package jalview.bin;
import jalview.datamodel.PDBEntry;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
import jalview.structure.StructureImportSettings;
import jalview.util.ColorUtils;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import java.util.Enumeration;
import java.util.Locale;
import java.util.Properties;
+import java.util.StringTokenizer;
import java.util.TreeSet;
import org.apache.log4j.ConsoleAppender;
setProperty("VERSION", codeVersion);
// LOAD USERDEFINED COLOURS
- jalview.gui.UserDefinedColours
+ jalview.bin.Cache
.initUserColourSchemes(getProperty("USER_DEFINED_COLOURS"));
jalview.io.PIRFile.useModellerOutput = Cache.getDefault("PIR_MODELLER",
false);
Cache.applicationProperties.setProperty(propName, value);
}
}
+
+ /**
+ * Loads in user colour schemes from files.
+ *
+ * @param files
+ * a '|'-delimited list of file paths
+ */
+ public static void initUserColourSchemes(String files)
+ {
+ 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 = ColourSchemes.loadColourScheme(file);
+ if (ucs != null)
+ {
+ if (coloursFound.length() > 0)
+ {
+ coloursFound.append("|");
+ }
+ coloursFound.append(file);
+ ColourSchemes.getInstance().registerColourScheme(ucs);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println("Error loading User ColourFile\n" + ex);
+ }
+ }
+ if (!files.equals(coloursFound.toString()))
+ {
+ if (coloursFound.toString().length() > 1)
+ {
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString());
+ }
+ else
+ {
+ applicationProperties.remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ }
+ }
+ }
}
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;
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.getSchemeName());
}
/**
- * 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
*/
UserColourScheme ucs = getSchemeFromButtons();
- String name = schemeName.getText();
- userColourSchemes.put(name, ucs);
-
ColourSchemes.getInstance().registerColourScheme(ucs);
/*
}
}
- 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);
- String name = ucs.getName();
- userColourSchemes.put(name, ucs);
- ColourSchemes.getInstance().registerColourScheme(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.getSchemeName().equals(target))
- {
- if (coloursFound.length() > 0)
- {
- coloursFound.append("|");
- }
- coloursFound.append(file);
- userColourSchemes.put(ucs.getSchemeName(), 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)
{
package jalview.schemes;
+import jalview.binding.JalviewUserColours;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import java.awt.Color;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
import java.util.LinkedHashMap;
import java.util.Map;
{
return schemes.values();
}
+
+ /**
+ * Answers true if there is a scheme with the given name, else false. The test
+ * is not case-sensitive.
+ *
+ * @param name
+ * @return
+ */
+ public boolean nameExists(String name)
+ {
+ if (name == null)
+ {
+ return false;
+ }
+ name = name.toLowerCase();
+ for (ColourSchemeI scheme : getColourSchemes())
+ {
+ if (name.equals(scheme.getSchemeName().toLowerCase()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Loads a user defined colour scheme from file. The file should contain a
+ * definition of residue colours in XML format as defined in
+ * JalviewUserColours.xsd.
+ *
+ * @param file
+ *
+ * @return
+ */
+ public static UserColourScheme loadColourScheme(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);
+
+ /*
+ * non-case-sensitive colours are for 20 amino acid codes,
+ * B, Z, X and Gap
+ * optionally, lower-case alternatives for all except Gap
+ */
+ newColours = new Color[24];
+ Color[] lowerCase = new Color[23];
+ 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;
+ }
+
+ Color color = new Color(Integer.parseInt(jucs.getColour(i)
+ .getRGB(), 16));
+ if (name.toLowerCase().equals(name))
+ {
+ caseSensitive = true;
+ lowerCase[index] = color;
+ }
+ else
+ {
+ newColours[index] = color;
+ }
+ }
+
+ /*
+ * instantiate the colour scheme
+ */
+ ucs = new UserColourScheme(newColours);
+ ucs.setName(jucs.getSchemeName());
+ if (caseSensitive)
+ {
+ ucs.setLowerCaseColours(lowerCase);
+ }
+ } catch (Exception ex)
+ {
+ // Could be old Jalview Archive format
+ try
+ {
+ InputStreamReader in = new InputStreamReader(new FileInputStream(
+ file), "UTF-8");
+
+ jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
+
+ jucs = JalviewUserColours.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));
+ }
+ 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;
+ }
}
git://source.jalview.org / jalview.git / commitdiff