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 final Color newColour = colorChooser.getColor();
254 for (int i = 0; i < selectedButtons.size(); i++)
256 button = (JButton) selectedButtons.elementAt(i);
257 button.setBackground(newColour);
258 button.setForeground(brighterThan(newColour));
260 if (button == lcaseColour)
262 for (int i = 0; i < lowerCaseButtons.size(); i++)
264 button = (JButton) lowerCaseButtons.elementAt(i);
265 button.setBackground(newColour);
266 button.setForeground(brighterThan(button.getBackground()));
278 public void colourButtonPressed(MouseEvent e)
280 if (selectedButtons == null)
282 selectedButtons = new Vector();
285 JButton pressed = (JButton) e.getSource();
289 JButton start, end = (JButton) e.getSource();
290 if (selectedButtons.size() > 0)
292 start = (JButton) selectedButtons
293 .elementAt(selectedButtons.size() - 1);
297 start = (JButton) e.getSource();
300 int startIndex = 0, endIndex = 0;
301 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
303 if (buttonPanel.getComponent(b) == start)
307 if (buttonPanel.getComponent(b) == end)
313 if (startIndex > endIndex)
315 int temp = startIndex;
316 startIndex = endIndex;
320 for (int b = startIndex; b <= endIndex; b++)
322 JButton button = (JButton) buttonPanel.getComponent(b);
323 if (!selectedButtons.contains(button))
325 button.setForeground(brighterThan(button.getBackground()));
326 selectedButtons.add(button);
330 else if (!e.isControlDown())
332 for (int b = 0; b < selectedButtons.size(); b++)
334 JButton button = (JButton) selectedButtons.elementAt(b);
335 button.setForeground(darkerThan(button.getBackground()));
337 selectedButtons.clear();
338 pressed.setForeground(brighterThan(pressed.getBackground()));
339 selectedButtons.addElement(pressed);
342 else if (e.isControlDown())
344 if (selectedButtons.contains(pressed))
346 pressed.setForeground(darkerThan(pressed.getBackground()));
347 selectedButtons.remove(pressed);
351 pressed.setForeground(brighterThan(pressed.getBackground()));
352 selectedButtons.addElement(pressed);
356 if (selectedButtons.size() > 0)
358 colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
371 JButton makeButton(String label, String aa, Vector caseSensitiveButtons,
374 final JButton button;
377 if (buttonIndex < caseSensitiveButtons.size())
379 button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
380 col = button.getBackground();
384 button = new JButton();
385 button.addMouseListener(new java.awt.event.MouseAdapter()
387 public void mouseClicked(MouseEvent e)
389 colourButtonPressed(e);
393 caseSensitiveButtons.addElement(button);
396 if (oldColourScheme != null)
400 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
401 } catch (Exception ex)
407 if (caseSensitive.isSelected())
409 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
413 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
416 button.setOpaque(true); // required for the next line to have effect
417 button.setBackground(col);
418 button.setText(label);
419 button.setForeground(darkerThan(col));
420 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
426 * Returns a colour three shades darker.
428 * We use darker text to indicate unselected buttons, lighter text for selected.
432 public static Color darkerThan(Color col) {
433 return col.darker().darker().darker();
437 * Returns a colour three shades brighter.
439 * We use darker text to indicate unselected buttons, lighter text for selected.
443 public static Color brighterThan(Color col) {
444 return col.brighter().brighter().brighter();
453 protected void okButton_actionPerformed(ActionEvent e)
455 applyButton_actionPerformed(null);
459 frame.setClosed(true);
460 } catch (Exception ex)
471 protected void applyButton_actionPerformed(ActionEvent e)
473 UserColourScheme ucs = getSchemeFromButtons();
474 ucs.setName(schemeName.getText());
476 if (seqGroup != null)
479 ap.paintAlignment(true);
483 ap.alignFrame.changeColour(ucs);
485 else if (jmol != null)
487 jmol.setJalviewColourScheme(ucs);
491 UserColourScheme getSchemeFromButtons()
494 Color[] newColours = new Color[24];
496 for (int i = 0; i < 24; i++)
498 JButton button = (JButton) upperCaseButtons.elementAt(i);
499 newColours[i] = button.getBackground();
502 UserColourScheme ucs = new UserColourScheme(newColours);
504 if (caseSensitive.isSelected())
506 newColours = new Color[23];
507 for (int i = 0; i < 23; i++)
509 JButton button = (JButton) lowerCaseButtons.elementAt(i);
510 newColours[i] = button.getBackground();
512 ucs.setLowerCaseColours(newColours);
517 ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
529 protected void loadbutton_actionPerformed(ActionEvent e)
531 upperCaseButtons = new Vector();
532 lowerCaseButtons = new Vector();
534 JalviewFileChooser chooser = new JalviewFileChooser(
535 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
536 { "jc" }, new String[]
537 { "Jalview User Colours" }, "Jalview User Colours");
538 chooser.setFileView(new jalview.io.JalviewFileView());
539 chooser.setDialogTitle(MessageManager
540 .getString("label.load_colour_scheme"));
541 chooser.setToolTipText(MessageManager.getString("action.load"));
543 int value = chooser.showOpenDialog(this);
545 if (value == JalviewFileChooser.APPROVE_OPTION)
547 File choice = chooser.getSelectedFile();
548 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
549 String defaultColours = jalview.bin.Cache.getDefault(
550 "USER_DEFINED_COLOURS", choice.getPath());
551 if (defaultColours.indexOf(choice.getPath()) == -1)
553 defaultColours = defaultColours.concat("|")
554 .concat(choice.getPath());
557 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
559 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
560 Color[] colors = ucs.getColours();
561 schemeName.setText(ucs.getName());
563 if (ucs.getLowerCaseColours() != null)
565 caseSensitive.setSelected(true);
566 lcaseColour.setEnabled(true);
567 resetButtonPanel(true);
568 for (int i = 0; i < lowerCaseButtons.size(); i++)
570 JButton button = (JButton) lowerCaseButtons.elementAt(i);
571 button.setBackground(ucs.getLowerCaseColours()[i]);
577 caseSensitive.setSelected(false);
578 lcaseColour.setEnabled(false);
579 resetButtonPanel(false);
582 for (int i = 0; i < upperCaseButtons.size(); i++)
584 JButton button = (JButton) upperCaseButtons.elementAt(i);
585 button.setBackground(colors[i]);
594 * @return DOCUMENT ME!
596 public static UserColourScheme loadDefaultColours()
598 UserColourScheme ret = null;
600 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
603 if (colours.indexOf("|") > -1)
605 colours = colours.substring(0, colours.indexOf("|"));
608 ret = loadColours(colours);
613 Color[] newColours = new Color[24];
614 for (int i = 0; i < 24; i++)
616 newColours[i] = Color.white;
618 ret = new UserColourScheme(newColours);
630 * @return DOCUMENT ME!
632 static UserColourScheme loadColours(String file)
634 UserColourScheme ucs = null;
635 Color[] newColours = null;
638 InputStreamReader in = new InputStreamReader(
639 new FileInputStream(file), "UTF-8");
641 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
643 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
645 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
648 newColours = new Color[24];
650 Color[] lowerCase = null;
651 boolean caseSensitive = false;
655 for (int i = 0; i < jucs.getColourCount(); i++)
657 name = jucs.getColour(i).getName();
658 if (ResidueProperties.aa3Hash.containsKey(name))
660 index = ((Integer) ResidueProperties.aa3Hash.get(name))
665 index = ResidueProperties.aaIndex[name.charAt(0)];
672 if (name.toLowerCase().equals(name))
674 if (lowerCase == null)
676 lowerCase = new Color[23];
678 caseSensitive = true;
679 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
684 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
689 if (newColours != null)
691 ucs = new UserColourScheme(newColours);
692 ucs.setName(jucs.getSchemeName());
695 ucs.setLowerCaseColours(lowerCase);
699 } catch (Exception ex)
701 // Could be Archive Jalview format
704 InputStreamReader in = new InputStreamReader(new FileInputStream(
707 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
709 jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
711 newColours = new Color[jucs.getColourCount()];
713 for (int i = 0; i < 24; i++)
715 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
718 if (newColours != null)
720 ucs = new UserColourScheme(newColours);
721 ucs.setName(jucs.getSchemeName());
723 } catch (Exception ex2)
725 ex2.printStackTrace();
728 if (newColours == null)
730 System.out.println("Error loading User ColourFile\n" + ex);
743 protected void savebutton_actionPerformed(ActionEvent e)
745 if (schemeName.getText().trim().length() < 1)
747 JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
748 .getString("label.user_colour_scheme_must_have_name"),
749 MessageManager.getString("label.no_name_colour_scheme"),
750 JOptionPane.WARNING_MESSAGE);
754 if (userColourSchemes != null
755 && userColourSchemes.containsKey(schemeName.getText()))
757 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
758 MessageManager.formatMessage(
759 "label.colour_scheme_exists_overwrite", new String[]
760 { schemeName.getText(), schemeName.getText() }),
761 MessageManager.getString("label.duplicate_scheme_name"),
762 JOptionPane.YES_NO_OPTION);
763 if (reply != JOptionPane.YES_OPTION)
768 userColourSchemes.remove(schemeName.getText());
770 JalviewFileChooser chooser = new JalviewFileChooser(
771 jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
772 { "jc" }, new String[]
773 { "Jalview User Colours" }, "Jalview User Colours");
775 chooser.setFileView(new jalview.io.JalviewFileView());
776 chooser.setDialogTitle("Save colour scheme");
777 chooser.setToolTipText(MessageManager.getString("action.save"));
779 int value = chooser.showSaveDialog(this);
781 if (value == JalviewFileChooser.APPROVE_OPTION)
783 String choice = chooser.getSelectedFile().getPath();
784 String defaultColours = jalview.bin.Cache.getDefault(
785 "USER_DEFINED_COLOURS", choice);
786 if (defaultColours.indexOf(choice) == -1)
788 if (defaultColours.length() > 0)
790 defaultColours = defaultColours.concat("|");
792 defaultColours = defaultColours.concat(choice);
795 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
797 ap.alignFrame.updateUserColourMenu();
799 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
801 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
803 ucs.setSchemeName(schemeName.getText());
806 PrintWriter out = new PrintWriter(new OutputStreamWriter(
807 new FileOutputStream(choice), "UTF-8"));
809 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
811 JButton button = (JButton) buttonPanel.getComponent(i);
812 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
813 col.setName(button.getText());
814 col.setRGB(jalview.util.Format.getHexString(button
821 } catch (Exception ex)
823 ex.printStackTrace();
834 protected void cancelButton_actionPerformed(ActionEvent e)
838 if (seqGroup != null)
840 seqGroup.cs = oldColourScheme;
844 ap.av.setGlobalColourScheme(oldColourScheme);
846 ap.paintAlignment(true);
851 jmol.setJalviewColourScheme(oldColourScheme);
856 frame.setClosed(true);
857 } catch (Exception ex)
862 static Hashtable userColourSchemes;
864 public static Hashtable getUserColourSchemes()
866 return userColourSchemes;
869 public static void initUserColourSchemes(String files)
871 userColourSchemes = new Hashtable();
873 if (files == null || files.length() == 0)
878 // In case colours can't be loaded, we'll remove them
879 // from the default list here.
880 StringBuffer coloursFound = new StringBuffer();
881 StringTokenizer st = new StringTokenizer(files, "|");
882 while (st.hasMoreElements())
884 String file = st.nextToken();
887 UserColourScheme ucs = loadColours(file);
890 if (coloursFound.length() > 0)
892 coloursFound.append("|");
894 coloursFound.append(file);
895 userColourSchemes.put(ucs.getName(), ucs);
897 } catch (Exception ex)
899 System.out.println("Error loading User ColourFile\n" + ex);
902 if (!files.equals(coloursFound.toString()))
904 if (coloursFound.toString().length() > 1)
906 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
907 coloursFound.toString());
911 jalview.bin.Cache.applicationProperties
912 .remove("USER_DEFINED_COLOURS");
917 public static void removeColourFromDefaults(String target)
919 // The only way to find colours by name is to load them in
920 // In case colours can't be loaded, we'll remove them
921 // from the default list here.
923 userColourSchemes = new Hashtable();
925 StringBuffer coloursFound = new StringBuffer();
926 StringTokenizer st = new StringTokenizer(
927 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
929 while (st.hasMoreElements())
931 String file = st.nextToken();
934 UserColourScheme ucs = loadColours(file);
935 if (ucs != null && !ucs.getName().equals(target))
937 if (coloursFound.length() > 0)
939 coloursFound.append("|");
941 coloursFound.append(file);
942 userColourSchemes.put(ucs.getName(), ucs);
944 } catch (Exception ex)
946 System.out.println("Error loading User ColourFile\n" + ex);
950 if (coloursFound.toString().length() > 1)
952 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
953 coloursFound.toString());
957 jalview.bin.Cache.applicationProperties
958 .remove("USER_DEFINED_COLOURS");
963 public void caseSensitive_actionPerformed(ActionEvent e)
965 resetButtonPanel(caseSensitive.isSelected());
966 lcaseColour.setEnabled(caseSensitive.isSelected());
969 public void lcaseColour_actionPerformed(ActionEvent e)
971 if (selectedButtons == null)
973 selectedButtons = new Vector();
977 selectedButtons.clear();
979 selectedButtons.add(lcaseColour);