n" + ex);
908 if (!files.equals(coloursFound.toString()))
910 if (coloursFound.toString().length() > 1)
912 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
913 coloursFound.toString());
917 jalview.bin.Cache.applicationProperties
918 .remove("USER_DEFINED_COLOURS");
923 public static void removeColourFromDefaults(String target)
925 // The only way to find colours by name is to load them in
926 // In case colours can't be loaded, we'll remove them
927 // from the default list here.
929 userColourSchemes = new Hashtable();
931 StringBuffer coloursFound = new StringBuffer();
932 StringTokenizer st = new StringTokenizer(
933 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
935 while (st.hasMoreElements())
937 String file = st.nextToken();
940 UserColourScheme ucs = loadColours(file);
941 if (ucs != null && !ucs.getName().equals(target))
943 if (coloursFound.length() > 0)
945 coloursFound.append("|");
947 coloursFound.append(file);
948 userColourSchemes.put(ucs.getName(), ucs);
950 } catch (Exception ex)
952 System.out.println("Error loading User ColourFile\n" + ex);
956 if (coloursFound.toString().length() > 1)
958 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
959 coloursFound.toString());
963 jalview.bin.Cache.applicationProperties
964 .remove("USER_DEFINED_COLOURS");
970 public void caseSensitive_actionPerformed(ActionEvent e)
972 resetButtonPanel(caseSensitive.isSelected());
973 lcaseColour.setEnabled(caseSensitive.isSelected());
977 public void lcaseColour_actionPerformed(ActionEvent e)
979 if (selectedButtons == null)
981 selectedButtons = new ArrayList<JButton>();
985 selectedButtons.clear();
987 selectedButtons.add(lcaseColour);