();
+ }
+
+ for (int i = 0; i < 20; i++)
+ {
+ int row = i / cols + 1;
+ int index = (row * cols) + i;
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
+
+ buttonPanel.add(button, index);
+ }
+ }
+
+ if (isCaseSensitive)
+ {
+ buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
+ buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
+ buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
+ }
+
+ // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
+ // codes
+ if (this.frame != null)
+ {
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ : MY_FRAME_WIDTH;
+ this.frame.setSize(newWidth, this.frame.getHeight());
+ }
+
+ buttonPanel.validate();
+ validate();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (selectedButtons != null)
+ {
+ JButton button = null;
+ final Color newColour = colorChooser.getColor();
+ for (int i = 0; i < selectedButtons.size(); i++)
+ {
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
+ }
+ if (button == lcaseColour)
+ {
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ button = lowerCaseButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(button
+ .getBackground()));
+ }
+ }
+ }
+ }
+
+ /**
+ * Performs actions when a residue button is clicked. This manages the button
+ * selection set (highlighted by brighter foreground text).
+ *
+ * On select button(s) with Ctrl/click or Shift/click: set button foreground
+ * text to brighter than background.
+ *
+ * On unselect button(s) with Ctrl/click on selected, or click to release
+ * current selection: reset foreground text to darker than background.
+ *
+ * Simple click: clear selection (resetting foreground to darker); set clicked
+ * button foreground to brighter
+ *
+ * Finally, synchronize the colour chooser to the colour of the first button
+ * in the selected set.
+ *
+ * @param e
+ */
+ public void colourButtonPressed(MouseEvent e)
+ {
+ if (selectedButtons == null)
+ {
+ selectedButtons = new ArrayList();
+ }
+
+ JButton pressed = (JButton) e.getSource();
+
+ if (e.isShiftDown())
+ {
+ JButton start, end = (JButton) e.getSource();
+ if (selectedButtons.size() > 0)
+ {
+ start = selectedButtons.get(selectedButtons.size() - 1);
+ }
+ else
+ {
+ start = (JButton) e.getSource();
+ }
+
+ int startIndex = 0, endIndex = 0;
+ for (int b = 0; b < buttonPanel.getComponentCount(); b++)
+ {
+ if (buttonPanel.getComponent(b) == start)
+ {
+ startIndex = b;
+ }
+ if (buttonPanel.getComponent(b) == end)
+ {
+ endIndex = b;
+ }
+ }
+
+ if (startIndex > endIndex)
+ {
+ int temp = startIndex;
+ startIndex = endIndex;
+ endIndex = temp;
+ }
+
+ for (int b = startIndex; b <= endIndex; b++)
+ {
+ JButton button = (JButton) buttonPanel.getComponent(b);
+ if (!selectedButtons.contains(button))
+ {
+ button.setForeground(ColorUtils.brighterThan(button
+ .getBackground()));
+ selectedButtons.add(button);
+ }
+ }
+ }
+ else if (!e.isControlDown())
+ {
+ for (int b = 0; b < selectedButtons.size(); b++)
+ {
+ JButton button = selectedButtons.get(b);
+ button.setForeground(ColorUtils.darkerThan(button.getBackground()));
+ }
+ selectedButtons.clear();
+ pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
+
+ }
+ else if (e.isControlDown())
+ {
+ if (selectedButtons.contains(pressed))
+ {
+ pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
+ selectedButtons.remove(pressed);
+ }
+ else
+ {
+ pressed.setForeground(ColorUtils.brighterThan(pressed
+ .getBackground()));
+ selectedButtons.add(pressed);
+ }
+ }
+
+ if (selectedButtons.size() > 0)
+ {
+ colorChooser.setColor((selectedButtons.get(0)).getBackground());
+ }
+ }
+
+ /**
+ * A helper method to update or make a colour button, whose background colour
+ * is the associated colour, and text colour a darker shade of the same. If
+ * the button is already in the list, then its text and margins are updated,
+ * if not then it is created and added. This method supports toggling between
+ * case-sensitive and case-insensitive button panels. The case-sensitive
+ * version has abbreviated button text in order to fit in more buttons.
+ *
+ * @param label
+ * @param residue
+ * @param the
+ * list of buttons
+ * @param buttonIndex
+ * the button's position in the list
+ */
+ JButton makeButton(String label, String residue, List buttons,
+ int buttonIndex)
+ {
+ final JButton button;
+ Color col;
+
+ if (buttonIndex < buttons.size())
+ {
+ button = buttons.get(buttonIndex);
+ col = button.getBackground();
+ }
+ else
+ {
+ button = new JButton();
+ button.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseClicked(MouseEvent e)
+ {
+ colourButtonPressed(e);
+ }
+ });
+
+ buttons.add(button);
+
+ /*
+ * make initial button colour that of the current colour scheme,
+ * if it is a simple per-residue colouring, else white
+ */
+ col = Color.white;
+ if (oldColourScheme != null && oldColourScheme.isSimple())
+ {
+ col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+ 0f);
+ }
+ }
+
+ if (caseSensitive.isSelected())
+ {
+ button.setMargin(new Insets(2, 2, 2, 2));
+ }
+ else
+ {
+ button.setMargin(new Insets(2, 14, 2, 14));
+ }
+
+ button.setOpaque(true); // required for the next line to have effect
+ button.setBackground(col);
+ button.setText(label);
+ button.setForeground(ColorUtils.darkerThan(col));
+ button.setFont(VERDANA_BOLD_10);
+
+ return button;
+ }
+
+ /**
+ * On 'OK', check that at least one colour has been assigned to a residue (and
+ * if not issue a warning), and apply the chosen colour scheme and close the
+ * panel.
+ */
+ @Override
+ protected void okButton_actionPerformed()
+ {
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ applyButton_actionPerformed();
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * Returns true if the user has not made any colour selection (including if
+ * 'case-sensitive' selected and no lower-case colour chosen).
+ *
+ * @return
+ */
+ protected boolean isNoSelectionMade()
+ {
+ final boolean noUpperCaseSelected = upperCaseButtons == null
+ || upperCaseButtons.isEmpty();
+ final boolean noLowerCaseSelected = caseSensitive.isSelected()
+ && (lowerCaseButtons == null || lowerCaseButtons.isEmpty());
+ final boolean noSelectionMade = noUpperCaseSelected
+ || noLowerCaseSelected;
+ return noSelectionMade;
+ }
+
+ /**
+ * Applies the current colour scheme to the alignment, sequence group or
+ * structure view.
+ */
+ @Override
+ protected void applyButton_actionPerformed()
+ {
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ UserColourScheme ucs = getSchemeFromButtons();
+
+ if (seqGroup != null)
+ {
+ seqGroup.setColourScheme(ucs);
+ ap.paintAlignment(true);
+ }
+ else if (ap != null)
+ {
+ ap.alignFrame.changeColour(ucs);
+ }
+ else if (structureViewer != null)
+ {
+ structureViewer.setJalviewColourScheme(ucs);
+ }
+ }
+
+ UserColourScheme getSchemeFromButtons()
+ {
+
+ Color[] newColours = new Color[24];
+
+ int length = upperCaseButtons.size();
+ if (length < 24)
+ {
+ int i = 0;
+ for (JButton btn : upperCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 24; i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
+ }
+
+ UserColourScheme ucs = new UserColourScheme(newColours);
+ ucs.setName(schemeName.getText());
+
+ if (caseSensitive.isSelected())
+ {
+ newColours = new Color[23];
+ length = lowerCaseButtons.size();
+ if (length < 23)
+ {
+ int i = 0;
+ for (JButton btn : lowerCaseButtons)
+ {
+ newColours[i] = btn.getBackground();
+ i++;
+ }
+ }
+ else
+ {
+ for (int i = 0; i < 23; i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ newColours[i] = button.getBackground();
+ }
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ // if (ap != null)
+ // {
+ // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ // }
+
+ return ucs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void loadbutton_actionPerformed(ActionEvent e)
+ {
+ upperCaseButtons = new ArrayList();
+ lowerCaseButtons = new ArrayList();
+
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value != JalviewFileChooser.APPROVE_OPTION)
+ {
+ return;
+ }
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
+
+ UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+ .getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
+
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
+ }
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
+
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
+ }
+
+ addNewColourScheme(choice.getPath());
+ }
+
+ /**
+ * Loads the user-defined colour scheme from the first file listed in property
+ * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme.
+ *
+ * @return
+ */
+ public static UserColourScheme loadDefaultColours()
+ {
+ UserColourScheme ret = null;
+
+ String colours = Cache.getProperty(USER_DEFINED_COLOURS);
+ if (colours != null)
+ {
+ if (colours.indexOf("|") > -1)
+ {
+ colours = colours.substring(0, colours.indexOf("|"));
+ }
+ ret = ColourSchemes.loadColourScheme(colours);
+ }
+
+ if (ret == null)
+ {
+ ret = new UserColourScheme("white");
+ }
+
+ return ret;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ protected void savebutton_actionPerformed(ActionEvent e)
+ {
+ String name = schemeName.getText().trim();
+ if (name.length() < 1)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.user_colour_scheme_must_have_name"),
+ MessageManager.getString("label.no_name_colour_scheme"),
+ JvOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ if (ColourSchemes.getInstance().nameExists(name))
+ {
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.colour_scheme_exists_overwrite", new Object[] {
+ name, name }),
+ MessageManager.getString("label.duplicate_scheme_name"),
+ JvOptionPane.YES_NO_OPTION);
+ if (reply != JvOptionPane.YES_OPTION)
+ {
+ return;
+ }
+ ColourSchemes.getInstance().removeColourScheme(name);
+ }
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
+
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int value = chooser.showSaveDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ addNewColourScheme(file.getPath());
+ saveToFile(file);
+ }
+ }
+
+ /**
+ * Adds the current colour scheme to the Jalview properties file so it is
+ * loaded on next startup, and updates the Colour menu in the parent
+ * AlignFrame (if there is one). Note this action does not including applying
+ * the colour scheme.
+ *
+ * @param filePath
+ */
+ protected void addNewColourScheme(String filePath)
+ {
+ /*
+ * update the delimited list of user defined colour files in
+ * Jalview property USER_DEFINED_COLOURS
+ */
+ String defaultColours = Cache
+ .getDefault(USER_DEFINED_COLOURS, filePath);
+ if (defaultColours.indexOf(filePath) == -1)
+ {
+ if (defaultColours.length() > 0)
+ {
+ defaultColours = defaultColours.concat("|");
+ }
+ defaultColours = defaultColours.concat(filePath);
+ }
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
+
+ /*
+ * construct and register the colour scheme
+ */
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
+
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
+ {
+ ap.alignFrame.buildColourMenu();
+ }
+ }
+
+ /**
+ * Saves the colour scheme to file in XML format
+ *
+ * @param path
+ */
+ protected void saveToFile(File toFile)
+ {
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName(schemeName.getText());
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(toFile), "UTF-8"));
+
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
+ {
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.addColour(col);
+ }
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * On cancel, restores the colour scheme before the dialogue was opened
+ *
+ * @param e
+ */
+ @Override
+ protected void cancelButton_actionPerformed(ActionEvent e)
+ {
+ if (ap != null)
+ {
+ if (seqGroup != null)
+ {
+ seqGroup.setColourScheme(oldColourScheme);
+ }
+ else
+ {
+ ap.alignFrame.changeColour(oldColourScheme);
+ }
+ ap.paintAlignment(true);
+ }
+
+ if (structureViewer != null)
+ {
+ structureViewer.setJalviewColourScheme(oldColourScheme);
+ }
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ @Override
+ public void caseSensitive_actionPerformed(ActionEvent e)
+ {
+ resetButtonPanel(caseSensitive.isSelected());
+ lcaseColour.setEnabled(caseSensitive.isSelected());
+ }
+
+ @Override
+ public void lcaseColour_actionPerformed(ActionEvent e)
+ {
+ if (selectedButtons == null)
+ {
+ selectedButtons = new ArrayList();
+ }
+ else
+ {
+ selectedButtons.clear();
+ }
+ selectedButtons.add(lcaseColour);
+ }
+}