2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.bin.Cache;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.io.JalviewFileChooser;
27 import jalview.jbgui.GUserDefinedColours;
28 import jalview.schemes.ColourSchemeI;
29 import jalview.schemes.ResidueProperties;
30 import jalview.schemes.UserColourScheme;
31 import jalview.util.ColorUtils;
32 import jalview.util.MessageManager;
34 import java.awt.Color;
36 import java.awt.event.ActionEvent;
37 import java.awt.event.MouseEvent;
39 import java.io.FileInputStream;
40 import java.io.FileOutputStream;
41 import java.io.InputStreamReader;
42 import java.io.OutputStreamWriter;
43 import java.io.PrintWriter;
44 import java.util.ArrayList;
45 import java.util.Hashtable;
46 import java.util.StringTokenizer;
48 import javax.swing.JButton;
49 import javax.swing.JInternalFrame;
50 import javax.swing.JOptionPane;
51 import javax.swing.event.ChangeEvent;
52 import javax.swing.event.ChangeListener;
55 * This panel allows the user to assign colours to Amino Acid residue codes, and
56 * save the colour scheme.
58 * @author Andrew Waterhouse
59 * @author Mungo Carstairs
61 public class UserDefinedColours extends GUserDefinedColours implements
64 private static final int MY_FRAME_HEIGHT = 420;
66 private static final int MY_FRAME_WIDTH = 810;
68 private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
72 SequenceGroup seqGroup;
74 ArrayList<JButton> selectedButtons;
76 ColourSchemeI oldColourScheme;
80 JalviewStructureDisplayI jmol;
82 ArrayList<JButton> upperCaseButtons;
84 ArrayList<JButton> lowerCaseButtons;
87 * Creates a new UserDefinedColours object.
94 public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
98 lcaseColour.setEnabled(false);
103 if (seqGroup != null)
105 oldColourScheme = seqGroup.cs;
109 oldColourScheme = ap.av.getGlobalColourScheme();
112 if (oldColourScheme instanceof UserColourScheme)
114 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
115 if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
117 caseSensitive.setSelected(true);
118 lcaseColour.setEnabled(true);
119 resetButtonPanel(true);
123 resetButtonPanel(false);
128 resetButtonPanel(false);
134 public UserDefinedColours(JalviewStructureDisplayI jmol,
140 colorChooser.getSelectionModel().addChangeListener(this);
142 oldColourScheme = oldcs;
144 if (oldColourScheme instanceof UserColourScheme)
146 schemeName.setText(((UserColourScheme) oldColourScheme).getName());
149 resetButtonPanel(false);
157 colorChooser.getSelectionModel().addChangeListener(this);
158 frame = new JInternalFrame();
159 frame.setContentPane(this);
160 Desktop.addInternalFrame(frame,
161 MessageManager.getString("label.user_defined_colours"),
162 MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
164 if (seqGroup != null)
166 frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
170 void resetButtonPanel(boolean caseSensitive)
172 buttonPanel.removeAll();
174 if (upperCaseButtons == null)
176 upperCaseButtons = new ArrayList<JButton>();
181 for (int i = 0; i < 20; i++)
185 label = ResidueProperties.aa[i];
189 label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
193 button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
196 buttonPanel.add(button);
199 buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
200 buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
201 buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
202 buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
206 gridLayout.setRows(6);
207 gridLayout.setColumns(4);
211 gridLayout.setRows(7);
213 gridLayout.setColumns(cols + 1);
215 if (lowerCaseButtons == null)
217 lowerCaseButtons = new ArrayList<JButton>();
220 for (int i = 0; i < 20; i++)
222 int row = i / cols + 1;
223 int index = (row * cols) + i;
224 button = makeButton(ResidueProperties.aa[i].toLowerCase(),
225 ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
227 buttonPanel.add(button, index);
233 buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
234 buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
235 buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
238 // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
240 if (this.frame != null)
242 int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
244 this.frame.setSize(newWidth, this.frame.getHeight());
247 buttonPanel.validate();
258 public void stateChanged(ChangeEvent evt)
260 if (selectedButtons != null)
262 JButton button = null;
263 final Color newColour = colorChooser.getColor();
264 for (int i = 0; i < selectedButtons.size(); i++)
266 button = selectedButtons.get(i);
267 button.setBackground(newColour);
268 button.setForeground(ColorUtils.brighterThan(newColour));
270 if (button == lcaseColour)
272 for (int i = 0; i < lowerCaseButtons.size(); i++)
274 button = lowerCaseButtons.get(i);
275 button.setBackground(newColour);
276 button.setForeground(ColorUtils.brighterThan(button
284 * Performs actions when a residue button is clicked. This manages the button
285 * selection set (highlighted by brighter foreground text).
287 * On select button(s) with Ctrl/click or Shift/click: set button foreground
288 * text to brighter than background.
290 * On unselect button(s) with Ctrl/click on selected, or click to release
291 * current selection: reset foreground text to darker than background.
293 * Simple click: clear selection (resetting foreground to darker); set clicked
294 * button foreground to brighter
296 * Finally, synchronize the colour chooser to the colour of the first button
297 * in the selected set.
301 public void colourButtonPressed(MouseEvent e)
303 if (selectedButtons == null)
305 selectedButtons = new ArrayList<JButton>();
308 JButton pressed = (JButton) e.getSource();
312 JButton start, end = (JButton) e.getSource();
313 if (selectedButtons.size() > 0)
315 start = selectedButtons.get(selectedButtons.size() - 1);
319 start = (JButton) e.getSource();
322 int startIndex = 0, endIndex = 0;
323 for (int b = 0; b < buttonPanel.getComponentCount(); b++)
325 if (buttonPanel.getComponent(b) == start)
329 if (buttonPanel.getComponent(b) == end)
335 if (startIndex > endIndex)
337 int temp = startIndex;
338 startIndex = endIndex;
342 for (int b = startIndex; b <= endIndex; b++)
344 JButton button = (JButton) buttonPanel.getComponent(b);
345 if (!selectedButtons.contains(button))
347 button.setForeground(ColorUtils.brighterThan(button
349 selectedButtons.add(button);
353 else if (!e.isControlDown())
355 for (int b = 0; b < selectedButtons.size(); b++)
357 JButton button = selectedButtons.get(b);
358 button.setForeground(ColorUtils.darkerThan(button.getBackground()));
360 selectedButtons.clear();
361 pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
362 selectedButtons.add(pressed);
365 else if (e.isControlDown())
367 if (selectedButtons.contains(pressed))
369 pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
370 selectedButtons.remove(pressed);
374 pressed.setForeground(ColorUtils.brighterThan(pressed
376 selectedButtons.add(pressed);
380 if (selectedButtons.size() > 0)
382 colorChooser.setColor((selectedButtons.get(0)).getBackground());
394 JButton makeButton(String label, String aa,
395 ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
397 final JButton button;
400 if (buttonIndex < caseSensitiveButtons.size())
402 button = caseSensitiveButtons.get(buttonIndex);
403 col = button.getBackground();
407 button = new JButton();
408 button.addMouseListener(new java.awt.event.MouseAdapter()
411 public void mouseClicked(MouseEvent e)
413 colourButtonPressed(e);
417 caseSensitiveButtons.add(button);
420 if (oldColourScheme != null)
424 col = oldColourScheme.findColour(aa.charAt(0), -1, null);
425 } catch (Exception ex)
431 if (caseSensitive.isSelected())
433 button.setMargin(new java.awt.Insets(2, 2, 2, 2));
437 button.setMargin(new java.awt.Insets(2, 14, 2, 14));
440 button.setOpaque(true); // required for the next line to have effect
441 button.setBackground(col);
442 button.setText(label);
443 button.setForeground(ColorUtils.darkerThan(col));
444 button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
456 protected void okButton_actionPerformed(ActionEvent e)
458 if (isNoSelectionMade())
460 JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
461 .getString("label.no_colour_selection_in_scheme"),
462 MessageManager.getString("label.no_colour_selection_warn"),
463 JvOptionPane.WARNING_MESSAGE);
467 applyButton_actionPerformed(null);
471 frame.setClosed(true);
472 } catch (Exception ex)
479 * Returns true if the user has not made any colour selection (including if
480 * 'case-sensitive' selected and no lower-case colour chosen).
484 protected boolean isNoSelectionMade()
486 final boolean noUpperCaseSelected = upperCaseButtons == null
487 || upperCaseButtons.isEmpty();
488 final boolean noLowerCaseSelected = caseSensitive.isSelected()
489 && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
490 final boolean noSelectionMade = noUpperCaseSelected
491 || noLowerCaseSelected;
492 return noSelectionMade;
502 protected void applyButton_actionPerformed(ActionEvent e)
504 if (isNoSelectionMade())
506 JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
507 .getString("label.no_colour_selection_in_scheme"),
508 MessageManager.getString("label.no_colour_selection_warn"),
509 JvOptionPane.WARNING_MESSAGE);
512 UserColourScheme ucs = getSchemeFromButtons();
513 ucs.setName(schemeName.getText());
515 if (seqGroup != null)
518 ap.paintAlignment(true);
522 ap.alignFrame.changeColour(ucs);
524 else if (jmol != null)
526 jmol.setJalviewColourScheme(ucs);
530 UserColourScheme getSchemeFromButtons()
533 Color[] newColours = new Color[24];
535 int length = upperCaseButtons.size();
539 for (JButton btn : upperCaseButtons)
541 newColours[i] = btn.getBackground();
547 for (int i = 0; i < 24; i++)
549 JButton button = upperCaseButtons.get(i);
550 newColours[i] = button.getBackground();
554 UserColourScheme ucs = new UserColourScheme(newColours);
556 if (caseSensitive.isSelected())
558 newColours = new Color[23];
559 length = lowerCaseButtons.size();
563 for (JButton btn : lowerCaseButtons)
565 newColours[i] = btn.getBackground();
571 for (int i = 0; i < 23; i++)
573 JButton button = lowerCaseButtons.get(i);
574 newColours[i] = button.getBackground();
577 ucs.setLowerCaseColours(newColours);
582 ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
595 protected void loadbutton_actionPerformed(ActionEvent e)
597 upperCaseButtons = new ArrayList<JButton>();
598 lowerCaseButtons = new ArrayList<JButton>();
600 JalviewFileChooser chooser = new JalviewFileChooser(
601 Cache.getProperty("LAST_DIRECTORY"), "jc",
602 "Jalview User Colours", "Jalview User Colours");
603 chooser.setFileView(new jalview.io.JalviewFileView());
604 chooser.setDialogTitle(MessageManager
605 .getString("label.load_colour_scheme"));
606 chooser.setToolTipText(MessageManager.getString("action.load"));
608 int value = chooser.showOpenDialog(this);
610 if (value == JalviewFileChooser.APPROVE_OPTION)
612 File choice = chooser.getSelectedFile();
613 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
614 String defaultColours = jalview.bin.Cache.getDefault(
615 "USER_DEFINED_COLOURS", choice.getPath());
616 if (defaultColours.indexOf(choice.getPath()) == -1)
618 defaultColours = defaultColours.concat("|")
619 .concat(choice.getPath());
622 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
624 UserColourScheme ucs = loadColours(choice.getAbsolutePath());
625 Color[] colors = ucs.getColours();
626 schemeName.setText(ucs.getName());
628 if (ucs.getLowerCaseColours() != null)
630 caseSensitive.setSelected(true);
631 lcaseColour.setEnabled(true);
632 resetButtonPanel(true);
633 for (int i = 0; i < lowerCaseButtons.size(); i++)
635 JButton button = lowerCaseButtons.get(i);
636 button.setBackground(ucs.getLowerCaseColours()[i]);
642 caseSensitive.setSelected(false);
643 lcaseColour.setEnabled(false);
644 resetButtonPanel(false);
647 for (int i = 0; i < upperCaseButtons.size(); i++)
649 JButton button = upperCaseButtons.get(i);
650 button.setBackground(colors[i]);
659 * @return DOCUMENT ME!
661 public static UserColourScheme loadDefaultColours()
663 UserColourScheme ret = null;
665 String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
668 if (colours.indexOf("|") > -1)
670 colours = colours.substring(0, colours.indexOf("|"));
673 ret = loadColours(colours);
678 Color[] newColours = new Color[24];
679 for (int i = 0; i < 24; i++)
681 newColours[i] = Color.white;
683 ret = new UserColourScheme(newColours);
695 * @return DOCUMENT ME!
697 static UserColourScheme loadColours(String file)
699 UserColourScheme ucs = null;
700 Color[] newColours = null;
703 InputStreamReader in = new InputStreamReader(
704 new FileInputStream(file), "UTF-8");
706 jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
708 org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
710 jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
713 newColours = new Color[24];
715 Color[] lowerCase = null;
716 boolean caseSensitive = false;
720 for (int i = 0; i < jucs.getColourCount(); i++)
722 name = jucs.getColour(i).getName();
723 if (ResidueProperties.aa3Hash.containsKey(name))
725 index = ResidueProperties.aa3Hash.get(name).intValue();
729 index = ResidueProperties.aaIndex[name.charAt(0)];
736 if (name.toLowerCase().equals(name))
738 if (lowerCase == null)
740 lowerCase = new Color[23];
742 caseSensitive = true;
743 lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
748 newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
753 if (newColours != null)
755 ucs = new UserColourScheme(newColours);
756 ucs.setName(jucs.getSchemeName());
759 ucs.setLowerCaseColours(lowerCase);
763 } catch (Exception ex)
765 // Could be Archive Jalview format
768 InputStreamReader in = new InputStreamReader(new FileInputStream(
771 jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
773 jucs = jucs.unmarshal(in);
775 newColours = new Color[jucs.getColourCount()];
777 for (int i = 0; i < 24; i++)
779 newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
782 if (newColours != null)
784 ucs = new UserColourScheme(newColours);
785 ucs.setName(jucs.getSchemeName());
787 } catch (Exception ex2)
789 ex2.printStackTrace();
792 if (newColours == null)
794 System.out.println("Error loading User ColourFile\n" + ex);
808 protected void savebutton_actionPerformed(ActionEvent e)
810 if (schemeName.getText().trim().length() < 1)
812 JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
813 .getString("label.user_colour_scheme_must_have_name"),
814 MessageManager.getString("label.no_name_colour_scheme"),
815 JvOptionPane.WARNING_MESSAGE);
819 if (userColourSchemes != null
820 && userColourSchemes.containsKey(schemeName.getText()))
822 int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
823 MessageManager.formatMessage(
824 "label.colour_scheme_exists_overwrite", new Object[] {
825 schemeName.getText(), schemeName.getText() }),
826 MessageManager.getString("label.duplicate_scheme_name"),
827 JvOptionPane.YES_NO_OPTION);
828 if (reply != JvOptionPane.YES_OPTION)
833 userColourSchemes.remove(schemeName.getText());
835 JalviewFileChooser chooser = new JalviewFileChooser(
836 Cache.getProperty("LAST_DIRECTORY"), "jc",
837 "Jalview User Colours", "Jalview User Colours");
839 chooser.setFileView(new jalview.io.JalviewFileView());
840 chooser.setDialogTitle(MessageManager
841 .getString("label.save_colour_scheme"));
842 chooser.setToolTipText(MessageManager.getString("action.save"));
844 int value = chooser.showSaveDialog(this);
846 if (value == JalviewFileChooser.APPROVE_OPTION)
848 String choice = chooser.getSelectedFile().getPath();
849 String defaultColours = jalview.bin.Cache.getDefault(
850 "USER_DEFINED_COLOURS", choice);
851 if (defaultColours.indexOf(choice) == -1)
853 if (defaultColours.length() > 0)
855 defaultColours = defaultColours.concat("|");
857 defaultColours = defaultColours.concat(choice);
860 userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
862 ap.alignFrame.updateUserColourMenu();
864 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
866 jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
868 ucs.setSchemeName(schemeName.getText());
871 PrintWriter out = new PrintWriter(new OutputStreamWriter(
872 new FileOutputStream(choice), "UTF-8"));
874 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
876 JButton button = (JButton) buttonPanel.getComponent(i);
877 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
878 col.setName(button.getText());
879 col.setRGB(jalview.util.Format.getHexString(button
886 } catch (Exception ex)
888 ex.printStackTrace();
900 protected void cancelButton_actionPerformed(ActionEvent e)
904 if (seqGroup != null)
906 seqGroup.cs = oldColourScheme;
910 ap.av.setGlobalColourScheme(oldColourScheme);
912 ap.paintAlignment(true);
917 jmol.setJalviewColourScheme(oldColourScheme);
922 frame.setClosed(true);
923 } catch (Exception ex)
928 static Hashtable userColourSchemes;
930 public static Hashtable getUserColourSchemes()
932 return userColourSchemes;
935 public static void initUserColourSchemes(String files)
937 userColourSchemes = new Hashtable();
939 if (files == null || files.length() == 0)
944 // In case colours can't be loaded, we'll remove them
945 // from the default list here.
946 StringBuffer coloursFound = new StringBuffer();
947 StringTokenizer st = new StringTokenizer(files, "|");
948 while (st.hasMoreElements())
950 String file = st.nextToken();
953 UserColourScheme ucs = loadColours(file);
956 if (coloursFound.length() > 0)
958 coloursFound.append("|");
960 coloursFound.append(file);
961 userColourSchemes.put(ucs.getName(), ucs);
963 } catch (Exception ex)
965 System.out.println("Error loading User ColourFile\n" + ex);
968 if (!files.equals(coloursFound.toString()))
970 if (coloursFound.toString().length() > 1)
972 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
973 coloursFound.toString());
977 jalview.bin.Cache.applicationProperties
978 .remove("USER_DEFINED_COLOURS");
983 public static void removeColourFromDefaults(String target)
985 // The only way to find colours by name is to load them in
986 // In case colours can't be loaded, we'll remove them
987 // from the default list here.
989 userColourSchemes = new Hashtable();
991 StringBuffer coloursFound = new StringBuffer();
992 StringTokenizer st = new StringTokenizer(
993 jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
995 while (st.hasMoreElements())
997 String file = st.nextToken();
1000 UserColourScheme ucs = loadColours(file);
1001 if (ucs != null && !ucs.getName().equals(target))
1003 if (coloursFound.length() > 0)
1005 coloursFound.append("|");
1007 coloursFound.append(file);
1008 userColourSchemes.put(ucs.getName(), ucs);
1010 } catch (Exception ex)
1012 System.out.println("Error loading User ColourFile\n" + ex);
1016 if (coloursFound.toString().length() > 1)
1018 jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
1019 coloursFound.toString());
1023 jalview.bin.Cache.applicationProperties
1024 .remove("USER_DEFINED_COLOURS");
1030 public void caseSensitive_actionPerformed(ActionEvent e)
1032 resetButtonPanel(caseSensitive.isSelected());
1033 lcaseColour.setEnabled(caseSensitive.isSelected());
1037 public void lcaseColour_actionPerformed(ActionEvent e)
1039 if (selectedButtons == null)
1041 selectedButtons = new ArrayList<JButton>();
1045 selectedButtons.clear();
1047 selectedButtons.add(lcaseColour);