/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.gui;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
import jalview.jbgui.GUserDefinedColours;
+import jalview.schemabinding.version2.Colour;
+import jalview.schemabinding.version2.JalviewUserColours;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.ColorUtils;
+import jalview.util.Format;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.Font;
+import java.awt.Insets;
import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.File;
import java.io.FileInputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.ArrayList;
-import java.util.Hashtable;
+import java.util.List;
+import java.util.SortedMap;
import java.util.StringTokenizer;
+import java.util.TreeMap;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
public class UserDefinedColours extends GUserDefinedColours implements
ChangeListener
{
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
+
+ private static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+ private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
+
private static final int MY_FRAME_HEIGHT = 420;
private static final int MY_FRAME_WIDTH = 810;
private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970;
+ static SortedMap<String, UserColourScheme> userColourSchemes;
+
AlignmentPanel ap;
SequenceGroup seqGroup;
- ArrayList<JButton> selectedButtons;
+ List<JButton> selectedButtons;
ColourSchemeI oldColourScheme;
JInternalFrame frame;
- JalviewStructureDisplayI jmol;
+ JalviewStructureDisplayI structureViewer;
- ArrayList<JButton> upperCaseButtons;
+ List<JButton> upperCaseButtons;
- ArrayList<JButton> lowerCaseButtons;
+ List<JButton> lowerCaseButtons;
/**
* Creates a new UserDefinedColours object.
*
* @param ap
- * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
*/
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
{
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
showFrame();
}
- public UserDefinedColours(JalviewStructureDisplayI jmol,
+ public UserDefinedColours(JalviewStructureDisplayI viewer,
ColourSchemeI oldcs)
{
super();
- this.jmol = jmol;
+ this.structureViewer = viewer;
colorChooser.getSelectionModel().addChangeListener(this);
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
}
resetButtonPanel(false);
}
/**
- * DOCUMENT ME!
+ * A helper method to update or make a colour button, whose background colour
+ * is the associated colour, and text colour a darker shade of the same. If
+ * the button is already in the list, then its text and margins are updated,
+ * if not then it is created and added. This method supports toggling between
+ * case-sensitive and case-insensitive button panels. The case-sensitive
+ * version has abbreviated button text in order to fit in more buttons.
*
* @param label
- * DOCUMENT ME!
- * @param aa
- * DOCUMENT ME!
+ * @param residue
+ * @param the
+ * list of buttons
+ * @param buttonIndex
+ * the button's position in the list
*/
- JButton makeButton(String label, String aa,
- ArrayList<JButton> caseSensitiveButtons, int buttonIndex)
+ JButton makeButton(String label, String residue,
+ List<JButton> buttons, int buttonIndex)
{
final JButton button;
Color col;
- if (buttonIndex < caseSensitiveButtons.size())
+ if (buttonIndex < buttons.size())
{
- button = caseSensitiveButtons.get(buttonIndex);
+ button = buttons.get(buttonIndex);
col = button.getBackground();
}
else
{
button = new JButton();
- button.addMouseListener(new java.awt.event.MouseAdapter()
+ button.addMouseListener(new MouseAdapter()
{
@Override
public void mouseClicked(MouseEvent e)
}
});
- caseSensitiveButtons.add(button);
+ buttons.add(button);
col = Color.white;
if (oldColourScheme != null)
{
try
{
- col = oldColourScheme.findColour(aa.charAt(0), -1, null);
+ col = oldColourScheme.findColour(residue.charAt(0), -1, null);
} catch (Exception ex)
{
}
if (caseSensitive.isSelected())
{
- button.setMargin(new java.awt.Insets(2, 2, 2, 2));
+ button.setMargin(new Insets(2, 2, 2, 2));
}
else
{
- button.setMargin(new java.awt.Insets(2, 14, 2, 14));
+ button.setMargin(new Insets(2, 14, 2, 14));
}
button.setOpaque(true); // required for the next line to have effect
button.setBackground(col);
button.setText(label);
button.setForeground(ColorUtils.darkerThan(col));
- button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
+ button.setFont(VERDANA_BOLD_10);
return button;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * On 'OK', check that at least one colour has been assigned to a residue (and
+ * if not issue a warning), and apply the chosen colour scheme and close the
+ * panel.
*/
@Override
- protected void okButton_actionPerformed(ActionEvent e)
+ protected void okButton_actionPerformed()
{
- //Check if the user have done any selection
- boolean showWarning = (upperCaseButtons==null) ||
- ((upperCaseButtons!=null) && (upperCaseButtons.size()==0)) ||
- (lowerCaseButtons==null) ||
- ((lowerCaseButtons!=null) && (lowerCaseButtons.size()==0));
- if (showWarning){
- JOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.getString("label.no_colour_selection_in_scheme"),MessageManager.getString("label.no_colour_selection_warn"),
- JOptionPane.WARNING_MESSAGE);
-
- }else{
- applyButton_actionPerformed(null);
-
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ applyButton_actionPerformed();
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
}
/**
- * DOCUMENT ME!
+ * Returns true if the user has not made any colour selection (including if
+ * 'case-sensitive' selected and no lower-case colour chosen).
*
- * @param e
- * DOCUMENT ME!
+ * @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;
+ }
+
+ /**
+ * Applies the current colour scheme to the alignment, sequence group or
+ * structure view.
*/
@Override
- protected void applyButton_actionPerformed(ActionEvent e)
+ protected void applyButton_actionPerformed()
{
- //Check if the user have done any selection
- boolean showWarning = (upperCaseButtons==null) ||
- ((upperCaseButtons!=null) && (upperCaseButtons.size()==0)) ||
- (lowerCaseButtons==null) ||
- ((lowerCaseButtons!=null) && (lowerCaseButtons.size()==0));
- if (showWarning){
- 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();
+ if (isNoSelectionMade())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.no_colour_selection_in_scheme"),
+ MessageManager.getString("label.no_colour_selection_warn"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ }
+ UserColourScheme ucs = getSchemeFromButtons();
ucs.setName(schemeName.getText());
if (seqGroup != null)
{
ap.alignFrame.changeColour(ucs);
}
- else if (jmol != null)
+ else if (structureViewer != null)
{
- jmol.setJalviewColourScheme(ucs);
+ structureViewer.setJalviewColourScheme(ucs);
}
}
Color[] newColours = new Color[24];
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 = (JButton) upperCaseButtons.get(i);
- newColours[i] = button.getBackground();
- }
+ 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);
{
newColours = new Color[23];
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 = (JButton) lowerCaseButtons.get(i);
- newColours[i] = button.getBackground();
- }
+ 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;
lowerCaseButtons = new ArrayList<JButton>();
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());
+ Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours");
+ chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
int value = chooser.showOpenDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- File choice = chooser.getSelectedFile();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice.getPath());
- if (defaultColours.indexOf(choice.getPath()) == -1)
- {
- defaultColours = defaultColours.concat("|")
- .concat(choice.getPath());
- }
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- UserColourScheme ucs = loadColours(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getName());
-
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
+ return;
+ }
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
+ UserColourScheme ucs = loadColours(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
- for (int i = 0; i < upperCaseButtons.size(); i++)
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
}
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
}
+
+ addNewColourScheme(choice.getPath());
}
/**
{
UserColourScheme ret = null;
- String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+ String colours = Cache.getProperty(USER_DEFINED_COLOURS);
if (colours != null)
{
if (colours.indexOf("|") > -1)
name = jucs.getColour(i).getName();
if (ResidueProperties.aa3Hash.containsKey(name))
{
- index = ((Integer) ResidueProperties.aa3Hash.get(name))
- .intValue();
+ index = ResidueProperties.aa3Hash.get(name).intValue();
}
else
{
{
if (schemeName.getText().trim().length() < 1)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.getString("label.user_colour_scheme_must_have_name"),
MessageManager.getString("label.no_name_colour_scheme"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
return;
}
if (userColourSchemes != null
&& userColourSchemes.containsKey(schemeName.getText()))
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.colour_scheme_exists_overwrite", new Object[]
- { schemeName.getText(), schemeName.getText() }),
+ "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)
+ JvOptionPane.YES_NO_OPTION);
+ if (reply != JvOptionPane.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");
+ Cache.getProperty(LAST_DIRECTORY), "jc",
+ "Jalview User Colours");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- String defaultColours = jalview.bin.Cache.getDefault(
- "USER_DEFINED_COLOURS", choice);
- if (defaultColours.indexOf(choice) == -1)
+ addNewColourScheme(choice);
+ saveToFile(choice);
+ }
+ }
+
+ /**
+ * Adds the current colour scheme to the Jalview properties file so it is
+ * loaded on next startup, and updates the Colour menu in the parent
+ * AlignFrame (if there is one). Note this action does not including applying
+ * the colour scheme.
+ *
+ * @param filePath
+ */
+ protected void addNewColourScheme(String filePath)
+ {
+ /*
+ * update the delimited list of user defined colour files in
+ * Jalview property USER_DEFINED_COLOURS
+ */
+ String defaultColours = Cache
+ .getDefault(USER_DEFINED_COLOURS, filePath);
+ if (defaultColours.indexOf(filePath) == -1)
+ {
+ if (defaultColours.length() > 0)
{
- if (defaultColours.length() > 0)
- {
- defaultColours = defaultColours.concat("|");
- }
- defaultColours = defaultColours.concat(choice);
+ defaultColours = defaultColours.concat("|");
}
+ defaultColours = defaultColours.concat(filePath);
+ }
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
- userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
-
- ap.alignFrame.updateUserColourMenu();
-
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
-
- jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
+ /*
+ * add to the cache in this object
+ */
+ userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
- ucs.setSchemeName(schemeName.getText());
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- new FileOutputStream(choice), "UTF-8"));
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
+ {
+ ap.alignFrame.buildColourMenu();// updateUserColourMenu();
+ }
+ }
- for (int i = 0; i < buttonPanel.getComponentCount(); i++)
- {
- JButton button = (JButton) buttonPanel.getComponent(i);
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
- col.setName(button.getText());
- col.setRGB(jalview.util.Format.getHexString(button
- .getBackground()));
- ucs.addColour(col);
- }
+ /**
+ * Saves the colour scheme to file in XML format
+ *
+ * @param filePath
+ */
+ protected void saveToFile(String filePath)
+ {
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName(schemeName.getText());
+ try
+ {
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(filePath), "UTF-8"));
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
- ex.printStackTrace();
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.addColour(col);
}
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
}
ap.paintAlignment(true);
}
- if (jmol != null)
+ if (structureViewer != null)
{
- jmol.setJalviewColourScheme(oldColourScheme);
+ structureViewer.setJalviewColourScheme(oldColourScheme);
}
try
}
}
- static Hashtable userColourSchemes;
-
- public static Hashtable getUserColourSchemes()
+ public static SortedMap<String, UserColourScheme> getUserColourSchemes()
{
return userColourSchemes;
}
public static void initUserColourSchemes(String files)
{
- userColourSchemes = new Hashtable();
+ userColourSchemes = new TreeMap<String, UserColourScheme>();
if (files == null || files.length() == 0)
{
coloursFound.append("|");
}
coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
+ userColourSchemes.put(ucs.getSchemeName(), ucs);
}
} catch (Exception ex)
{
{
if (coloursFound.toString().length() > 1)
{
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
+ Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
}
else
{
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
+ Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
}
}
}
// In case colours can't be loaded, we'll remove them
// from the default list here.
- userColourSchemes = new Hashtable();
+ userColourSchemes = new TreeMap<String, UserColourScheme>();
StringBuffer coloursFound = new StringBuffer();
StringTokenizer st = new StringTokenizer(
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+ Cache.getProperty(USER_DEFINED_COLOURS), "|");
while (st.hasMoreElements())
{
try
{
UserColourScheme ucs = loadColours(file);
- if (ucs != null && !ucs.getName().equals(target))
+ if (ucs != null && !ucs.getSchemeName().equals(target))
{
if (coloursFound.length() > 0)
{
coloursFound.append("|");
}
coloursFound.append(file);
- userColourSchemes.put(ucs.getName(), ucs);
+ userColourSchemes.put(ucs.getSchemeName(), ucs);
}
} catch (Exception ex)
{
if (coloursFound.toString().length() > 1)
{
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
+ Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString());
}
else
{
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
+ Cache.applicationProperties.remove(USER_DEFINED_COLOURS);
}
}
git://source.jalview.org / jalview.git / blobdiff