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.MessageManager;
32 import java.awt.Color;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.MouseEvent;
37 import java.io.FileInputStream;
38 import java.io.FileOutputStream;
39 import java.io.InputStreamReader;
40 import java.io.OutputStreamWriter;
41 import java.io.PrintWriter;
42 import java.util.Hashtable;
43 import java.util.StringTokenizer;
44 import java.util.Vector;
46 import javax.swing.JButton;
47 import javax.swing.JInternalFrame;
48 import javax.swing.JOptionPane;
49 import javax.swing.event.ChangeEvent;
50 import javax.swing.event.ChangeListener;
58 public class UserDefinedColours extends GUserDefinedColours implements
61 private static final int MY_FRAME_HEIGHT = 420;
62 private static final int MY_FRAME_WIDTH = 810;
63 private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
67 SequenceGroup seqGroup;
69 Vector selectedButtons;
71 ColourSchemeI oldColourScheme;
75 JalviewStructureDisplayI jmol;
77 Vector upperCaseButtons;
79 Vector lowerCaseButtons;
82 * Creates a new UserDefinedColours object.
89 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
93 lcaseColour.setEnabled(false);
100 oldColourScheme = seqGroup.cs;
104 oldColourScheme = ap.av.getGlobalColourScheme();
107 if (oldColourScheme instanceof UserColourScheme)
109 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
110 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
112 caseSensitive.setSelected(true);
113 lcaseColour.setEnabled(true);
114 resetButtonPanel(true);
118 resetButtonPanel(false);
123 resetButtonPanel(false);
129 public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs)
134 colorChooser.getSelectionModel().addChangeListener(this);
136 oldColourScheme = oldcs;
138 if (oldColourScheme instanceof UserColourScheme)
140 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
143 resetButtonPanel(false);
151 colorChooser.getSelectionModel().addChangeListener(this);
152 frame = new JInternalFrame();
153 frame.setContentPane(this);
154 Desktop.addInternalFrame(frame,
155 MessageManager.getString("label.user_defined_colours"), MY_FRAME_WIDTH,
156 MY_FRAME_HEIGHT, true);
158 if (seqGroup != null)
160 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
164 void resetButtonPanel(boolean caseSensitive)
166 buttonPanel.removeAll();
168 if (upperCaseButtons == null)
170 upperCaseButtons = new Vector();
175 for (int i = 0; i < 20; i++)
179 label = ResidueProperties.aa[i];
183 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
187 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
190 buttonPanel.add(button);
193 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
194 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
195 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
196 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
200 gridLayout.setRows(6);
201 gridLayout.setColumns(4);
205 gridLayout.setRows(7);
207 gridLayout.setColumns(cols + 1);
209 if (lowerCaseButtons == null)
211 lowerCaseButtons = new Vector();
214 for (int i = 0; i < 20; i++)
216 int row = i / cols + 1;
217 int index = (row * cols) + i;
218 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
219 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
221 buttonPanel.add(button, index);
227 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
228 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
229 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
232 // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA codes
233 if (this.frame != null) {
234 int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE : MY_FRAME_WIDTH;
235 this.frame.setSize(newWidth, this.frame.getHeight());
238 buttonPanel.validate();
248 public void stateChanged(ChangeEvent evt)
250 if (selectedButtons != null)
252 JButton button = null;
253 for (int i = 0; i < selectedButtons.size(); i++)
255 button = (JButton) selectedButtons.elementAt(i);
256 button.setBackground(colorChooser.getColor());
257 button.setForeground(brighterThan(button.getBackground()));
259 if (button == lcaseColour)
261 for (int i = 0; i < lowerCaseButtons.size(); i++)
263 button = (JButton) lowerCaseButtons.elementAt(i);
264 button.setBackground(colorChooser.getColor());
265 button.setForeground(brighterThan(button.getBackground()));
277 public void colourButtonPressed(MouseEvent e)
279 if (selectedButtons == null)
281 selectedButtons = new Vector();
284 JButton pressed = (JButton) e.getSource();
288 JButton start, end = (JButton) e.getSource();
289 if (selectedButtons.size() > 0)
291 start = (JButton) selectedButtons
292 .elementAt(selectedButtons.size() - 1);
296 start = (JButton) e.getSource();
299 int startIndex = 0, endIndex = 0;
300 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
302 if (buttonPanel.getComponent(b) == start)
306 if (buttonPanel.getComponent(b) == end)
312 if (startIndex > endIndex)
314 int temp = startIndex;
315 startIndex = endIndex;
319 for (int b = startIndex; b <= endIndex; b++)
321 JButton button = (JButton) buttonPanel.getComponent(b);
322 if (!selectedButtons.contains(button))
324 button.setForeground(brighterThan(button.getBackground()));
325 selectedButtons.add(button);
329 else if (!e.isControlDown())
331 for (int b = 0; b < selectedButtons.size(); b++)
333 JButton button = (JButton) selectedButtons.elementAt(b);
334 button.setForeground(darkerThan(button.getBackground()));
336 selectedButtons.clear();
337 pressed.setForeground(brighterThan(pressed.getBackground()));
338 selectedButtons.addElement(pressed);
341 else if (e.isControlDown())
343 if (selectedButtons.contains(pressed))
345 pressed.setForeground(darkerThan(pressed.getBackground()));
346 selectedButtons.remove(pressed);
350 pressed.setForeground(brighterThan(pressed.getBackground()));
351 selectedButtons.addElement(pressed);
355 if (selectedButtons.size() > 0)
357 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
370 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
373 final JButton button;
376 if (buttonIndex < caseSensitiveButtons.size())
378 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
379 col = button.getBackground();
383 button = new JButton();
384 button.addMouseListener(new java.awt.event.MouseAdapter()
386 public void mouseClicked(MouseEvent e)
388 colourButtonPressed(e);
392 caseSensitiveButtons.addElement(button);
395 if (oldColourScheme != null)
399 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
400 } catch (Exception ex)
406 if (caseSensitive.isSelected())
408 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
412 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
415 button.setOpaque(true); // required for the next line to have effect
416 button.setBackground(col);
417 button.setText(label);
418 button.setForeground(darkerThan(col));
419 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
425 * Returns a colour three shades darker.
427 * We use darker text to indicate unselected buttons, lighter text for selected.
431 public static Color darkerThan(Color col) {
432 return col.darker().darker().darker();
436 * Returns a colour three shades brighter.
438 * We use darker text to indicate unselected buttons, lighter text for selected.
442 public static Color brighterThan(Color col) {
443 return col.brighter().brighter().brighter();
452 protected void okButton_actionPerformed(ActionEvent e)
454 applyButton_actionPerformed(null);
458 frame.setClosed(true);
459 } catch (Exception ex)
470 protected void applyButton_actionPerformed(ActionEvent e)
472 UserColourScheme ucs = getSchemeFromButtons();
473 ucs.setName(schemeName.getText());
475 if (seqGroup != null)
478 ap.paintAlignment(true);
482 ap.alignFrame.changeColour(ucs);
484 else if (jmol != null)
486 jmol.setJalviewColourScheme(ucs);
490 UserColourScheme getSchemeFromButtons()
493 Color[] newColours = new Color[24];
495 for (int i = 0; i < 24; i++)
497 JButton button = (JButton) upperCaseButtons.elementAt(i);
498 newColours[i] = button.getBackground();
501 UserColourScheme ucs = new UserColourScheme(newColours);
503 if (caseSensitive.isSelected())
505 newColours = new Color[23];
506 for (int i = 0; i < 23; i++)
508 JButton button = (JButton) lowerCaseButtons.elementAt(i);
509 newColours[i] = button.getBackground();
511 ucs.setLowerCaseColours(newColours);
516 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
528 protected void loadbutton_actionPerformed(ActionEvent e)
530 upperCaseButtons = new Vector();
531 lowerCaseButtons = new Vector();
533 JalviewFileChooser chooser = new JalviewFileChooser(
534 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
535 { "jc" }, new String[]
536 { "Jalview User Colours" }, "Jalview User Colours");
537 chooser.setFileView(new jalview.io.JalviewFileView());
538 chooser.setDialogTitle(MessageManager
539 .getString("label.load_colour_scheme"));
540 chooser.setToolTipText(MessageManager.getString("action.load"));
542 int value = chooser.showOpenDialog(this);
544 if (value == JalviewFileChooser.APPROVE_OPTION)
546 File choice = chooser.getSelectedFile();
547 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
548 String defaultColours = jalview.bin.Cache.getDefault(
549 "USER_DEFINED_COLOURS", choice.getPath());
550 if (defaultColours.indexOf(choice.getPath()) == -1)
552 defaultColours = defaultColours.concat("|")
553 .concat(choice.getPath());
556 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
558 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
559 Color[] colors = ucs.getColours();
560 schemeName.setText(ucs.getName());
562 if (ucs.getLowerCaseColours() != null)
564 caseSensitive.setSelected(true);
565 lcaseColour.setEnabled(true);
566 resetButtonPanel(true);
567 for (int i = 0; i < lowerCaseButtons.size(); i++)
569 JButton button = (JButton) lowerCaseButtons.elementAt(i);
570 button.setBackground(ucs.getLowerCaseColours()[i]);
576 caseSensitive.setSelected(false);
577 lcaseColour.setEnabled(false);
578 resetButtonPanel(false);
581 for (int i = 0; i < upperCaseButtons.size(); i++)
583 JButton button = (JButton) upperCaseButtons.elementAt(i);
584 button.setBackground(colors[i]);
593 * @return DOCUMENT ME!
595 public static UserColourScheme loadDefaultColours()
597 UserColourScheme ret = null;
599 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
602 if (colours.indexOf("|") > -1)
604 colours = colours.substring(0, colours.indexOf("|"));
607 ret = loadColours(colours);
612 Color[] newColours = new Color[24];
613 for (int i = 0; i < 24; i++)
615 newColours[i] = Color.white;
617 ret = new UserColourScheme(newColours);
629 * @return DOCUMENT ME!
631 static UserColourScheme loadColours(String file)
633 UserColourScheme ucs = null;
634 Color[] newColours = null;
637 InputStreamReader in = new InputStreamReader(
638 new FileInputStream(file), "UTF-8");
640 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
642 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
644 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
647 newColours = new Color[24];
649 Color[] lowerCase = null;
650 boolean caseSensitive = false;
654 for (int i = 0; i < jucs.getColourCount(); i++)
656 name = jucs.getColour(i).getName();
657 if (ResidueProperties.aa3Hash.containsKey(name))
659 index = ((Integer) ResidueProperties.aa3Hash.get(name))
664 index = ResidueProperties.aaIndex[name.charAt(0)];
671 if (name.toLowerCase().equals(name))
673 if (lowerCase == null)
675 lowerCase = new Color[23];
677 caseSensitive = true;
678 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
683 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
688 if (newColours != null)
690 ucs = new UserColourScheme(newColours);
691 ucs.setName(jucs.getSchemeName());
694 ucs.setLowerCaseColours(lowerCase);
698 } catch (Exception ex)
700 // Could be Archive Jalview format
703 InputStreamReader in = new InputStreamReader(new FileInputStream(
706 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
708 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
710 newColours = new Color[jucs.getColourCount()];
712 for (int i = 0; i < 24; i++)
714 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
717 if (newColours != null)
719 ucs = new UserColourScheme(newColours);
720 ucs.setName(jucs.getSchemeName());
722 } catch (Exception ex2)
724 ex2.printStackTrace();
727 if (newColours == null)
729 System.out.println("Error loading User ColourFile\n" + ex);
742 protected void savebutton_actionPerformed(ActionEvent e)
744 if (schemeName.getText().trim().length() < 1)
746 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
747 .getString("label.user_colour_scheme_must_have_name"),
748 MessageManager.getString("label.no_name_colour_scheme"),
749 JOptionPane.WARNING_MESSAGE);
753 if (userColourSchemes != null
754 && userColourSchemes.containsKey(schemeName.getText()))
756 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
757 MessageManager.formatMessage(
758 "label.colour_scheme_exists_overwrite", new String[]
759 { schemeName.getText(), schemeName.getText() }),
760 MessageManager.getString("label.duplicate_scheme_name"),
761 JOptionPane.YES_NO_OPTION);
762 if (reply != JOptionPane.YES_OPTION)
767 userColourSchemes.remove(schemeName.getText());
769 JalviewFileChooser chooser = new JalviewFileChooser(
770 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
771 { "jc" }, new String[]
772 { "Jalview User Colours" }, "Jalview User Colours");
774 chooser.setFileView(new jalview.io.JalviewFileView());
775 chooser.setDialogTitle("Save colour scheme");
776 chooser.setToolTipText(MessageManager.getString("action.save"));
778 int value = chooser.showSaveDialog(this);
780 if (value == JalviewFileChooser.APPROVE_OPTION)
782 String choice = chooser.getSelectedFile().getPath();
783 String defaultColours = jalview.bin.Cache.getDefault(
784 "USER_DEFINED_COLOURS", choice);
785 if (defaultColours.indexOf(choice) == -1)
787 if (defaultColours.length() > 0)
789 defaultColours = defaultColours.concat("|");
791 defaultColours = defaultColours.concat(choice);
794 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
796 ap.alignFrame.updateUserColourMenu();
798 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
800 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
802 ucs.setSchemeName(schemeName.getText());
805 PrintWriter out = new PrintWriter(new OutputStreamWriter(
806 new FileOutputStream(choice), "UTF-8"));
808 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
810 JButton button = (JButton) buttonPanel.getComponent(i);
811 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
812 col.setName(button.getText());
813 col.setRGB(jalview.util.Format.getHexString(button
820 } catch (Exception ex)
822 ex.printStackTrace();
833 protected void cancelButton_actionPerformed(ActionEvent e)
837 if (seqGroup != null)
839 seqGroup.cs = oldColourScheme;
843 ap.av.setGlobalColourScheme(oldColourScheme);
845 ap.paintAlignment(true);
850 jmol.setJalviewColourScheme(oldColourScheme);
855 frame.setClosed(true);
856 } catch (Exception ex)
861 static Hashtable userColourSchemes;
863 public static Hashtable getUserColourSchemes()
865 return userColourSchemes;
868 public static void initUserColourSchemes(String files)
870 userColourSchemes = new Hashtable();
872 if (files == null || files.length() == 0)
877 // In case colours can't be loaded, we'll remove them
878 // from the default list here.
879 StringBuffer coloursFound = new StringBuffer();
880 StringTokenizer st = new StringTokenizer(files, "|");
881 while (st.hasMoreElements())
883 String file = st.nextToken();
886 UserColourScheme ucs = loadColours(file);
889 if (coloursFound.length() > 0)
891 coloursFound.append("|");
893 coloursFound.append(file);
894 userColourSchemes.put(ucs.getName(), ucs);
896 } catch (Exception ex)
898 System.out.println("Error loading User ColourFile\n" + ex);
901 if (!files.equals(coloursFound.toString()))
903 if (coloursFound.toString().length() > 1)
905 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
906 coloursFound.toString());
910 jalview.bin.Cache.applicationProperties
911 .remove("USER_DEFINED_COLOURS");
916 public static void removeColourFromDefaults(String target)
918 // The only way to find colours by name is to load them in
919 // In case colours can't be loaded, we'll remove them
920 // from the default list here.
922 userColourSchemes = new Hashtable();
924 StringBuffer coloursFound = new StringBuffer();
925 StringTokenizer st = new StringTokenizer(
926 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
928 while (st.hasMoreElements())
930 String file = st.nextToken();
933 UserColourScheme ucs = loadColours(file);
934 if (ucs != null && !ucs.getName().equals(target))
936 if (coloursFound.length() > 0)
938 coloursFound.append("|");
940 coloursFound.append(file);
941 userColourSchemes.put(ucs.getName(), ucs);
943 } catch (Exception ex)
945 System.out.println("Error loading User ColourFile\n" + ex);
949 if (coloursFound.toString().length() > 1)
951 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
952 coloursFound.toString());
956 jalview.bin.Cache.applicationProperties
957 .remove("USER_DEFINED_COLOURS");
962 public void caseSensitive_actionPerformed(ActionEvent e)
964 resetButtonPanel(caseSensitive.isSelected());
965 lcaseColour.setEnabled(caseSensitive.isSelected());
968 public void lcaseColour_actionPerformed(ActionEvent e)
970 if (selectedButtons == null)
972 selectedButtons = new Vector();
976 selectedButtons.clear();
978 selectedButtons.add(lcaseColour);