2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import jalview.datamodel.SequenceGroup;
22 import jalview.io.JalviewFileChooser;
23 import jalview.jbgui.GUserDefinedColours;
24 import jalview.schemes.ColourSchemeI;
25 import jalview.schemes.ResidueProperties;
26 import jalview.schemes.UserColourScheme;
27 import jalview.util.MessageManager;
29 import java.awt.Color;
31 import java.awt.event.ActionEvent;
32 import java.awt.event.MouseEvent;
34 import java.io.FileInputStream;
35 import java.io.FileOutputStream;
36 import java.io.InputStreamReader;
37 import java.io.OutputStreamWriter;
38 import java.io.PrintWriter;
39 import java.util.Hashtable;
40 import java.util.StringTokenizer;
41 import java.util.Vector;
43 import javax.swing.JButton;
44 import javax.swing.JInternalFrame;
45 import javax.swing.JOptionPane;
46 import javax.swing.event.ChangeEvent;
47 import javax.swing.event.ChangeListener;
55 public class UserDefinedColours extends GUserDefinedColours implements
60 SequenceGroup seqGroup;
62 Vector selectedButtons;
64 ColourSchemeI oldColourScheme;
70 Vector upperCaseButtons;
72 Vector lowerCaseButtons;
75 * Creates a new UserDefinedColours object.
82 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
86 lcaseColour.setEnabled(false);
93 oldColourScheme = seqGroup.cs;
97 oldColourScheme = ap.av.getGlobalColourScheme();
100 if (oldColourScheme instanceof UserColourScheme)
102 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
103 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
105 caseSensitive.setSelected(true);
106 lcaseColour.setEnabled(true);
107 resetButtonPanel(true);
111 resetButtonPanel(false);
116 resetButtonPanel(false);
122 public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)
127 colorChooser.getSelectionModel().addChangeListener(this);
129 oldColourScheme = oldcs;
131 if (oldColourScheme instanceof UserColourScheme)
133 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
136 resetButtonPanel(false);
144 colorChooser.getSelectionModel().addChangeListener(this);
145 frame = new JInternalFrame();
146 frame.setContentPane(this);
147 Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);
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149 if (seqGroup != null)
151 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
154 if (new jalview.util.Platform().isAMac())
156 frame.setSize(760, 370);
160 void resetButtonPanel(boolean caseSensitive)
162 buttonPanel.removeAll();
164 if (upperCaseButtons == null)
166 upperCaseButtons = new Vector();
171 for (int i = 0; i < 20; i++)
175 label = ResidueProperties.aa[i];
179 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
183 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
186 buttonPanel.add(button);
189 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
190 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
191 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
192 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
196 gridLayout.setRows(6);
197 gridLayout.setColumns(4);
201 gridLayout.setRows(7);
203 gridLayout.setColumns(cols + 1);
205 if (lowerCaseButtons == null)
207 lowerCaseButtons = new Vector();
210 for (int i = 0; i < 20; i++)
212 int row = i / cols + 1;
213 int index = (row * cols) + i;
214 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
215 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
217 buttonPanel.add(button, index);
223 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
224 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
225 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
228 buttonPanel.validate();
238 public void stateChanged(ChangeEvent evt)
240 if (selectedButtons != null)
242 JButton button = null;
243 for (int i = 0; i < selectedButtons.size(); i++)
245 button = (JButton) selectedButtons.elementAt(i);
246 button.setBackground(colorChooser.getColor());
247 button.setForeground(button.getBackground().brighter().brighter()
250 if (button == lcaseColour)
252 for (int i = 0; i < lowerCaseButtons.size(); i++)
254 button = (JButton) lowerCaseButtons.elementAt(i);
255 button.setBackground(colorChooser.getColor());
256 button.setForeground(button.getBackground().brighter().brighter()
269 public void colourButtonPressed(MouseEvent e)
271 if (selectedButtons == null)
273 selectedButtons = new Vector();
276 JButton pressed = (JButton) e.getSource();
280 JButton start, end = (JButton) e.getSource();
281 if (selectedButtons.size() > 0)
283 start = (JButton) selectedButtons
284 .elementAt(selectedButtons.size() - 1);
288 start = (JButton) e.getSource();
291 int startIndex = 0, endIndex = 0;
292 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
294 if (buttonPanel.getComponent(b) == start)
298 if (buttonPanel.getComponent(b) == end)
304 if (startIndex > endIndex)
306 int temp = startIndex;
307 startIndex = endIndex;
311 for (int b = startIndex; b <= endIndex; b++)
313 JButton button = (JButton) buttonPanel.getComponent(b);
314 if (!selectedButtons.contains(button))
316 button.setForeground(button.getBackground().brighter().brighter());
317 selectedButtons.add(button);
321 else if (!e.isControlDown())
323 for (int b = 0; b < selectedButtons.size(); b++)
325 JButton button = (JButton) selectedButtons.elementAt(b);
326 button.setForeground(button.getBackground().darker().darker());
328 selectedButtons.clear();
329 pressed.setForeground(pressed.getBackground().brighter().brighter());
330 selectedButtons.addElement(pressed);
333 else if (e.isControlDown())
335 if (selectedButtons.contains(pressed))
337 pressed.setForeground(pressed.getBackground().darker().darker());
338 selectedButtons.remove(pressed);
342 pressed.setForeground(pressed.getBackground().brighter().brighter());
343 selectedButtons.addElement(pressed);
347 if (selectedButtons.size() > 0)
349 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
362 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
365 final JButton button;
368 if (buttonIndex < caseSensitiveButtons.size())
370 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
371 col = button.getBackground();
375 button = new JButton();
376 button.addMouseListener(new java.awt.event.MouseAdapter()
378 public void mouseClicked(MouseEvent e)
380 colourButtonPressed(e);
384 caseSensitiveButtons.addElement(button);
387 if (oldColourScheme != null)
391 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
392 } catch (Exception ex)
398 if (caseSensitive.isSelected())
400 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
404 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
407 button.setBackground(col);
408 button.setText(label);
409 button.setForeground(col.darker().darker().darker());
410 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
421 protected void okButton_actionPerformed(ActionEvent e)
423 applyButton_actionPerformed(null);
427 frame.setClosed(true);
428 } catch (Exception ex)
439 protected void applyButton_actionPerformed(ActionEvent e)
441 UserColourScheme ucs = getSchemeFromButtons();
442 ucs.setName(schemeName.getText());
444 if (seqGroup != null)
447 ap.paintAlignment(true);
451 ap.alignFrame.changeColour(ucs);
453 else if (jmol != null)
455 jmol.setJalviewColourScheme(ucs);
459 UserColourScheme getSchemeFromButtons()
462 Color[] newColours = new Color[24];
464 for (int i = 0; i < 24; i++)
466 JButton button = (JButton) upperCaseButtons.elementAt(i);
467 newColours[i] = button.getBackground();
470 UserColourScheme ucs = new UserColourScheme(newColours);
472 if (caseSensitive.isSelected())
474 newColours = new Color[23];
475 for (int i = 0; i < 23; i++)
477 JButton button = (JButton) lowerCaseButtons.elementAt(i);
478 newColours[i] = button.getBackground();
480 ucs.setLowerCaseColours(newColours);
485 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
497 protected void loadbutton_actionPerformed(ActionEvent e)
499 upperCaseButtons = new Vector();
500 lowerCaseButtons = new Vector();
502 JalviewFileChooser chooser = new JalviewFileChooser(
503 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
504 { "jc" }, new String[]
505 { "Jalview User Colours" }, "Jalview User Colours");
506 chooser.setFileView(new jalview.io.JalviewFileView());
507 chooser.setDialogTitle(MessageManager.getString("label.load_colour_scheme"));
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508 chooser.setToolTipText(MessageManager.getString("action.load"));
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510 int value = chooser.showOpenDialog(this);
512 if (value == JalviewFileChooser.APPROVE_OPTION)
514 File choice = chooser.getSelectedFile();
515 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
516 String defaultColours = jalview.bin.Cache.getDefault(
517 "USER_DEFINED_COLOURS", choice.getPath());
518 if (defaultColours.indexOf(choice.getPath()) == -1)
520 defaultColours = defaultColours.concat("|")
521 .concat(choice.getPath());
524 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
526 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
527 Color[] colors = ucs.getColours();
528 schemeName.setText(ucs.getName());
530 if (ucs.getLowerCaseColours() != null)
532 caseSensitive.setSelected(true);
533 lcaseColour.setEnabled(true);
534 resetButtonPanel(true);
535 for (int i = 0; i < lowerCaseButtons.size(); i++)
537 JButton button = (JButton) lowerCaseButtons.elementAt(i);
538 button.setBackground(ucs.getLowerCaseColours()[i]);
544 caseSensitive.setSelected(false);
545 lcaseColour.setEnabled(false);
546 resetButtonPanel(false);
549 for (int i = 0; i < upperCaseButtons.size(); i++)
551 JButton button = (JButton) upperCaseButtons.elementAt(i);
552 button.setBackground(colors[i]);
561 * @return DOCUMENT ME!
563 public static UserColourScheme loadDefaultColours()
565 UserColourScheme ret = null;
567 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
570 if (colours.indexOf("|") > -1)
572 colours = colours.substring(0, colours.indexOf("|"));
575 ret = loadColours(colours);
580 Color[] newColours = new Color[24];
581 for (int i = 0; i < 24; i++)
583 newColours[i] = Color.white;
585 ret = new UserColourScheme(newColours);
597 * @return DOCUMENT ME!
599 static UserColourScheme loadColours(String file)
601 UserColourScheme ucs = null;
602 Color[] newColours = null;
605 InputStreamReader in = new InputStreamReader(
606 new FileInputStream(file), "UTF-8");
608 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
610 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
612 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
615 newColours = new Color[24];
617 Color[] lowerCase = null;
618 boolean caseSensitive = false;
622 for (int i = 0; i < jucs.getColourCount(); i++)
624 name = jucs.getColour(i).getName();
625 if (ResidueProperties.aa3Hash.containsKey(name))
627 index = ((Integer) ResidueProperties.aa3Hash.get(name))
632 index = ResidueProperties.aaIndex[name.charAt(0)];
639 if (name.toLowerCase().equals(name))
641 if (lowerCase == null)
643 lowerCase = new Color[23];
645 caseSensitive = true;
646 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
651 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
656 if (newColours != null)
658 ucs = new UserColourScheme(newColours);
659 ucs.setName(jucs.getSchemeName());
662 ucs.setLowerCaseColours(lowerCase);
666 } catch (Exception ex)
668 // Could be Archive Jalview format
671 InputStreamReader in = new InputStreamReader(new FileInputStream(
674 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
676 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
678 newColours = new Color[jucs.getColourCount()];
680 for (int i = 0; i < 24; i++)
682 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
685 if (newColours != null)
687 ucs = new UserColourScheme(newColours);
688 ucs.setName(jucs.getSchemeName());
690 } catch (Exception ex2)
692 ex2.printStackTrace();
695 if (newColours == null)
697 System.out.println("Error loading User ColourFile\n" + ex);
710 protected void savebutton_actionPerformed(ActionEvent e)
712 if (schemeName.getText().trim().length() < 1)
714 JOptionPane.showInternalMessageDialog(Desktop.desktop,
715 MessageManager.getString("label.user_colour_scheme_must_have_name"),
716 MessageManager.getString("label.no_name_colour_scheme"), JOptionPane.WARNING_MESSAGE);
720 if (userColourSchemes != null
721 && userColourSchemes.containsKey(schemeName.getText()))
723 int reply = JOptionPane.showInternalConfirmDialog(
725 MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
726 MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
727 if (reply != JOptionPane.YES_OPTION)
732 userColourSchemes.remove(schemeName.getText());
734 JalviewFileChooser chooser = new JalviewFileChooser(
735 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
736 { "jc" }, new String[]
737 { "Jalview User Colours" }, "Jalview User Colours");
739 chooser.setFileView(new jalview.io.JalviewFileView());
740 chooser.setDialogTitle("Save colour scheme");
741 chooser.setToolTipText(MessageManager.getString("action.save"));
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743 int value = chooser.showSaveDialog(this);
745 if (value == JalviewFileChooser.APPROVE_OPTION)
747 String choice = chooser.getSelectedFile().getPath();
748 String defaultColours = jalview.bin.Cache.getDefault(
749 "USER_DEFINED_COLOURS", choice);
750 if (defaultColours.indexOf(choice) == -1)
752 if (defaultColours.length() > 0)
754 defaultColours = defaultColours.concat("|");
756 defaultColours = defaultColours.concat(choice);
759 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
761 ap.alignFrame.updateUserColourMenu();
763 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
765 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
767 ucs.setSchemeName(schemeName.getText());
770 PrintWriter out = new PrintWriter(new OutputStreamWriter(
771 new FileOutputStream(choice), "UTF-8"));
773 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
775 JButton button = (JButton) buttonPanel.getComponent(i);
776 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
777 col.setName(button.getText());
778 col.setRGB(jalview.util.Format.getHexString(button
785 } catch (Exception ex)
787 ex.printStackTrace();
798 protected void cancelButton_actionPerformed(ActionEvent e)
802 if (seqGroup != null)
804 seqGroup.cs = oldColourScheme;
808 ap.av.setGlobalColourScheme(oldColourScheme);
810 ap.paintAlignment(true);
815 jmol.setJalviewColourScheme(oldColourScheme);
820 frame.setClosed(true);
821 } catch (Exception ex)
826 static Hashtable userColourSchemes;
828 public static Hashtable getUserColourSchemes()
830 return userColourSchemes;
833 public static void initUserColourSchemes(String files)
835 userColourSchemes = new Hashtable();
837 if (files == null || files.length() == 0)
842 // In case colours can't be loaded, we'll remove them
843 // from the default list here.
844 StringBuffer coloursFound = new StringBuffer();
845 StringTokenizer st = new StringTokenizer(files, "|");
846 while (st.hasMoreElements())
848 String file = st.nextToken();
851 UserColourScheme ucs = loadColours(file);
854 if (coloursFound.length() > 0)
856 coloursFound.append("|");
858 coloursFound.append(file);
859 userColourSchemes.put(ucs.getName(), ucs);
861 } catch (Exception ex)
863 System.out.println("Error loading User ColourFile\n" + ex);
866 if (!files.equals(coloursFound.toString()))
868 if (coloursFound.toString().length() > 1)
870 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
871 coloursFound.toString());
875 jalview.bin.Cache.applicationProperties
876 .remove("USER_DEFINED_COLOURS");
881 public static void removeColourFromDefaults(String target)
883 // The only way to find colours by name is to load them in
884 // In case colours can't be loaded, we'll remove them
885 // from the default list here.
887 userColourSchemes = new Hashtable();
889 StringBuffer coloursFound = new StringBuffer();
890 StringTokenizer st = new StringTokenizer(
891 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
893 while (st.hasMoreElements())
895 String file = st.nextToken();
898 UserColourScheme ucs = loadColours(file);
899 if (ucs != null && !ucs.getName().equals(target))
901 if (coloursFound.length() > 0)
903 coloursFound.append("|");
905 coloursFound.append(file);
906 userColourSchemes.put(ucs.getName(), ucs);
908 } catch (Exception ex)
910 System.out.println("Error loading User ColourFile\n" + ex);
914 if (coloursFound.toString().length() > 1)
916 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
917 coloursFound.toString());
921 jalview.bin.Cache.applicationProperties
922 .remove("USER_DEFINED_COLOURS");
927 public void caseSensitive_actionPerformed(ActionEvent e)
929 resetButtonPanel(caseSensitive.isSelected());
930 lcaseColour.setEnabled(caseSensitive.isSelected());
933 public void lcaseColour_actionPerformed(ActionEvent e)
935 if (selectedButtons == null)
937 selectedButtons = new Vector();
941 selectedButtons.clear();
943 selectedButtons.add(lcaseColour);