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.datamodel.SequenceGroup;
24 import jalview.io.JalviewFileChooser;
25 import jalview.jbgui.GUserDefinedColours;
26 import jalview.schemes.ColourSchemeI;
27 import jalview.schemes.ResidueProperties;
28 import jalview.schemes.UserColourScheme;
29 import jalview.util.MessageManager;
31 import java.awt.Color;
33 import java.awt.event.ActionEvent;
34 import java.awt.event.MouseEvent;
36 import java.io.FileInputStream;
37 import java.io.FileOutputStream;
38 import java.io.InputStreamReader;
39 import java.io.OutputStreamWriter;
40 import java.io.PrintWriter;
41 import java.util.Hashtable;
42 import java.util.StringTokenizer;
43 import java.util.Vector;
45 import javax.swing.JButton;
46 import javax.swing.JInternalFrame;
47 import javax.swing.JOptionPane;
48 import javax.swing.event.ChangeEvent;
49 import javax.swing.event.ChangeListener;
57 public class UserDefinedColours extends GUserDefinedColours implements
62 SequenceGroup seqGroup;
64 Vector selectedButtons;
66 ColourSchemeI oldColourScheme;
72 Vector upperCaseButtons;
74 Vector lowerCaseButtons;
77 * Creates a new UserDefinedColours object.
84 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
88 lcaseColour.setEnabled(false);
95 oldColourScheme = seqGroup.cs;
99 oldColourScheme = ap.av.getGlobalColourScheme();
102 if (oldColourScheme instanceof UserColourScheme)
104 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
105 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
107 caseSensitive.setSelected(true);
108 lcaseColour.setEnabled(true);
109 resetButtonPanel(true);
113 resetButtonPanel(false);
118 resetButtonPanel(false);
124 public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
129 colorChooser.getSelectionModel().addChangeListener(this);
131 oldColourScheme = oldcs;
133 if (oldColourScheme instanceof UserColourScheme)
135 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
138 resetButtonPanel(false);
146 colorChooser.getSelectionModel().addChangeListener(this);
147 frame = new JInternalFrame();
148 frame.setContentPane(this);
149 Desktop.addInternalFrame(frame,
150 MessageManager.getString("label.user_defined_colours"), 720,
153 if (seqGroup != null)
155 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
158 if (new jalview.util.Platform().isAMac())
160 frame.setSize(760, 370);
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 buttonPanel.validate();
242 public void stateChanged(ChangeEvent evt)
244 if (selectedButtons != null)
246 JButton button = null;
247 for (int i = 0; i < selectedButtons.size(); i++)
249 button = (JButton) selectedButtons.elementAt(i);
250 button.setBackground(colorChooser.getColor());
251 button.setForeground(button.getBackground().brighter().brighter()
254 if (button == lcaseColour)
256 for (int i = 0; i < lowerCaseButtons.size(); i++)
258 button = (JButton) lowerCaseButtons.elementAt(i);
259 button.setBackground(colorChooser.getColor());
260 button.setForeground(button.getBackground().brighter().brighter()
273 public void colourButtonPressed(MouseEvent e)
275 if (selectedButtons == null)
277 selectedButtons = new Vector();
280 JButton pressed = (JButton) e.getSource();
284 JButton start, end = (JButton) e.getSource();
285 if (selectedButtons.size() > 0)
287 start = (JButton) selectedButtons
288 .elementAt(selectedButtons.size() - 1);
292 start = (JButton) e.getSource();
295 int startIndex = 0, endIndex = 0;
296 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
298 if (buttonPanel.getComponent(b) == start)
302 if (buttonPanel.getComponent(b) == end)
308 if (startIndex > endIndex)
310 int temp = startIndex;
311 startIndex = endIndex;
315 for (int b = startIndex; b <= endIndex; b++)
317 JButton button = (JButton) buttonPanel.getComponent(b);
318 if (!selectedButtons.contains(button))
320 button.setForeground(button.getBackground().brighter().brighter());
321 selectedButtons.add(button);
325 else if (!e.isControlDown())
327 for (int b = 0; b < selectedButtons.size(); b++)
329 JButton button = (JButton) selectedButtons.elementAt(b);
330 button.setForeground(button.getBackground().darker().darker());
332 selectedButtons.clear();
333 pressed.setForeground(pressed.getBackground().brighter().brighter());
334 selectedButtons.addElement(pressed);
337 else if (e.isControlDown())
339 if (selectedButtons.contains(pressed))
341 pressed.setForeground(pressed.getBackground().darker().darker());
342 selectedButtons.remove(pressed);
346 pressed.setForeground(pressed.getBackground().brighter().brighter());
347 selectedButtons.addElement(pressed);
351 if (selectedButtons.size() > 0)
353 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
366 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
369 final JButton button;
372 if (buttonIndex < caseSensitiveButtons.size())
374 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
375 col = button.getBackground();
379 button = new JButton();
380 button.addMouseListener(new java.awt.event.MouseAdapter()
382 public void mouseClicked(MouseEvent e)
384 colourButtonPressed(e);
388 caseSensitiveButtons.addElement(button);
391 if (oldColourScheme != null)
395 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
396 } catch (Exception ex)
402 if (caseSensitive.isSelected())
404 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
408 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
411 button.setBackground(col);
412 button.setText(label);
413 button.setForeground(col.darker().darker().darker());
414 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
425 protected void okButton_actionPerformed(ActionEvent e)
427 applyButton_actionPerformed(null);
431 frame.setClosed(true);
432 } catch (Exception ex)
443 protected void applyButton_actionPerformed(ActionEvent e)
445 UserColourScheme ucs = getSchemeFromButtons();
446 ucs.setName(schemeName.getText());
448 if (seqGroup != null)
451 ap.paintAlignment(true);
455 ap.alignFrame.changeColour(ucs);
457 else if (jmol != null)
459 jmol.setJalviewColourScheme(ucs);
463 UserColourScheme getSchemeFromButtons()
466 Color[] newColours = new Color[24];
468 for (int i = 0; i < 24; i++)
470 JButton button = (JButton) upperCaseButtons.elementAt(i);
471 newColours[i] = button.getBackground();
474 UserColourScheme ucs = new UserColourScheme(newColours);
476 if (caseSensitive.isSelected())
478 newColours = new Color[23];
479 for (int i = 0; i < 23; i++)
481 JButton button = (JButton) lowerCaseButtons.elementAt(i);
482 newColours[i] = button.getBackground();
484 ucs.setLowerCaseColours(newColours);
489 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
501 protected void loadbutton_actionPerformed(ActionEvent e)
503 upperCaseButtons = new Vector();
504 lowerCaseButtons = new Vector();
506 JalviewFileChooser chooser = new JalviewFileChooser(
507 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
508 { "jc" }, new String[]
509 { "Jalview User Colours" }, "Jalview User Colours");
510 chooser.setFileView(new jalview.io.JalviewFileView());
511 chooser.setDialogTitle(MessageManager
512 .getString("label.load_colour_scheme"));
513 chooser.setToolTipText(MessageManager.getString("action.load"));
515 int value = chooser.showOpenDialog(this);
517 if (value == JalviewFileChooser.APPROVE_OPTION)
519 File choice = chooser.getSelectedFile();
520 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
521 String defaultColours = jalview.bin.Cache.getDefault(
522 "USER_DEFINED_COLOURS", choice.getPath());
523 if (defaultColours.indexOf(choice.getPath()) == -1)
525 defaultColours = defaultColours.concat("|")
526 .concat(choice.getPath());
529 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
531 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
532 Color[] colors = ucs.getColours();
533 schemeName.setText(ucs.getName());
535 if (ucs.getLowerCaseColours() != null)
537 caseSensitive.setSelected(true);
538 lcaseColour.setEnabled(true);
539 resetButtonPanel(true);
540 for (int i = 0; i < lowerCaseButtons.size(); i++)
542 JButton button = (JButton) lowerCaseButtons.elementAt(i);
543 button.setBackground(ucs.getLowerCaseColours()[i]);
549 caseSensitive.setSelected(false);
550 lcaseColour.setEnabled(false);
551 resetButtonPanel(false);
554 for (int i = 0; i < upperCaseButtons.size(); i++)
556 JButton button = (JButton) upperCaseButtons.elementAt(i);
557 button.setBackground(colors[i]);
566 * @return DOCUMENT ME!
568 public static UserColourScheme loadDefaultColours()
570 UserColourScheme ret = null;
572 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
575 if (colours.indexOf("|") > -1)
577 colours = colours.substring(0, colours.indexOf("|"));
580 ret = loadColours(colours);
585 Color[] newColours = new Color[24];
586 for (int i = 0; i < 24; i++)
588 newColours[i] = Color.white;
590 ret = new UserColourScheme(newColours);
602 * @return DOCUMENT ME!
604 static UserColourScheme loadColours(String file)
606 UserColourScheme ucs = null;
607 Color[] newColours = null;
610 InputStreamReader in = new InputStreamReader(
611 new FileInputStream(file), "UTF-8");
613 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
615 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
617 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
620 newColours = new Color[24];
622 Color[] lowerCase = null;
623 boolean caseSensitive = false;
627 for (int i = 0; i < jucs.getColourCount(); i++)
629 name = jucs.getColour(i).getName();
630 if (ResidueProperties.aa3Hash.containsKey(name))
632 index = ((Integer) ResidueProperties.aa3Hash.get(name))
637 index = ResidueProperties.aaIndex[name.charAt(0)];
644 if (name.toLowerCase().equals(name))
646 if (lowerCase == null)
648 lowerCase = new Color[23];
650 caseSensitive = true;
651 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
656 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
661 if (newColours != null)
663 ucs = new UserColourScheme(newColours);
664 ucs.setName(jucs.getSchemeName());
667 ucs.setLowerCaseColours(lowerCase);
671 } catch (Exception ex)
673 // Could be Archive Jalview format
676 InputStreamReader in = new InputStreamReader(new FileInputStream(
679 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
681 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
683 newColours = new Color[jucs.getColourCount()];
685 for (int i = 0; i < 24; i++)
687 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
690 if (newColours != null)
692 ucs = new UserColourScheme(newColours);
693 ucs.setName(jucs.getSchemeName());
695 } catch (Exception ex2)
697 ex2.printStackTrace();
700 if (newColours == null)
702 System.out.println("Error loading User ColourFile\n" + ex);
715 protected void savebutton_actionPerformed(ActionEvent e)
717 if (schemeName.getText().trim().length() < 1)
719 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
720 .getString("label.user_colour_scheme_must_have_name"),
721 MessageManager.getString("label.no_name_colour_scheme"),
722 JOptionPane.WARNING_MESSAGE);
726 if (userColourSchemes != null
727 && userColourSchemes.containsKey(schemeName.getText()))
729 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
730 MessageManager.formatMessage(
731 "label.colour_scheme_exists_overwrite", new String[]
732 { schemeName.getText(), schemeName.getText() }),
733 MessageManager.getString("label.duplicate_scheme_name"),
734 JOptionPane.YES_NO_OPTION);
735 if (reply != JOptionPane.YES_OPTION)
740 userColourSchemes.remove(schemeName.getText());
742 JalviewFileChooser chooser = new JalviewFileChooser(
743 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
744 { "jc" }, new String[]
745 { "Jalview User Colours" }, "Jalview User Colours");
747 chooser.setFileView(new jalview.io.JalviewFileView());
748 chooser.setDialogTitle("Save colour scheme");
749 chooser.setToolTipText(MessageManager.getString("action.save"));
751 int value = chooser.showSaveDialog(this);
753 if (value == JalviewFileChooser.APPROVE_OPTION)
755 String choice = chooser.getSelectedFile().getPath();
756 String defaultColours = jalview.bin.Cache.getDefault(
757 "USER_DEFINED_COLOURS", choice);
758 if (defaultColours.indexOf(choice) == -1)
760 if (defaultColours.length() > 0)
762 defaultColours = defaultColours.concat("|");
764 defaultColours = defaultColours.concat(choice);
767 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
769 ap.alignFrame.updateUserColourMenu();
771 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
773 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
775 ucs.setSchemeName(schemeName.getText());
778 PrintWriter out = new PrintWriter(new OutputStreamWriter(
779 new FileOutputStream(choice), "UTF-8"));
781 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
783 JButton button = (JButton) buttonPanel.getComponent(i);
784 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
785 col.setName(button.getText());
786 col.setRGB(jalview.util.Format.getHexString(button
793 } catch (Exception ex)
795 ex.printStackTrace();
806 protected void cancelButton_actionPerformed(ActionEvent e)
810 if (seqGroup != null)
812 seqGroup.cs = oldColourScheme;
816 ap.av.setGlobalColourScheme(oldColourScheme);
818 ap.paintAlignment(true);
823 jmol.setJalviewColourScheme(oldColourScheme);
828 frame.setClosed(true);
829 } catch (Exception ex)
834 static Hashtable userColourSchemes;
836 public static Hashtable getUserColourSchemes()
838 return userColourSchemes;
841 public static void initUserColourSchemes(String files)
843 userColourSchemes = new Hashtable();
845 if (files == null || files.length() == 0)
850 // In case colours can't be loaded, we'll remove them
851 // from the default list here.
852 StringBuffer coloursFound = new StringBuffer();
853 StringTokenizer st = new StringTokenizer(files, "|");
854 while (st.hasMoreElements())
856 String file = st.nextToken();
859 UserColourScheme ucs = loadColours(file);
862 if (coloursFound.length() > 0)
864 coloursFound.append("|");
866 coloursFound.append(file);
867 userColourSchemes.put(ucs.getName(), ucs);
869 } catch (Exception ex)
871 System.out.println("Error loading User ColourFile\n" + ex);
874 if (!files.equals(coloursFound.toString()))
876 if (coloursFound.toString().length() > 1)
878 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
879 coloursFound.toString());
883 jalview.bin.Cache.applicationProperties
884 .remove("USER_DEFINED_COLOURS");
889 public static void removeColourFromDefaults(String target)
891 // The only way to find colours by name is to load them in
892 // In case colours can't be loaded, we'll remove them
893 // from the default list here.
895 userColourSchemes = new Hashtable();
897 StringBuffer coloursFound = new StringBuffer();
898 StringTokenizer st = new StringTokenizer(
899 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
901 while (st.hasMoreElements())
903 String file = st.nextToken();
906 UserColourScheme ucs = loadColours(file);
907 if (ucs != null && !ucs.getName().equals(target))
909 if (coloursFound.length() > 0)
911 coloursFound.append("|");
913 coloursFound.append(file);
914 userColourSchemes.put(ucs.getName(), ucs);
916 } catch (Exception ex)
918 System.out.println("Error loading User ColourFile\n" + ex);
922 if (coloursFound.toString().length() > 1)
924 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
925 coloursFound.toString());
929 jalview.bin.Cache.applicationProperties
930 .remove("USER_DEFINED_COLOURS");
935 public void caseSensitive_actionPerformed(ActionEvent e)
937 resetButtonPanel(caseSensitive.isSelected());
938 lcaseColour.setEnabled(caseSensitive.isSelected());
941 public void lcaseColour_actionPerformed(ActionEvent e)
943 if (selectedButtons == null)
945 selectedButtons = new Vector();
949 selectedButtons.clear();
951 selectedButtons.add(lcaseColour);