/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class UserDefinedColours
- extends GUserDefinedColours implements ChangeListener
+public class UserDefinedColours extends GUserDefinedColours implements
+ ChangeListener
{
AlignmentPanel ap;
+
SequenceGroup seqGroup;
+
Vector selectedButtons;
+
ColourSchemeI oldColourScheme;
+
JInternalFrame frame;
+
AppJmol jmol;
+
Vector upperCaseButtons;
+
Vector lowerCaseButtons;
/**
* Creates a new UserDefinedColours object.
- *
- * @param ap DOCUMENT ME!
- * @param sg DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param sg
+ * DOCUMENT ME!
*/
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
{
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
- if ( ( (UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
+ schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
lcaseColour.setEnabled(true);
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getName());
}
resetButtonPanel(false);
colorChooser.getSelectionModel().addChangeListener(this);
frame = new JInternalFrame();
frame.setContentPane(this);
- Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), 720, 370, true);\r
if (seqGroup != null)
{
}
else
{
- label = ResidueProperties.aa2Triplet.get
- (ResidueProperties.aa[i]).toString();
+ label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+ .toString();
}
- button = makeButton(label,
- ResidueProperties.aa[i],
- upperCaseButtons, i);
+ button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
+ i);
buttonPanel.add(button);
}
{
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);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void stateChanged(ChangeEvent evt)
{
{
button = (JButton) selectedButtons.elementAt(i);
button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter().
- brighter());
+ button.setForeground(button.getBackground().brighter().brighter()
+ .brighter());
}
if (button == lcaseColour)
{
{
button = (JButton) lowerCaseButtons.elementAt(i);
button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter().
- brighter());
+ button.setForeground(button.getBackground().brighter().brighter()
+ .brighter());
}
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void colourButtonPressed(MouseEvent e)
{
JButton start, end = (JButton) e.getSource();
if (selectedButtons.size() > 0)
{
- start = (JButton) selectedButtons.elementAt(selectedButtons.size() - 1);
+ start = (JButton) selectedButtons
+ .elementAt(selectedButtons.size() - 1);
}
else
{
if (selectedButtons.size() > 0)
{
- colorChooser.setColor( ( (JButton) selectedButtons.elementAt(0)).
- getBackground());
+ colorChooser.setColor(((JButton) selectedButtons.elementAt(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, Vector caseSensitiveButtons,
+ int buttonIndex)
{
final JButton button;
Color col;
caseSensitiveButtons.addElement(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())
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void okButton_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void applyButton_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
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");
+ 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"));\r
+ chooser.setToolTipText(MessageManager.getString("action.load"));\r
int value = chooser.showOpenDialog(this);
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);
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public static UserColourScheme loadDefaultColours()
/**
* DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- *
+ *
+ * @param file
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
static UserColourScheme loadColours(String file)
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];
name = jucs.getColour(i).getName();
if (ResidueProperties.aa3Hash.containsKey(name))
{
- index = ( (Integer) ResidueProperties.aa3Hash.get(name)).intValue();
+ index = ((Integer) ResidueProperties.aa3Hash.get(name))
+ .intValue();
}
else
{
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));
}
}
}
}
- }
- 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);
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();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
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);
+ 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);
+ int reply = JOptionPane.showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage("label.colour_scheme_exists_overwrite", new String[]{schemeName.getText(),schemeName.getText()}),
+ MessageManager.getString("label.duplicate_scheme_name"), JOptionPane.YES_NO_OPTION);
if (reply != JOptionPane.YES_OPTION)
{
return;
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.setToolTipText(MessageManager.getString("action.save"));\r
int value = chooser.showSaveDialog(this);
{
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)
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();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void cancelButton_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
}
coloursFound.append(file);
userColourSchemes.put(ucs.getName(), ucs);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
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");
}
}
}
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())
{
coloursFound.append(file);
userColourSchemes.put(ucs.getName(), ucs);
}
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
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");
}
}
git://source.jalview.org / jalview.git / blobdiff