();
}
for (int i = 0; i < 20; i++)
{
int row = i / cols + 1;
int index = (row * cols) + i;
- button = makeButton(
- ResidueProperties.aa[i].toLowerCase(),
- ResidueProperties.aa[i].toLowerCase(),
- lowerCaseButtons,
- i);
+ button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
@@ -205,50 +234,74 @@ public class UserDefinedColours
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 = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ : MY_FRAME_WIDTH;
+ this.frame.setSize(newWidth, this.frame.getHeight());
+ }
+
buttonPanel.validate();
validate();
}
/**
* DOCUMENT ME!
- *
- * @param evt 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 = (JButton) selectedButtons.elementAt(i);
- button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter().
- brighter());
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
}
if (button == lcaseColour)
{
for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- button = (JButton) lowerCaseButtons.elementAt(i);
- button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter().
- brighter());
+ button = lowerCaseButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(button
+ .getBackground()));
}
}
}
}
/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ * 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 Vector();
+ selectedButtons = new ArrayList();
}
JButton pressed = (JButton) e.getSource();
@@ -258,7 +311,7 @@ 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 +343,8 @@ 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);
}
}
@@ -299,52 +353,52 @@ 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!
+ *
+ * @param label
+ * DOCUMENT ME!
+ * @param aa
+ * DOCUMENT ME!
*/
- JButton makeButton(String label,
- String aa,
- Vector caseSensitiveButtons,
- int buttonIndex)
+ JButton makeButton(String label, String aa,
+ ArrayList caseSensitiveButtons, int buttonIndex)
{
final JButton button;
Color col;
if (buttonIndex < caseSensitiveButtons.size())
{
- button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
+ button = caseSensitiveButtons.get(buttonIndex);
col = button.getBackground();
}
else
@@ -352,22 +406,25 @@ public class UserDefinedColours
button = new JButton();
button.addMouseListener(new java.awt.event.MouseAdapter()
{
+ @Override
public void mouseClicked(MouseEvent e)
{
colourButtonPressed(e);
}
});
- caseSensitiveButtons.addElement(button);
+ caseSensitiveButtons.add(button);
col = Color.white;
-
- try
+ if (oldColourScheme != null)
{
- col = oldColourScheme.findColour(aa.charAt(0), -1);
+ try
+ {
+ col = oldColourScheme.findColour(aa.charAt(0), -1, null);
+ } catch (Exception ex)
+ {
+ }
}
- catch (Exception ex)
- {}
}
if (caseSensitive.isSelected())
@@ -379,9 +436,10 @@ public class UserDefinedColours
button.setMargin(new java.awt.Insets(2, 14, 2, 14));
}
+ button.setOpaque(true); // required for the next line to have effect
button.setBackground(col);
button.setText(label);
- button.setForeground(col.darker().darker().darker());
+ button.setForeground(ColorUtils.darkerThan(col));
button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
return button;
@@ -389,30 +447,66 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void okButton_actionPerformed(ActionEvent e)
{
- applyButton_actionPerformed(null);
-
- try
+ if (isNoSelectionMade())
{
- frame.setClosed(true);
+ JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JOptionPane.WARNING_MESSAGE);
}
- catch (Exception ex)
+ else
{
+ applyButton_actionPerformed(null);
+
+ 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;
+ }
+
+ /**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void applyButton_actionPerformed(ActionEvent e)
{
- UserColourScheme ucs = getSchemeFromButtons();
+ if (isNoSelectionMade())
+ {
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
+ JOptionPane.WARNING_MESSAGE);
+
+ }
+ UserColourScheme ucs = getSchemeFromButtons();
ucs.setName(schemeName.getText());
if (seqGroup != null)
@@ -435,10 +529,18 @@ public class UserDefinedColours
Color[] newColours = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- JButton button = (JButton) upperCaseButtons.elementAt(i);
- newColours[i] = button.getBackground();
+ 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);
@@ -446,17 +548,25 @@ public class UserDefinedColours
if (caseSensitive.isSelected())
{
newColours = new Color[23];
- for (int i = 0; i < 23; i++)
- {
- JButton button = (JButton) lowerCaseButtons.elementAt(i);
- newColours[i] = button.getBackground();
+ 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.getIgnoreGapsConsensus());
+ ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
return ucs;
@@ -464,23 +574,24 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void loadbutton_actionPerformed(ActionEvent e)
{
- 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");
+ upperCaseButtons = new ArrayList();
+ lowerCaseButtons = new ArrayList();
+
+ 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");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.load_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
@@ -489,11 +600,11 @@ public class UserDefinedColours
File choice = chooser.getSelectedFile();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS",
- choice.getPath());
+ "USER_DEFINED_COLOURS", choice.getPath());
if (defaultColours.indexOf(choice.getPath()) == -1)
{
- defaultColours = defaultColours.concat("|").concat(choice.getPath());
+ defaultColours = defaultColours.concat("|")
+ .concat(choice.getPath());
}
jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
@@ -509,7 +620,7 @@ public class UserDefinedColours
resetButtonPanel(true);
for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- JButton button = (JButton) lowerCaseButtons.elementAt(i);
+ JButton button = lowerCaseButtons.get(i);
button.setBackground(ucs.getLowerCaseColours()[i]);
}
@@ -523,7 +634,7 @@ public class UserDefinedColours
for (int i = 0; i < upperCaseButtons.size(); i++)
{
- JButton button = (JButton) upperCaseButtons.elementAt(i);
+ JButton button = upperCaseButtons.get(i);
button.setBackground(colors[i]);
}
@@ -532,7 +643,7 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static UserColourScheme loadDefaultColours()
@@ -565,9 +676,10 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- *
+ *
+ * @param file
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
static UserColourScheme loadColours(String file)
@@ -576,16 +688,15 @@ public class UserDefinedColours
Color[] newColours = null;
try
{
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
- jalview.schemabinding.version2.JalviewUserColours jucs
- = new jalview.schemabinding.version2.JalviewUserColours();
+ 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);
+ 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];
@@ -599,7 +710,8 @@ public class UserDefinedColours
name = jucs.getColour(i).getName();
if (ResidueProperties.aa3Hash.containsKey(name))
{
- index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
+ index = ResidueProperties.aa3Hash.get(name)
+ .intValue();
}
else
{
@@ -617,13 +729,13 @@ public class UserDefinedColours
lowerCase = new Color[23];
}
caseSensitive = true;
- lowerCase[index] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
+ lowerCase[index] = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
}
else
{
- newColours[index] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
+ newColours[index] = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
}
}
@@ -637,34 +749,31 @@ public class UserDefinedColours
}
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
- //Could be Archive Jalview format
+ // Could be Archive Jalview format
try
{
InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
+ file), "UTF-8");
- jalview.binding.JalviewUserColours jucs
- = new jalview.binding.JalviewUserColours();
+ jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
+ jucs = jucs.unmarshal(in);
newColours = new Color[jucs.getColourCount()];
for (int i = 0; i < 24; i++)
{
- newColours[i] = new Color(Integer.parseInt(
- jucs.getColour(i).getRGB(), 16));
+ 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)
+ } catch (Exception ex2)
{
ex2.printStackTrace();
}
@@ -680,27 +789,31 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void savebutton_actionPerformed(ActionEvent e)
{
if (schemeName.getText().trim().length() < 1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "User colour scheme must have a name!",
- "No name for colour scheme",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.user_colour_scheme_must_have_name"),
+ MessageManager.getString("label.no_name_colour_scheme"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
- if (userColourSchemes != null &&
- userColourSchemes.containsKey(schemeName.getText()))
+ 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);
+ MessageManager.formatMessage(
+ "label.colour_scheme_exists_overwrite", new Object[]
+ { schemeName.getText(), schemeName.getText() }),
+ MessageManager.getString("label.duplicate_scheme_name"),
+ JOptionPane.YES_NO_OPTION);
if (reply != JOptionPane.YES_OPTION)
{
return;
@@ -708,16 +821,14 @@ public class UserDefinedColours
userColourSchemes.remove(schemeName.getText());
}
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"), new String[]
- {"jc"},
- new String[]
- {"Jalview User Colours"}, "Jalview User Colours");
+ 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");
+ chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -725,7 +836,7 @@ public class UserDefinedColours
{
String choice = chooser.getSelectedFile().getPath();
String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice);
+ "USER_DEFINED_COLOURS", choice);
if (defaultColours.indexOf(choice) == -1)
{
if (defaultColours.length() > 0)
@@ -741,30 +852,27 @@ public class UserDefinedColours
jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
- jalview.schemabinding.version2.JalviewUserColours ucs
- = new jalview.schemabinding.version2.JalviewUserColours();
+ 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"));
+ 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();
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
col.setName(button.getText());
- col.setRGB(jalview.util.Format.getHexString(
- button.getBackground()));
+ col.setRGB(jalview.util.Format.getHexString(button
+ .getBackground()));
ucs.addColour(col);
}
ucs.marshal(out);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -773,9 +881,11 @@ public class UserDefinedColours
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
protected void cancelButton_actionPerformed(ActionEvent e)
{
if (ap != null)
@@ -799,8 +909,7 @@ public class UserDefinedColours
try
{
frame.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
@@ -840,8 +949,7 @@ public class UserDefinedColours
coloursFound.append(file);
userColourSchemes.put(ucs.getName(), ucs);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
@@ -851,11 +959,12 @@ public class UserDefinedColours
if (coloursFound.toString().length() > 1)
{
jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
+ coloursFound.toString());
}
else
{
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+ jalview.bin.Cache.applicationProperties
+ .remove("USER_DEFINED_COLOURS");
}
}
}
@@ -870,7 +979,7 @@ public class UserDefinedColours
StringBuffer coloursFound = new StringBuffer();
StringTokenizer st = new StringTokenizer(
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+ jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
while (st.hasMoreElements())
{
@@ -887,8 +996,7 @@ public class UserDefinedColours
coloursFound.append(file);
userColourSchemes.put(ucs.getName(), ucs);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
@@ -897,26 +1005,29 @@ public class UserDefinedColours
if (coloursFound.toString().length() > 1)
{
jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
+ coloursFound.toString());
}
else
{
- jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
+ jalview.bin.Cache.applicationProperties
+ .remove("USER_DEFINED_COLOURS");
}
}
+ @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 Vector();
+ selectedButtons = new ArrayList();
}
else
{
@@ -924,5 +1035,4 @@ public class UserDefinedColours
}
selectedButtons.add(lcaseColour);
}
-
}