import jalview.schemabinding.version2.Colour;
import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.ColorUtils;
import java.awt.event.MouseAdapter;
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.ArrayList;
import java.util.List;
-import java.util.SortedMap;
-import java.util.StringTokenizer;
-import java.util.TreeMap;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
{
private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
- private static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+ public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
- static SortedMap<String, UserColourScheme> userColourSchemes;
-
AlignmentPanel ap;
SequenceGroup seqGroup;
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
}
resetButtonPanel(false);
}
UserColourScheme ucs = getSchemeFromButtons();
- ucs.setName(schemeName.getText());
if (seqGroup != null)
{
}
UserColourScheme ucs = new UserColourScheme(newColours);
+ ucs.setName(schemeName.getText());
if (caseSensitive.isSelected())
{
File choice = chooser.getSelectedFile();
Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+ UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getName());
+ schemeName.setText(ucs.getSchemeName());
if (ucs.getLowerCaseColours() != null)
{
}
/**
- * 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 DOCUMENT ME!
+ * @return
*/
public static UserColourScheme loadDefaultColours()
{
{
colours = colours.substring(0, colours.indexOf("|"));
}
-
- ret = loadColours(colours);
+ ret = ColourSchemes.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!
- */
- static UserColourScheme loadColours(String file)
- {
- 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 = ResidueProperties.aa3Hash.get(name).intValue();
- }
- else
- {
- index = ResidueProperties.aaIndex[name.charAt(0)];
- }
- if (index == -1)
- {
- 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));
- }
- }
-
- 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 = 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));
- }
- if (newColours != null)
- {
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- }
- } catch (Exception ex2)
- {
- ex2.printStackTrace();
- }
-
- if (newColours == null)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
-
- return ucs;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param e
* DOCUMENT ME!
*/
@Override
protected void savebutton_actionPerformed(ActionEvent e)
{
- if (schemeName.getText().trim().length() < 1)
+ String name = schemeName.getText().trim();
+ if (name.length() < 1)
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.user_colour_scheme_must_have_name"),
return;
}
- if (userColourSchemes != null
- && userColourSchemes.containsKey(schemeName.getText()))
+ if (ColourSchemes.getInstance().nameExists(name))
{
int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.colour_scheme_exists_overwrite", new Object[] {
- schemeName.getText(), schemeName.getText() }),
+ name, name }),
MessageManager.getString("label.duplicate_scheme_name"),
JvOptionPane.YES_NO_OPTION);
if (reply != JvOptionPane.YES_OPTION)
{
return;
}
-
- userColourSchemes.remove(schemeName.getText());
+ ColourSchemes.getInstance().removeColourScheme(name);
}
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty(LAST_DIRECTORY), "jc",
Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
/*
- * add to the cache in this object
+ * construct and register the colour scheme
*/
- userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
/*
* update the Colour menu items
*/
if (ap != null)
{
- ap.alignFrame.buildColourMenu();// updateUserColourMenu();
+ ap.alignFrame.buildColourMenu();
}
}
}
/**
- * DOCUMENT ME!
+ * On cancel, restores the colour scheme before the dialogue was opened
*
* @param e
- * DOCUMENT ME!
*/
@Override
protected void cancelButton_actionPerformed(ActionEvent e)
{
seqGroup.cs = oldColourScheme;
}
- else if (ap != null)
+ else
{
- ap.av.setGlobalColourScheme(oldColourScheme);
+ ap.alignFrame.changeColour(oldColourScheme);
}
ap.paintAlignment(true);
}
}
}
- public static SortedMap<String, UserColourScheme> getUserColourSchemes()
- {
- return userColourSchemes;
- }
-
- public static void initUserColourSchemes(String files)
- {
- userColourSchemes = new TreeMap<String, UserColourScheme>();
-
- 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)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
- if (!files.equals(coloursFound.toString()))
- {
- if (coloursFound.toString().length() > 1)
- {
- Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
- }
- else
- {
- Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
- }
- }
- }
-
- public static void removeColourFromDefaults(String target)
- {
- // 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 TreeMap<String, UserColourScheme>();
-
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(
- 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);
- }
- }
-
- if (coloursFound.toString().length() > 1)
- {
- Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
- }
- else
- {
- Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
- }
-
- }
-
@Override
public void caseSensitive_actionPerformed(ActionEvent e)
{