+ * 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 Vector();
- }
-
JButton pressed = (JButton) e.getSource();
if (e.isShiftDown())
@@ -258,7 +297,7 @@ public class UserDefinedColours
JButton start, end = (JButton) e.getSource();
if (selectedButtons.size() > 0)
{
- start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
+ start = selectedButtons.get(selectedButtons.size() - 1);
}
else
{
@@ -290,7 +329,8 @@ public class UserDefinedColours
JButton button = (JButton) buttonPanel.getComponent(b);
if (!selectedButtons.contains(button))
{
- button.setForeground(button.getBackground().brighter().brighter());
+ button.setForeground(
+ ColorUtils.brighterThan(button.getBackground()));
selectedButtons.add(button);
}
}
@@ -299,630 +339,581 @@ public class UserDefinedColours
{
for (int b = 0; b < selectedButtons.size(); b++)
{
- JButton button = (JButton) selectedButtons.elementAt(b);
- button.setForeground(button.getBackground().darker().darker());
+ JButton button = selectedButtons.get(b);
+ button.setForeground(ColorUtils.darkerThan(button.getBackground()));
}
selectedButtons.clear();
- pressed.setForeground(pressed.getBackground().brighter().brighter());
- selectedButtons.addElement(pressed);
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
}
else if (e.isControlDown())
{
if (selectedButtons.contains(pressed))
{
- pressed.setForeground(pressed.getBackground().darker().darker());
+ pressed.setForeground(
+ ColorUtils.darkerThan(pressed.getBackground()));
selectedButtons.remove(pressed);
}
else
{
- pressed.setForeground(pressed.getBackground().brighter().brighter());
- selectedButtons.addElement(pressed);
+ pressed.setForeground(
+ ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
}
}
if (selectedButtons.size() > 0)
{
- colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).
- getBackground());
+ colorChooser.setColor((selectedButtons.get(0)).getBackground());
}
}
/**
- * DOCUMENT ME!
- *
- * @param label DOCUMENT ME!
- * @param aa DOCUMENT ME!
+ * 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 aa,
- Vector caseSensitiveButtons,
- int buttonIndex)
+ JButton makeButton(String label, String residue, List
+ *
*/
- protected void loadbutton_actionPerformed(ActionEvent e)
+ @Override
+ protected void loadbutton_actionPerformed()
{
- upperCaseButtons = new Vector();
- lowerCaseButtons = new Vector();
-
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"jc"},
- new String[]
- {"Jalview User Colours"}, "Jalview User Colours");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Load colour scheme");
- chooser.setToolTipText("Load");
-
- int value = chooser.showOpenDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS",
- choice.getPath());
- if (defaultColours.indexOf(choice.getPath()) == -1)
- {
- defaultColours = defaultColours.concat("|").concat(choice.getPath());
- }
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getName());
-
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = (JButton) lowerCaseButtons.elementAt(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 = (JButton) upperCaseButtons.elementAt(i);
- button.setBackground(colors[i]);
- }
-
- }
+ 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"));
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
+
+ UserColourScheme ucs = ColourSchemeLoader
+ .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());
+ }
+ });
+
+ chooser.showOpenDialog(this);
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * 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 = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+ String colours = Cache.getProperty(USER_DEFINED_COLOURS);
if (colours != null)
{
if (colours.indexOf("|") > -1)
{
colours = colours.substring(0, colours.indexOf("|"));
}
-
- ret = loadColours(colours);
+ ret = ColourSchemeLoader.loadColourScheme(colours);
}
if (ret == null)
{
- Color[] newColours = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = Color.white;
- }
- ret = new UserColourScheme(newColours);
+ ret = new UserColourScheme("white");
}
return ret;
}
/**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Action on pressing the Save button.
+ *
+ *
+ * If the scheme is saved to file, the 'changed' flag field is reset to false.
*/
- static UserColourScheme loadColours(String file)
+ @Override
+ protected void savebutton_actionPerformed()
{
- UserColourScheme ucs = null;
- Color[] newColours = null;
- try
- {
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
- jalview.schemabinding.version2.JalviewUserColours jucs
- = new jalview.schemabinding.version2.JalviewUserColours();
-
- org.exolab.castor.xml.Unmarshaller unmar
- = new org.exolab.castor.xml.Unmarshaller(jucs);
- jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.
- unmarshal(in);
-
- newColours = new Color[24];
-
- Color[] lowerCase = null;
- boolean caseSensitive = false;
-
- String name;
- int index;
- for (int i = 0; i < jucs.getColourCount(); i++)
- {
- name = jucs.getColour(i).getName();
- if (ResidueProperties.aa3Hash.containsKey(name))
- {
- index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
- }
- else
- {
- index = ResidueProperties.aaIndex[name.charAt(0)];
- }
- if (index == -1)
+ 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);
+ }
+
+ if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name))
+ {
+ /**
+ * java only
+ *
+ * @j2sIgnore
+ */
+ {
+ 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)
{
- continue;
- }
-
- if (name.toLowerCase().equals(name))
- {
- if (lowerCase == null)
- {
- lowerCase = new Color[23];
- }
- caseSensitive = true;
- lowerCase[index] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
- }
- else
- {
- newColours[index] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
+ return;
}
}
-
- if (newColours != null)
- {
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- if (caseSensitive)
- {
- ucs.setLowerCaseColours(lowerCase);
- }
- }
-
}
- catch (Exception ex)
- {
- //Could be Archive Jalview format
- try
- {
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
- jalview.binding.JalviewUserColours jucs
- = new jalview.binding.JalviewUserColours();
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+ JalviewFileChooser chooser = new JalviewFileChooser("jc",
+ "Jalview User Colours");
- newColours = new Color[jucs.getColourCount()];
-
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
- }
- if (newColours != null)
- {
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- }
- }
- catch (Exception ex2)
- {
- ex2.printStackTrace();
- }
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
+ chooser.setDialogTitle(
+ MessageManager.getString("label.save_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
+ int option = chooser.showSaveDialog(this);
+ if (option == JalviewFileChooser.APPROVE_OPTION)
+ {
+ File file = chooser.getSelectedFile();
+ UserColourScheme updatedScheme = addNewColourScheme(file.getPath());
+ saveToFile(file);
+ changedButNotSaved = false;
- if (newColours == null)
+ /*
+ * changes saved - apply to alignment if we are changing
+ * the currently selected colour scheme; also make the updated
+ * colours the 'backout' scheme on Cancel
+ */
+ if (oldColourScheme != null
+ && name.equals(oldColourScheme.getSchemeName()))
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ oldColourScheme = updatedScheme;
+ applyButton_actionPerformed();
}
}
-
- return ucs;
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * 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
+ * @return
*/
- protected void savebutton_actionPerformed(ActionEvent e)
+ protected UserColourScheme addNewColourScheme(String filePath)
{
- if (schemeName.getText().trim().length() < 1)
+ /*
+ * 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)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "User colour scheme must have a name!",
- "No name for colour scheme",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- if (userColourSchemes != null &&
- userColourSchemes.containsKey(schemeName.getText()))
- {
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- "Colour scheme " + schemeName.getText() + " exists."
- + "\nContinue saving colour scheme as " + schemeName.getText() + "?",
- "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
- if (reply != JOptionPane.YES_OPTION)
+ if (defaultColours.length() > 0)
{
- return;
+ defaultColours = defaultColours.concat("|");
}
-
- userColourSchemes.remove(schemeName.getText());
+ defaultColours = defaultColours.concat(filePath);
}
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"jc"},
- new String[]
- {"Jalview User Colours"}, "Jalview User Colours");
-
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Save colour scheme");
- chooser.setToolTipText("Save");
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
- int value = chooser.showSaveDialog(this);
+ /*
+ * construct and register the colour scheme
+ */
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
{
- String choice = chooser.getSelectedFile().getPath();
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice);
- if (defaultColours.indexOf(choice) == -1)
- {
- if (defaultColours.length() > 0)
- {
- defaultColours = defaultColours.concat("|");
- }
- defaultColours = defaultColours.concat(choice);
- }
-
- userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
-
- ap.alignFrame.updateUserColourMenu();
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- jalview.schemabinding.version2.JalviewUserColours ucs
- = new jalview.schemabinding.version2.JalviewUserColours();
-
- ucs.setSchemeName(schemeName.getText());
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
-
- for (int i = 0; i < buttonPanel.getComponentCount(); i++)
- {
- JButton button = (JButton) buttonPanel.getComponent(i);
- jalview.schemabinding.version2.Colour col
- = new jalview.schemabinding.version2.Colour();
- col.setName(button.getText());
- col.setRGB(jalview.util.Format.getHexString(
- button.getBackground()));
- ucs.addColour(col);
- }
-
- ucs.marshal(out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ ap.alignFrame.buildColourMenu();
}
+
+ return ucs;
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * Saves the colour scheme to file in XML format
+ *
+ * @param path
*/
- protected void cancelButton_actionPerformed(ActionEvent e)
+ protected void saveToFile(File toFile)
{
- if (ap != null)
- {
- if (seqGroup != null)
- {
- seqGroup.cs = oldColourScheme;
- }
- else if (ap != null)
- {
- ap.av.setGlobalColourScheme(oldColourScheme);
- }
- ap.paintAlignment(true);
- }
-
- if (jmol != null)
- {
- jmol.setJalviewColourScheme(oldColourScheme);
- }
-
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ String name = schemeName.getText();
+ ucs.setSchemeName(name);
try
{
- frame.setClosed(true);
- }
- catch (Exception ex)
- {
- }
- }
-
- static Hashtable userColourSchemes;
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(toFile), "UTF-8"));
- public static Hashtable getUserColourSchemes()
- {
- return userColourSchemes;
- }
-
- public static void initUserColourSchemes(String files)
- {
- userColourSchemes = new Hashtable();
-
- if (files == null || files.length() == 0)
- {
- return;
- }
-
- // In case colours can't be loaded, we'll remove them
- // from the default list here.
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(files, "|");
- while (st.hasMoreElements())
- {
- String file = st.nextToken();
- try
- {
- UserColourScheme ucs = loadColours(file);
- if (ucs != null)
- {
- if (coloursFound.length() > 0)
- {
- coloursFound.append("|");
- }
- coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
- }
- }
- catch (Exception ex)
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.getColour().add(col);
}
- }
- if (!files.equals(coloursFound.toString()))
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewUserColours.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewUserColours(ucs), out);
+ // ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
{
- if (coloursFound.toString().length() > 1)
- {
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
- }
- else
- {
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
- }
+ ex.printStackTrace();
}
}
- public static void removeColourFromDefaults(String target)
+ /**
+ * On cancel, restores the colour scheme that was selected before the dialogue
+ * was opened
+ */
+ @Override
+ protected void cancelButton_actionPerformed()
{
- // The only way to find colours by name is to load them in
- // In case colours can't be loaded, we'll remove them
- // from the default list here.
-
- userColourSchemes = new Hashtable();
-
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
-
- while (st.hasMoreElements())
- {
- String file = st.nextToken();
- try
- {
- UserColourScheme ucs = loadColours(file);
- if (ucs != null && !ucs.getName().equals(target))
- {
- if (coloursFound.length() > 0)
- {
- coloursFound.append("|");
- }
- coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
- }
- }
- catch (Exception ex)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
+ ap.alignFrame.changeColour(oldColourScheme);
+ ap.paintAlignment(true, true);
- if (coloursFound.toString().length() > 1)
+ try
{
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
- }
- else
+ frame.setClosed(true);
+ } catch (Exception ex)
{
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
}
-
}
- public void caseSensitive_actionPerformed(ActionEvent e)
- {
- resetButtonPanel(caseSensitive.isSelected());
- lcaseColour.setEnabled(caseSensitive.isSelected());
- }
-
- public void lcaseColour_actionPerformed(ActionEvent e)
+ /**
+ * Action on selecting or deselecting the Case Sensitive option. When
+ * selected, separate buttons are shown for lower case residues, and the panel
+ * is resized to accommodate them. Also, the checkbox for 'apply colour to all
+ * lower case' is enabled.
+ */
+ @Override
+ public void caseSensitive_actionPerformed()
{
- if (selectedButtons == null)
- {
- selectedButtons = new Vector();
- }
- else
- {
- selectedButtons.clear();
- }
- selectedButtons.add(lcaseColour);
+ boolean selected = caseSensitive.isSelected();
+ resetButtonPanel(selected);
+ lcaseColour.setEnabled(selected);
}
-
}