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
63 SequenceGroup seqGroup;
65 Vector selectedButtons;
67 ColourSchemeI oldColourScheme;
71 JalviewStructureDisplayI jmol;
73 Vector upperCaseButtons;
75 Vector lowerCaseButtons;
78 * Creates a new UserDefinedColours object.
85 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
89 lcaseColour.setEnabled(false);
96 oldColourScheme = seqGroup.cs;
100 oldColourScheme = ap.av.getGlobalColourScheme();
103 if (oldColourScheme instanceof UserColourScheme)
105 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
106 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
108 caseSensitive.setSelected(true);
109 lcaseColour.setEnabled(true);
110 resetButtonPanel(true);
114 resetButtonPanel(false);
119 resetButtonPanel(false);
125 public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs)
130 colorChooser.getSelectionModel().addChangeListener(this);
132 oldColourScheme = oldcs;
134 if (oldColourScheme instanceof UserColourScheme)
136 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
139 resetButtonPanel(false);
147 colorChooser.getSelectionModel().addChangeListener(this);
148 frame = new JInternalFrame();
149 frame.setContentPane(this);
150 Desktop.addInternalFrame(frame,
151 MessageManager.getString("label.user_defined_colours"), 720,
154 if (seqGroup != null)
156 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
159 if (new jalview.util.Platform().isAMac())
161 frame.setSize(760, 370);
165 void resetButtonPanel(boolean caseSensitive)
167 buttonPanel.removeAll();
169 if (upperCaseButtons == null)
171 upperCaseButtons = new Vector();
176 for (int i = 0; i < 20; i++)
180 label = ResidueProperties.aa[i];
184 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
188 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
191 buttonPanel.add(button);
194 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
195 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
196 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
197 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
201 gridLayout.setRows(6);
202 gridLayout.setColumns(4);
206 gridLayout.setRows(7);
208 gridLayout.setColumns(cols + 1);
210 if (lowerCaseButtons == null)
212 lowerCaseButtons = new Vector();
215 for (int i = 0; i < 20; i++)
217 int row = i / cols + 1;
218 int index = (row * cols) + i;
219 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
220 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
222 buttonPanel.add(button, index);
228 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
229 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
230 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
233 buttonPanel.validate();
243 public void stateChanged(ChangeEvent evt)
245 if (selectedButtons != null)
247 JButton button = null;
248 for (int i = 0; i < selectedButtons.size(); i++)
250 button = (JButton) selectedButtons.elementAt(i);
251 button.setBackground(colorChooser.getColor());
252 button.setForeground(button.getBackground().brighter().brighter()
255 if (button == lcaseColour)
257 for (int i = 0; i < lowerCaseButtons.size(); i++)
259 button = (JButton) lowerCaseButtons.elementAt(i);
260 button.setBackground(colorChooser.getColor());
261 button.setForeground(button.getBackground().brighter().brighter()
274 public void colourButtonPressed(MouseEvent e)
276 if (selectedButtons == null)
278 selectedButtons = new Vector();
281 JButton pressed = (JButton) e.getSource();
285 JButton start, end = (JButton) e.getSource();
286 if (selectedButtons.size() > 0)
288 start = (JButton) selectedButtons
289 .elementAt(selectedButtons.size() - 1);
293 start = (JButton) e.getSource();
296 int startIndex = 0, endIndex = 0;
297 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
299 if (buttonPanel.getComponent(b) == start)
303 if (buttonPanel.getComponent(b) == end)
309 if (startIndex > endIndex)
311 int temp = startIndex;
312 startIndex = endIndex;
316 for (int b = startIndex; b <= endIndex; b++)
318 JButton button = (JButton) buttonPanel.getComponent(b);
319 if (!selectedButtons.contains(button))
321 button.setForeground(button.getBackground().brighter().brighter());
322 selectedButtons.add(button);
326 else if (!e.isControlDown())
328 for (int b = 0; b < selectedButtons.size(); b++)
330 JButton button = (JButton) selectedButtons.elementAt(b);
331 button.setForeground(button.getBackground().darker().darker());
333 selectedButtons.clear();
334 pressed.setForeground(pressed.getBackground().brighter().brighter());
335 selectedButtons.addElement(pressed);
338 else if (e.isControlDown())
340 if (selectedButtons.contains(pressed))
342 pressed.setForeground(pressed.getBackground().darker().darker());
343 selectedButtons.remove(pressed);
347 pressed.setForeground(pressed.getBackground().brighter().brighter());
348 selectedButtons.addElement(pressed);
352 if (selectedButtons.size() > 0)
354 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
367 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
370 final JButton button;
373 if (buttonIndex < caseSensitiveButtons.size())
375 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
376 col = button.getBackground();
380 button = new JButton();
381 button.addMouseListener(new java.awt.event.MouseAdapter()
383 public void mouseClicked(MouseEvent e)
385 colourButtonPressed(e);
389 caseSensitiveButtons.addElement(button);
392 if (oldColourScheme != null)
396 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
397 } catch (Exception ex)
403 if (caseSensitive.isSelected())
405 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
409 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
412 button.setBackground(col);
413 button.setText(label);
414 button.setForeground(col.darker().darker().darker());
415 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
426 protected void okButton_actionPerformed(ActionEvent e)
428 applyButton_actionPerformed(null);
432 frame.setClosed(true);
433 } catch (Exception ex)
444 protected void applyButton_actionPerformed(ActionEvent e)
446 UserColourScheme ucs = getSchemeFromButtons();
447 ucs.setName(schemeName.getText());
449 if (seqGroup != null)
452 ap.paintAlignment(true);
456 ap.alignFrame.changeColour(ucs);
458 else if (jmol != null)
460 jmol.setJalviewColourScheme(ucs);
464 UserColourScheme getSchemeFromButtons()
467 Color[] newColours = new Color[24];
469 for (int i = 0; i < 24; i++)
471 JButton button = (JButton) upperCaseButtons.elementAt(i);
472 newColours[i] = button.getBackground();
475 UserColourScheme ucs = new UserColourScheme(newColours);
477 if (caseSensitive.isSelected())
479 newColours = new Color[23];
480 for (int i = 0; i < 23; i++)
482 JButton button = (JButton) lowerCaseButtons.elementAt(i);
483 newColours[i] = button.getBackground();
485 ucs.setLowerCaseColours(newColours);
490 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
502 protected void loadbutton_actionPerformed(ActionEvent e)
504 upperCaseButtons = new Vector();
505 lowerCaseButtons = new Vector();
507 JalviewFileChooser chooser = new JalviewFileChooser(
508 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
509 { "jc" }, new String[]
510 { "Jalview User Colours" }, "Jalview User Colours");
511 chooser.setFileView(new jalview.io.JalviewFileView());
512 chooser.setDialogTitle(MessageManager
513 .getString("label.load_colour_scheme"));
514 chooser.setToolTipText(MessageManager.getString("action.load"));
516 int value = chooser.showOpenDialog(this);
518 if (value == JalviewFileChooser.APPROVE_OPTION)
520 File choice = chooser.getSelectedFile();
521 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
522 String defaultColours = jalview.bin.Cache.getDefault(
523 "USER_DEFINED_COLOURS", choice.getPath());
524 if (defaultColours.indexOf(choice.getPath()) == -1)
526 defaultColours = defaultColours.concat("|")
527 .concat(choice.getPath());
530 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
532 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
533 Color[] colors = ucs.getColours();
534 schemeName.setText(ucs.getName());
536 if (ucs.getLowerCaseColours() != null)
538 caseSensitive.setSelected(true);
539 lcaseColour.setEnabled(true);
540 resetButtonPanel(true);
541 for (int i = 0; i < lowerCaseButtons.size(); i++)
543 JButton button = (JButton) lowerCaseButtons.elementAt(i);
544 button.setBackground(ucs.getLowerCaseColours()[i]);
550 caseSensitive.setSelected(false);
551 lcaseColour.setEnabled(false);
552 resetButtonPanel(false);
555 for (int i = 0; i < upperCaseButtons.size(); i++)
557 JButton button = (JButton) upperCaseButtons.elementAt(i);
558 button.setBackground(colors[i]);
567 * @return DOCUMENT ME!
569 public static UserColourScheme loadDefaultColours()
571 UserColourScheme ret = null;
573 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
576 if (colours.indexOf("|") > -1)
578 colours = colours.substring(0, colours.indexOf("|"));
581 ret = loadColours(colours);
586 Color[] newColours = new Color[24];
587 for (int i = 0; i < 24; i++)
589 newColours[i] = Color.white;
591 ret = new UserColourScheme(newColours);
603 * @return DOCUMENT ME!
605 static UserColourScheme loadColours(String file)
607 UserColourScheme ucs = null;
608 Color[] newColours = null;
611 InputStreamReader in = new InputStreamReader(
612 new FileInputStream(file), "UTF-8");
614 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
616 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
618 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
621 newColours = new Color[24];
623 Color[] lowerCase = null;
624 boolean caseSensitive = false;
628 for (int i = 0; i < jucs.getColourCount(); i++)
630 name = jucs.getColour(i).getName();
631 if (ResidueProperties.aa3Hash.containsKey(name))
633 index = ((Integer) ResidueProperties.aa3Hash.get(name))
638 index = ResidueProperties.aaIndex[name.charAt(0)];
645 if (name.toLowerCase().equals(name))
647 if (lowerCase == null)
649 lowerCase = new Color[23];
651 caseSensitive = true;
652 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
657 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
662 if (newColours != null)
664 ucs = new UserColourScheme(newColours);
665 ucs.setName(jucs.getSchemeName());
668 ucs.setLowerCaseColours(lowerCase);
672 } catch (Exception ex)
674 // Could be Archive Jalview format
677 InputStreamReader in = new InputStreamReader(new FileInputStream(
680 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
682 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
684 newColours = new Color[jucs.getColourCount()];
686 for (int i = 0; i < 24; i++)
688 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
691 if (newColours != null)
693 ucs = new UserColourScheme(newColours);
694 ucs.setName(jucs.getSchemeName());
696 } catch (Exception ex2)
698 ex2.printStackTrace();
701 if (newColours == null)
703 System.out.println("Error loading User ColourFile\n" + ex);
716 protected void savebutton_actionPerformed(ActionEvent e)
718 if (schemeName.getText().trim().length() < 1)
720 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
721 .getString("label.user_colour_scheme_must_have_name"),
722 MessageManager.getString("label.no_name_colour_scheme"),
723 JOptionPane.WARNING_MESSAGE);
727 if (userColourSchemes != null
728 && userColourSchemes.containsKey(schemeName.getText()))
730 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
731 MessageManager.formatMessage(
732 "label.colour_scheme_exists_overwrite", new String[]
733 { schemeName.getText(), schemeName.getText() }),
734 MessageManager.getString("label.duplicate_scheme_name"),
735 JOptionPane.YES_NO_OPTION);
736 if (reply != JOptionPane.YES_OPTION)
741 userColourSchemes.remove(schemeName.getText());
743 JalviewFileChooser chooser = new JalviewFileChooser(
744 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
745 { "jc" }, new String[]
746 { "Jalview User Colours" }, "Jalview User Colours");
748 chooser.setFileView(new jalview.io.JalviewFileView());
749 chooser.setDialogTitle("Save colour scheme");
750 chooser.setToolTipText(MessageManager.getString("action.save"));
752 int value = chooser.showSaveDialog(this);
754 if (value == JalviewFileChooser.APPROVE_OPTION)
756 String choice = chooser.getSelectedFile().getPath();
757 String defaultColours = jalview.bin.Cache.getDefault(
758 "USER_DEFINED_COLOURS", choice);
759 if (defaultColours.indexOf(choice) == -1)
761 if (defaultColours.length() > 0)
763 defaultColours = defaultColours.concat("|");
765 defaultColours = defaultColours.concat(choice);
768 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
770 ap.alignFrame.updateUserColourMenu();
772 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
774 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
776 ucs.setSchemeName(schemeName.getText());
779 PrintWriter out = new PrintWriter(new OutputStreamWriter(
780 new FileOutputStream(choice), "UTF-8"));
782 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
784 JButton button = (JButton) buttonPanel.getComponent(i);
785 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
786 col.setName(button.getText());
787 col.setRGB(jalview.util.Format.getHexString(button
794 } catch (Exception ex)
796 ex.printStackTrace();
807 protected void cancelButton_actionPerformed(ActionEvent e)
811 if (seqGroup != null)
813 seqGroup.cs = oldColourScheme;
817 ap.av.setGlobalColourScheme(oldColourScheme);
819 ap.paintAlignment(true);
824 jmol.setJalviewColourScheme(oldColourScheme);
829 frame.setClosed(true);
830 } catch (Exception ex)
835 static Hashtable userColourSchemes;
837 public static Hashtable getUserColourSchemes()
839 return userColourSchemes;
842 public static void initUserColourSchemes(String files)
844 userColourSchemes = new Hashtable();
846 if (files == null || files.length() == 0)
851 // In case colours can't be loaded, we'll remove them
852 // from the default list here.
853 StringBuffer coloursFound = new StringBuffer();
854 StringTokenizer st = new StringTokenizer(files, "|");
855 while (st.hasMoreElements())
857 String file = st.nextToken();
860 UserColourScheme ucs = loadColours(file);
863 if (coloursFound.length() > 0)
865 coloursFound.append("|");
867 coloursFound.append(file);
868 userColourSchemes.put(ucs.getName(), ucs);
870 } catch (Exception ex)
872 System.out.println("Error loading User ColourFile\n" + ex);
875 if (!files.equals(coloursFound.toString()))
877 if (coloursFound.toString().length() > 1)
879 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
880 coloursFound.toString());
884 jalview.bin.Cache.applicationProperties
885 .remove("USER_DEFINED_COLOURS");
890 public static void removeColourFromDefaults(String target)
892 // The only way to find colours by name is to load them in
893 // In case colours can't be loaded, we'll remove them
894 // from the default list here.
896 userColourSchemes = new Hashtable();
898 StringBuffer coloursFound = new StringBuffer();
899 StringTokenizer st = new StringTokenizer(
900 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
902 while (st.hasMoreElements())
904 String file = st.nextToken();
907 UserColourScheme ucs = loadColours(file);
908 if (ucs != null && !ucs.getName().equals(target))
910 if (coloursFound.length() > 0)
912 coloursFound.append("|");
914 coloursFound.append(file);
915 userColourSchemes.put(ucs.getName(), ucs);
917 } catch (Exception ex)
919 System.out.println("Error loading User ColourFile\n" + ex);
923 if (coloursFound.toString().length() > 1)
925 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
926 coloursFound.toString());
930 jalview.bin.Cache.applicationProperties
931 .remove("USER_DEFINED_COLOURS");
936 public void caseSensitive_actionPerformed(ActionEvent e)
938 resetButtonPanel(caseSensitive.isSelected());
939 lcaseColour.setEnabled(caseSensitive.isSelected());
942 public void lcaseColour_actionPerformed(ActionEvent e)
944 if (selectedButtons == null)
946 selectedButtons = new Vector();
950 selectedButtons.clear();
952 selectedButtons.add(lcaseColour);