2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
\r
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
\r
5 * This file is part of Jalview.
\r
7 * Jalview is free software: you can redistribute it and/or
\r
8 * modify it under the terms of the GNU General Public License
\r
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
11 * Jalview is distributed in the hope that it will be useful, but
\r
12 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
14 * PURPOSE. See the GNU General Public License for more details.
\r
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
18 package jalview.gui;
\r
20 import jalview.datamodel.SequenceGroup;
\r
21 import jalview.io.JalviewFileChooser;
\r
22 import jalview.jbgui.GUserDefinedColours;
\r
23 import jalview.schemes.ColourSchemeI;
\r
24 import jalview.schemes.ResidueProperties;
\r
25 import jalview.schemes.UserColourScheme;
\r
26 import jalview.util.MessageManager;
\r
28 import java.awt.Color;
\r
29 import java.awt.Font;
\r
30 import java.awt.event.ActionEvent;
\r
31 import java.awt.event.MouseEvent;
\r
32 import java.io.File;
\r
33 import java.io.FileInputStream;
\r
34 import java.io.FileOutputStream;
\r
35 import java.io.InputStreamReader;
\r
36 import java.io.OutputStreamWriter;
\r
37 import java.io.PrintWriter;
\r
38 import java.util.Hashtable;
\r
39 import java.util.StringTokenizer;
\r
40 import java.util.Vector;
\r
42 import javax.swing.JButton;
\r
43 import javax.swing.JInternalFrame;
\r
44 import javax.swing.JOptionPane;
\r
45 import javax.swing.event.ChangeEvent;
\r
46 import javax.swing.event.ChangeListener;
\r
52 * @version $Revision$
\r
54 public class UserDefinedColours extends GUserDefinedColours implements
\r
59 SequenceGroup seqGroup;
\r
61 Vector selectedButtons;
\r
63 ColourSchemeI oldColourScheme;
\r
65 JInternalFrame frame;
\r
69 Vector upperCaseButtons;
\r
71 Vector lowerCaseButtons;
\r
74 * Creates a new UserDefinedColours object.
\r
81 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
\r
85 lcaseColour.setEnabled(false);
\r
90 if (seqGroup != null)
\r
92 oldColourScheme = seqGroup.cs;
\r
96 oldColourScheme = ap.av.getGlobalColourScheme();
\r
99 if (oldColourScheme instanceof UserColourScheme)
\r
101 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
\r
102 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
\r
104 caseSensitive.setSelected(true);
\r
105 lcaseColour.setEnabled(true);
\r
106 resetButtonPanel(true);
\r
110 resetButtonPanel(false);
\r
115 resetButtonPanel(false);
\r
121 public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
\r
126 colorChooser.getSelectionModel().addChangeListener(this);
\r
128 oldColourScheme = oldcs;
\r
130 if (oldColourScheme instanceof UserColourScheme)
\r
132 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
\r
135 resetButtonPanel(false);
\r
143 colorChooser.getSelectionModel().addChangeListener(this);
\r
144 frame = new JInternalFrame();
\r
145 frame.setContentPane(this);
\r
146 Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);
\r
148 if (seqGroup != null)
\r
150 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
\r
153 if (new jalview.util.Platform().isAMac())
\r
155 frame.setSize(760, 370);
\r
159 void resetButtonPanel(boolean caseSensitive)
\r
161 buttonPanel.removeAll();
\r
163 if (upperCaseButtons == null)
\r
165 upperCaseButtons = new Vector();
\r
170 for (int i = 0; i < 20; i++)
\r
174 label = ResidueProperties.aa[i];
\r
178 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
\r
182 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
\r
185 buttonPanel.add(button);
\r
188 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
\r
189 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
\r
190 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
\r
191 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
\r
193 if (!caseSensitive)
\r
195 gridLayout.setRows(6);
\r
196 gridLayout.setColumns(4);
\r
200 gridLayout.setRows(7);
\r
202 gridLayout.setColumns(cols + 1);
\r
204 if (lowerCaseButtons == null)
\r
206 lowerCaseButtons = new Vector();
\r
209 for (int i = 0; i < 20; i++)
\r
211 int row = i / cols + 1;
\r
212 int index = (row * cols) + i;
\r
213 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
\r
214 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
\r
216 buttonPanel.add(button, index);
\r
222 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
\r
223 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
\r
224 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
\r
227 buttonPanel.validate();
\r
237 public void stateChanged(ChangeEvent evt)
\r
239 if (selectedButtons != null)
\r
241 JButton button = null;
\r
242 for (int i = 0; i < selectedButtons.size(); i++)
\r
244 button = (JButton) selectedButtons.elementAt(i);
\r
245 button.setBackground(colorChooser.getColor());
\r
246 button.setForeground(button.getBackground().brighter().brighter()
\r
249 if (button == lcaseColour)
\r
251 for (int i = 0; i < lowerCaseButtons.size(); i++)
\r
253 button = (JButton) lowerCaseButtons.elementAt(i);
\r
254 button.setBackground(colorChooser.getColor());
\r
255 button.setForeground(button.getBackground().brighter().brighter()
\r
268 public void colourButtonPressed(MouseEvent e)
\r
270 if (selectedButtons == null)
\r
272 selectedButtons = new Vector();
\r
275 JButton pressed = (JButton) e.getSource();
\r
277 if (e.isShiftDown())
\r
279 JButton start, end = (JButton) e.getSource();
\r
280 if (selectedButtons.size() > 0)
\r
282 start = (JButton) selectedButtons
\r
283 .elementAt(selectedButtons.size() - 1);
\r
287 start = (JButton) e.getSource();
\r
290 int startIndex = 0, endIndex = 0;
\r
291 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
\r
293 if (buttonPanel.getComponent(b) == start)
\r
297 if (buttonPanel.getComponent(b) == end)
\r
303 if (startIndex > endIndex)
\r
305 int temp = startIndex;
\r
306 startIndex = endIndex;
\r
310 for (int b = startIndex; b <= endIndex; b++)
\r
312 JButton button = (JButton) buttonPanel.getComponent(b);
\r
313 if (!selectedButtons.contains(button))
\r
315 button.setForeground(button.getBackground().brighter().brighter());
\r
316 selectedButtons.add(button);
\r
320 else if (!e.isControlDown())
\r
322 for (int b = 0; b < selectedButtons.size(); b++)
\r
324 JButton button = (JButton) selectedButtons.elementAt(b);
\r
325 button.setForeground(button.getBackground().darker().darker());
\r
327 selectedButtons.clear();
\r
328 pressed.setForeground(pressed.getBackground().brighter().brighter());
\r
329 selectedButtons.addElement(pressed);
\r
332 else if (e.isControlDown())
\r
334 if (selectedButtons.contains(pressed))
\r
336 pressed.setForeground(pressed.getBackground().darker().darker());
\r
337 selectedButtons.remove(pressed);
\r
341 pressed.setForeground(pressed.getBackground().brighter().brighter());
\r
342 selectedButtons.addElement(pressed);
\r
346 if (selectedButtons.size() > 0)
\r
348 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
\r
361 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
\r
364 final JButton button;
\r
367 if (buttonIndex < caseSensitiveButtons.size())
\r
369 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
\r
370 col = button.getBackground();
\r
374 button = new JButton();
\r
375 button.addMouseListener(new java.awt.event.MouseAdapter()
\r
377 public void mouseClicked(MouseEvent e)
\r
379 colourButtonPressed(e);
\r
383 caseSensitiveButtons.addElement(button);
\r
386 if (oldColourScheme != null)
\r
390 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
\r
391 } catch (Exception ex)
\r
397 if (caseSensitive.isSelected())
\r
399 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
\r
403 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
\r
406 button.setBackground(col);
\r
407 button.setText(label);
\r
408 button.setForeground(col.darker().darker().darker());
\r
409 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
\r
420 protected void okButton_actionPerformed(ActionEvent e)
\r
422 applyButton_actionPerformed(null);
\r
426 frame.setClosed(true);
\r
427 } catch (Exception ex)
\r
438 protected void applyButton_actionPerformed(ActionEvent e)
\r
440 UserColourScheme ucs = getSchemeFromButtons();
\r
441 ucs.setName(schemeName.getText());
\r
443 if (seqGroup != null)
\r
446 ap.paintAlignment(true);
\r
448 else if (ap != null)
\r
450 ap.alignFrame.changeColour(ucs);
\r
452 else if (jmol != null)
\r
454 jmol.setJalviewColourScheme(ucs);
\r
458 UserColourScheme getSchemeFromButtons()
\r
461 Color[] newColours = new Color[24];
\r
463 for (int i = 0; i < 24; i++)
\r
465 JButton button = (JButton) upperCaseButtons.elementAt(i);
\r
466 newColours[i] = button.getBackground();
\r
469 UserColourScheme ucs = new UserColourScheme(newColours);
\r
471 if (caseSensitive.isSelected())
\r
473 newColours = new Color[23];
\r
474 for (int i = 0; i < 23; i++)
\r
476 JButton button = (JButton) lowerCaseButtons.elementAt(i);
\r
477 newColours[i] = button.getBackground();
\r
479 ucs.setLowerCaseColours(newColours);
\r
484 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
496 protected void loadbutton_actionPerformed(ActionEvent e)
\r
498 upperCaseButtons = new Vector();
\r
499 lowerCaseButtons = new Vector();
\r
501 JalviewFileChooser chooser = new JalviewFileChooser(
\r
502 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
\r
503 { "jc" }, new String[]
\r
504 { "Jalview User Colours" }, "Jalview User Colours");
\r
505 chooser.setFileView(new jalview.io.JalviewFileView());
\r
506 chooser.setDialogTitle(MessageManager.getString("label.load_colour_scheme"));
\r
507 chooser.setToolTipText(MessageManager.getString("action.load"));
\r
509 int value = chooser.showOpenDialog(this);
\r
511 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
513 File choice = chooser.getSelectedFile();
\r
514 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
\r
515 String defaultColours = jalview.bin.Cache.getDefault(
\r
516 "USER_DEFINED_COLOURS", choice.getPath());
\r
517 if (defaultColours.indexOf(choice.getPath()) == -1)
\r
519 defaultColours = defaultColours.concat("|")
\r
520 .concat(choice.getPath());
\r
523 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
\r
525 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
\r
526 Color[] colors = ucs.getColours();
\r
527 schemeName.setText(ucs.getName());
\r
529 if (ucs.getLowerCaseColours() != null)
\r
531 caseSensitive.setSelected(true);
\r
532 lcaseColour.setEnabled(true);
\r
533 resetButtonPanel(true);
\r
534 for (int i = 0; i < lowerCaseButtons.size(); i++)
\r
536 JButton button = (JButton) lowerCaseButtons.elementAt(i);
\r
537 button.setBackground(ucs.getLowerCaseColours()[i]);
\r
543 caseSensitive.setSelected(false);
\r
544 lcaseColour.setEnabled(false);
\r
545 resetButtonPanel(false);
\r
548 for (int i = 0; i < upperCaseButtons.size(); i++)
\r
550 JButton button = (JButton) upperCaseButtons.elementAt(i);
\r
551 button.setBackground(colors[i]);
\r
560 * @return DOCUMENT ME!
\r
562 public static UserColourScheme loadDefaultColours()
\r
564 UserColourScheme ret = null;
\r
566 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
\r
567 if (colours != null)
\r
569 if (colours.indexOf("|") > -1)
\r
571 colours = colours.substring(0, colours.indexOf("|"));
\r
574 ret = loadColours(colours);
\r
579 Color[] newColours = new Color[24];
\r
580 for (int i = 0; i < 24; i++)
\r
582 newColours[i] = Color.white;
\r
584 ret = new UserColourScheme(newColours);
\r
596 * @return DOCUMENT ME!
\r
598 static UserColourScheme loadColours(String file)
\r
600 UserColourScheme ucs = null;
\r
601 Color[] newColours = null;
\r
604 InputStreamReader in = new InputStreamReader(
\r
605 new FileInputStream(file), "UTF-8");
\r
607 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
\r
609 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
\r
611 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
\r
614 newColours = new Color[24];
\r
616 Color[] lowerCase = null;
\r
617 boolean caseSensitive = false;
\r
621 for (int i = 0; i < jucs.getColourCount(); i++)
\r
623 name = jucs.getColour(i).getName();
\r
624 if (ResidueProperties.aa3Hash.containsKey(name))
\r
626 index = ((Integer) ResidueProperties.aa3Hash.get(name))
\r
631 index = ResidueProperties.aaIndex[name.charAt(0)];
\r
638 if (name.toLowerCase().equals(name))
\r
640 if (lowerCase == null)
\r
642 lowerCase = new Color[23];
\r
644 caseSensitive = true;
\r
645 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
\r
650 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
\r
655 if (newColours != null)
\r
657 ucs = new UserColourScheme(newColours);
\r
658 ucs.setName(jucs.getSchemeName());
\r
661 ucs.setLowerCaseColours(lowerCase);
\r
665 } catch (Exception ex)
\r
667 // Could be Archive Jalview format
\r
670 InputStreamReader in = new InputStreamReader(new FileInputStream(
\r
673 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
\r
675 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
\r
677 newColours = new Color[jucs.getColourCount()];
\r
679 for (int i = 0; i < 24; i++)
\r
681 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
\r
684 if (newColours != null)
\r
686 ucs = new UserColourScheme(newColours);
\r
687 ucs.setName(jucs.getSchemeName());
\r
689 } catch (Exception ex2)
\r
691 ex2.printStackTrace();
\r
694 if (newColours == null)
\r
696 System.out.println("Error loading User ColourFile\n" + ex);
\r
709 protected void savebutton_actionPerformed(ActionEvent e)
\r
711 if (schemeName.getText().trim().length() < 1)
\r
713 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
714 MessageManager.getString("label.user_colour_scheme_must_have_name"),
\r
715 MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
\r
719 if (userColourSchemes != null
\r
720 && userColourSchemes.containsKey(schemeName.getText()))
\r
722 int reply = JOptionPane.showInternalConfirmDialog(
\r
724 MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
\r
725 MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
\r
726 if (reply != JOptionPane.YES_OPTION)
\r
731 userColourSchemes.remove(schemeName.getText());
\r
733 JalviewFileChooser chooser = new JalviewFileChooser(
\r
734 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
\r
735 { "jc" }, new String[]
\r
736 { "Jalview User Colours" }, "Jalview User Colours");
\r
738 chooser.setFileView(new jalview.io.JalviewFileView());
\r
739 chooser.setDialogTitle("Save colour scheme");
\r
740 chooser.setToolTipText(MessageManager.getString("action.save"));
\r
742 int value = chooser.showSaveDialog(this);
\r
744 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
746 String choice = chooser.getSelectedFile().getPath();
\r
747 String defaultColours = jalview.bin.Cache.getDefault(
\r
748 "USER_DEFINED_COLOURS", choice);
\r
749 if (defaultColours.indexOf(choice) == -1)
\r
751 if (defaultColours.length() > 0)
\r
753 defaultColours = defaultColours.concat("|");
\r
755 defaultColours = defaultColours.concat(choice);
\r
758 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
\r
760 ap.alignFrame.updateUserColourMenu();
\r
762 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
\r
764 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
\r
766 ucs.setSchemeName(schemeName.getText());
\r
769 PrintWriter out = new PrintWriter(new OutputStreamWriter(
\r
770 new FileOutputStream(choice), "UTF-8"));
\r
772 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
\r
774 JButton button = (JButton) buttonPanel.getComponent(i);
\r
775 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
\r
776 col.setName(button.getText());
\r
777 col.setRGB(jalview.util.Format.getHexString(button
\r
778 .getBackground()));
\r
779 ucs.addColour(col);
\r
784 } catch (Exception ex)
\r
786 ex.printStackTrace();
\r
797 protected void cancelButton_actionPerformed(ActionEvent e)
\r
801 if (seqGroup != null)
\r
803 seqGroup.cs = oldColourScheme;
\r
805 else if (ap != null)
\r
807 ap.av.setGlobalColourScheme(oldColourScheme);
\r
809 ap.paintAlignment(true);
\r
814 jmol.setJalviewColourScheme(oldColourScheme);
\r
819 frame.setClosed(true);
\r
820 } catch (Exception ex)
\r
825 static Hashtable userColourSchemes;
\r
827 public static Hashtable getUserColourSchemes()
\r
829 return userColourSchemes;
\r
832 public static void initUserColourSchemes(String files)
\r
834 userColourSchemes = new Hashtable();
\r
836 if (files == null || files.length() == 0)
\r
841 // In case colours can't be loaded, we'll remove them
\r
842 // from the default list here.
\r
843 StringBuffer coloursFound = new StringBuffer();
\r
844 StringTokenizer st = new StringTokenizer(files, "|");
\r
845 while (st.hasMoreElements())
\r
847 String file = st.nextToken();
\r
850 UserColourScheme ucs = loadColours(file);
\r
853 if (coloursFound.length() > 0)
\r
855 coloursFound.append("|");
\r
857 coloursFound.append(file);
\r
858 userColourSchemes.put(ucs.getName(), ucs);
\r
860 } catch (Exception ex)
\r
862 System.out.println("Error loading User ColourFile\n" + ex);
\r
865 if (!files.equals(coloursFound.toString()))
\r
867 if (coloursFound.toString().length() > 1)
\r
869 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
\r
870 coloursFound.toString());
\r
874 jalview.bin.Cache.applicationProperties
\r
875 .remove("USER_DEFINED_COLOURS");
\r
880 public static void removeColourFromDefaults(String target)
\r
882 // The only way to find colours by name is to load them in
\r
883 // In case colours can't be loaded, we'll remove them
\r
884 // from the default list here.
\r
886 userColourSchemes = new Hashtable();
\r
888 StringBuffer coloursFound = new StringBuffer();
\r
889 StringTokenizer st = new StringTokenizer(
\r
890 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
\r
892 while (st.hasMoreElements())
\r
894 String file = st.nextToken();
\r
897 UserColourScheme ucs = loadColours(file);
\r
898 if (ucs != null && !ucs.getName().equals(target))
\r
900 if (coloursFound.length() > 0)
\r
902 coloursFound.append("|");
\r
904 coloursFound.append(file);
\r
905 userColourSchemes.put(ucs.getName(), ucs);
\r
907 } catch (Exception ex)
\r
909 System.out.println("Error loading User ColourFile\n" + ex);
\r
913 if (coloursFound.toString().length() > 1)
\r
915 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
\r
916 coloursFound.toString());
\r
920 jalview.bin.Cache.applicationProperties
\r
921 .remove("USER_DEFINED_COLOURS");
\r
926 public void caseSensitive_actionPerformed(ActionEvent e)
\r
928 resetButtonPanel(caseSensitive.isSelected());
\r
929 lcaseColour.setEnabled(caseSensitive.isSelected());
\r
932 public void lcaseColour_actionPerformed(ActionEvent e)
\r
934 if (selectedButtons == null)
\r
936 selectedButtons = new Vector();
\r
940 selectedButtons.clear();
\r
942 selectedButtons.add(lcaseColour);
\r