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 (seqGroup != null)
{
- oldColourScheme = seqGroup.cs;
+ oldColourScheme = seqGroup.getColourScheme();
}
else
{
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
+ schemeName.setText(oldColourScheme.getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
}
}
- void resetButtonPanel(boolean caseSensitive)
+ /**
+ * Rebuilds the panel with coloured buttons for residues. If not case
+ * sensitive colours, show 3-letter amino acid code as button text. If case
+ * sensitive, just show the single letter code, in order to make space for the
+ * additional buttons.
+ *
+ * @param isCaseSensitive
+ */
+ void resetButtonPanel(boolean isCaseSensitive)
{
buttonPanel.removeAll();
upperCaseButtons = new ArrayList<JButton>();
}
- JButton button;
- String label;
for (int i = 0; i < 20; i++)
{
- if (caseSensitive)
- {
- label = ResidueProperties.aa[i];
- }
- else
- {
- label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
- .toString();
- }
-
- button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons,
- i);
-
+ String label = isCaseSensitive ? ResidueProperties.aa[i]
+ : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i])
+ .toString();
+ JButton button = makeButton(label, ResidueProperties.aa[i],
+ upperCaseButtons, i);
buttonPanel.add(button);
}
buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
- if (!caseSensitive)
+ if (!isCaseSensitive)
{
gridLayout.setRows(6);
gridLayout.setColumns(4);
{
int row = i / cols + 1;
int index = (row * cols) + i;
- button = makeButton(ResidueProperties.aa[i].toLowerCase(),
+ JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(),
ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i);
buttonPanel.add(button, index);
}
}
- if (caseSensitive)
+ if (isCaseSensitive)
{
buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
// codes
if (this.frame != null)
{
- int newWidth = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
: MY_FRAME_WIDTH;
this.frame.setSize(newWidth, this.frame.getHeight());
}
buttons.add(button);
+ /*
+ * make initial button colour that of the current colour scheme,
+ * if it is a simple per-residue colouring, else white
+ */
col = Color.white;
- if (oldColourScheme != null)
+ if (oldColourScheme != null && oldColourScheme.isSimple())
{
- try
- {
- col = oldColourScheme.findColour(residue.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+ 0f);
}
}
}
UserColourScheme ucs = getSchemeFromButtons();
- ucs.setName(schemeName.getText());
if (seqGroup != null)
{
- seqGroup.cs = ucs;
+ seqGroup.setColourScheme(ucs);
ap.paintAlignment(true);
}
else if (ap != null)
}
UserColourScheme ucs = new UserColourScheme(newColours);
+ ucs.setName(schemeName.getText());
if (caseSensitive.isSelected())
{
ucs.setLowerCaseColours(newColours);
}
- if (ap != null)
- {
- ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
- }
+ // if (ap != null)
+ // {
+ // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ // }
return ucs;
}
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",
"Jalview User Colours");
- chooser.setFileView(new JalviewFileView());
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
chooser.setDialogTitle(MessageManager
.getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
if (value == JalviewFileChooser.APPROVE_OPTION)
{
- String choice = chooser.getSelectedFile().getPath();
- addNewColourScheme(choice);
- saveToFile(choice);
+ File file = chooser.getSelectedFile();
+ addNewColourScheme(file.getPath());
+ saveToFile(file);
}
}
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);
/*
/**
* Saves the colour scheme to file in XML format
*
- * @param filePath
+ * @param path
*/
- protected void saveToFile(String filePath)
+ protected void saveToFile(File toFile)
{
/*
* build a Java model of colour scheme as XML, and
try
{
PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(filePath), "UTF-8"));
+ new FileOutputStream(toFile), "UTF-8"));
for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
{
if (seqGroup != null)
{
- seqGroup.cs = oldColourScheme;
+ seqGroup.setColourScheme(oldColourScheme);
}
else
{
}
}
- 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)
{
git://source.jalview.org / jalview.git / blobdiff