/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.ColourSchemes;
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.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 java.util.ArrayList;
+import java.util.List;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
/**
- * DOCUMENT ME!
+ * This panel allows the user to assign colours to Amino Acid residue codes, and
+ * save the colour scheme.
*
- * @author $author$
- * @version $Revision$
+ * @author Andrew Waterhouse
+ * @author Mungo Carstairs
*/
public class UserDefinedColours extends GUserDefinedColours implements
ChangeListener
{
+ private static final Font VERDANA_BOLD_10 = new Font("Verdana",
+ Font.BOLD, 10);
+
+ public 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;
+
AlignmentPanel ap;
SequenceGroup seqGroup;
- Vector selectedButtons;
+ List<JButton> selectedButtons;
ColourSchemeI oldColourScheme;
JInternalFrame frame;
- JalviewStructureDisplayI jmol;
+ JalviewStructureDisplayI structureViewer;
- Vector upperCaseButtons;
+ List<JButton> upperCaseButtons;
- Vector lowerCaseButtons;
+ List<JButton> lowerCaseButtons;
/**
* Creates a new UserDefinedColours object.
*
* @param ap
- * DOCUMENT ME!
* @param sg
- * DOCUMENT ME!
*/
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
{
if (seqGroup != null)
{
- oldColourScheme = seqGroup.cs;
+ oldColourScheme = seqGroup.getColourScheme();
}
else
{
if (oldColourScheme instanceof UserColourScheme)
{
- schemeName.setText(((UserColourScheme) oldColourScheme).getName());
+ schemeName.setText(oldColourScheme.getSchemeName());
if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null)
{
caseSensitive.setSelected(true);
showFrame();
}
- public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs)
+ 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);
frame = new JInternalFrame();
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
- MessageManager.getString("label.user_defined_colours"), 720,
- 370, true);
+ MessageManager.getString("label.user_defined_colours"),
+ MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
if (seqGroup != null)
{
frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
}
-
- if (new jalview.util.Platform().isAMac())
- {
- frame.setSize(760, 370);
- }
}
- 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();
if (upperCaseButtons == null)
{
- upperCaseButtons = new Vector();
+ 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);
if (lowerCaseButtons == null)
{
- lowerCaseButtons = new Vector();
+ lowerCaseButtons = new ArrayList<JButton>();
}
for (int i = 0; i < 20; i++)
{
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));
buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
}
+ // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA
+ // codes
+ if (this.frame != null)
+ {
+ int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE
+ : MY_FRAME_WIDTH;
+ this.frame.setSize(newWidth, this.frame.getHeight());
+ }
+
buttonPanel.validate();
validate();
}
/**
- * DOCUMENT ME!
+ * ChangeListener handler for when a colour is picked in the colour chooser.
+ * The action is to apply the colour to all selected buttons as their
+ * background colour. Foreground colour (text) is set to a lighter shade in
+ * order to highlight which buttons are selected. If 'Lower Case Colour' is
+ * active, then the colour is applied to all lower case buttons (as well as
+ * the Lower Case Colour button itself).
*
* @param evt
- * DOCUMENT ME!
*/
+ @Override
public void stateChanged(ChangeEvent evt)
{
- if (selectedButtons != null)
+ JButton button = null;
+ final Color newColour = colorChooser.getColor();
+ for (int i = 0; i < selectedButtons.size(); i++)
{
- JButton button = null;
- for (int i = 0; i < selectedButtons.size(); i++)
- {
- button = (JButton) selectedButtons.elementAt(i);
- button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter()
- .brighter());
- }
- if (button == lcaseColour)
+ button = selectedButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(newColour));
+ }
+ if (button == lcaseColour)
+ {
+ button.setForeground(Color.black);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- button = (JButton) lowerCaseButtons.elementAt(i);
- button.setBackground(colorChooser.getColor());
- button.setForeground(button.getBackground().brighter().brighter()
- .brighter());
- }
+ button = lowerCaseButtons.get(i);
+ button.setBackground(newColour);
+ button.setForeground(ColorUtils.brighterThan(button.getBackground()));
}
}
}
/**
- * DOCUMENT ME!
+ * Performs actions when a residue button is clicked. This manages the button
+ * selection set (highlighted by brighter foreground text).
+ * <p>
+ * On select button(s) with Ctrl/click or Shift/click: set button foreground
+ * text to brighter than background.
+ * <p>
+ * On unselect button(s) with Ctrl/click on selected, or click to release
+ * current selection: reset foreground text to darker than background.
+ * <p>
+ * Simple click: clear selection (resetting foreground to darker); set clicked
+ * button foreground to brighter
+ * <p>
+ * Finally, synchronize the colour chooser to the colour of the first button
+ * in the selected set.
*
* @param e
- * DOCUMENT ME!
*/
public void colourButtonPressed(MouseEvent e)
{
- if (selectedButtons == null)
- {
- selectedButtons = new Vector();
- }
-
JButton pressed = (JButton) e.getSource();
if (e.isShiftDown())
JButton start, end = (JButton) e.getSource();
if (selectedButtons.size() > 0)
{
- start = (JButton) selectedButtons
- .elementAt(selectedButtons.size() - 1);
+ start = selectedButtons.get(selectedButtons.size() - 1);
}
else
{
JButton button = (JButton) buttonPanel.getComponent(b);
if (!selectedButtons.contains(button))
{
- button.setForeground(button.getBackground().brighter().brighter());
+ button.setForeground(ColorUtils.brighterThan(button
+ .getBackground()));
selectedButtons.add(button);
}
}
{
for (int b = 0; b < selectedButtons.size(); b++)
{
- JButton button = (JButton) selectedButtons.elementAt(b);
- button.setForeground(button.getBackground().darker().darker());
+ JButton button = selectedButtons.get(b);
+ button.setForeground(ColorUtils.darkerThan(button.getBackground()));
}
selectedButtons.clear();
- pressed.setForeground(pressed.getBackground().brighter().brighter());
- selectedButtons.addElement(pressed);
+ pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground()));
+ selectedButtons.add(pressed);
}
else if (e.isControlDown())
{
if (selectedButtons.contains(pressed))
{
- pressed.setForeground(pressed.getBackground().darker().darker());
+ pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground()));
selectedButtons.remove(pressed);
}
else
{
- pressed.setForeground(pressed.getBackground().brighter().brighter());
- selectedButtons.addElement(pressed);
+ pressed.setForeground(ColorUtils.brighterThan(pressed
+ .getBackground()));
+ selectedButtons.add(pressed);
}
}
if (selectedButtons.size() > 0)
{
- colorChooser.setColor(((JButton) selectedButtons.elementAt(0))
- .getBackground());
+ colorChooser.setColor((selectedButtons.get(0)).getBackground());
}
}
/**
- * 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, Vector caseSensitiveButtons,
+ 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 = (JButton) caseSensitiveButtons.elementAt(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)
{
colourButtonPressed(e);
}
});
- caseSensitiveButtons.addElement(button);
+ 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(aa.charAt(0), -1, null);
- } catch (Exception ex)
- {
- }
+ col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+ 0f);
}
}
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(col.darker().darker().darker());
- button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
+ button.setForeground(ColorUtils.darkerThan(col));
+ 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.
*/
- protected void okButton_actionPerformed(ActionEvent e)
+ @Override
+ protected void okButton_actionPerformed()
{
- applyButton_actionPerformed(null);
-
- try
+ if (isNoSelectionMade())
{
- frame.setClosed(true);
- } catch (Exception ex)
+ 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.
*/
- protected void applyButton_actionPerformed(ActionEvent e)
+ @Override
+ protected void applyButton_actionPerformed()
{
+ 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)
{
- seqGroup.cs = ucs;
+ seqGroup.setColourScheme(ucs);
ap.paintAlignment(true);
}
else if (ap != null)
{
ap.alignFrame.changeColour(ucs);
}
- else if (jmol != null)
+ else if (structureViewer != null)
{
- jmol.setJalviewColourScheme(ucs);
+ structureViewer.setJalviewColourScheme(ucs);
}
}
Color[] newColours = new Color[24];
- for (int i = 0; i < 24; i++)
+ int length = upperCaseButtons.size();
+ if (length < 24)
{
- JButton button = (JButton) upperCaseButtons.elementAt(i);
- newColours[i] = button.getBackground();
+ 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);
+ ucs.setName(schemeName.getText());
if (caseSensitive.isSelected())
{
newColours = new Color[23];
- for (int i = 0; i < 23; i++)
+ length = lowerCaseButtons.size();
+ if (length < 23)
{
- JButton button = (JButton) lowerCaseButtons.elementAt(i);
- newColours[i] = button.getBackground();
+ 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());
- }
+ // if (ap != null)
+ // {
+ // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ // }
return ucs;
}
* @param e
* DOCUMENT ME!
*/
+ @Override
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");
- chooser.setFileView(new jalview.io.JalviewFileView());
+ upperCaseButtons = new ArrayList<JButton>();
+ lowerCaseButtons = new ArrayList<JButton>();
+
+ JalviewFileChooser chooser = new JalviewFileChooser("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 = (JButton) lowerCaseButtons.elementAt(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 = ColourSchemes.loadColourScheme(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 = (JButton) upperCaseButtons.elementAt(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());
}
/**
- * 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()
{
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)
{
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 = ((Integer) 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 = (jalview.binding.JalviewUserColours) 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)
{
- 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()))
+ if (ColourSchemes.getInstance().nameExists(name))
{
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage(
- "label.colour_scheme_exists_overwrite", new String[]
- { schemeName.getText(), schemeName.getText() }),
+ "label.colour_scheme_exists_overwrite", new Object[] {
+ name, name }),
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());
+ ColourSchemes.getInstance().removeColourScheme(name);
}
- 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("jc",
+ "Jalview User Colours");
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
+ JalviewFileView fileView = new JalviewFileView();
+ chooser.setFileView(fileView);
+ 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)
- {
- if (defaultColours.length() > 0)
- {
- defaultColours = defaultColours.concat("|");
- }
- defaultColours = defaultColours.concat(choice);
- }
-
- 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();
-
- ucs.setSchemeName(schemeName.getText());
- try
- {
- PrintWriter out = new PrintWriter(new OutputStreamWriter(
- 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();
- col.setName(button.getText());
- col.setRGB(jalview.util.Format.getHexString(button
- .getBackground()));
- ucs.addColour(col);
- }
-
- ucs.marshal(out);
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ File file = chooser.getSelectedFile();
+ addNewColourScheme(file.getPath());
+ saveToFile(file);
}
}
/**
- * DOCUMENT ME!
+ * 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 e
- * DOCUMENT ME!
+ * @param filePath
*/
- protected void cancelButton_actionPerformed(ActionEvent e)
+ protected void addNewColourScheme(String filePath)
{
- if (ap != null)
+ /*
+ * 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 (seqGroup != null)
+ if (defaultColours.length() > 0)
{
- seqGroup.cs = oldColourScheme;
+ defaultColours = defaultColours.concat("|");
}
- else if (ap != null)
- {
- ap.av.setGlobalColourScheme(oldColourScheme);
- }
- ap.paintAlignment(true);
+ defaultColours = defaultColours.concat(filePath);
}
+ Cache.setProperty(USER_DEFINED_COLOURS, defaultColours);
- if (jmol != null)
- {
- jmol.setJalviewColourScheme(oldColourScheme);
- }
+ /*
+ * construct and register the colour scheme
+ */
+ UserColourScheme ucs = getSchemeFromButtons();
+ ColourSchemes.getInstance().registerColourScheme(ucs);
- try
- {
- frame.setClosed(true);
- } catch (Exception ex)
+ /*
+ * update the Colour menu items
+ */
+ if (ap != null)
{
+ ap.alignFrame.buildColourMenu();
}
}
- static Hashtable userColourSchemes;
-
- public static Hashtable getUserColourSchemes()
- {
- return userColourSchemes;
- }
-
- public static void initUserColourSchemes(String files)
+ /**
+ * Saves the colour scheme to file in XML format
+ *
+ * @param path
+ */
+ protected void saveToFile(File toFile)
{
- userColourSchemes = new Hashtable();
-
- if (files == null || files.length() == 0)
+ /*
+ * build a Java model of colour scheme as XML, and
+ * marshal to file
+ */
+ JalviewUserColours ucs = new JalviewUserColours();
+ ucs.setSchemeName(schemeName.getText());
+ try
{
- return;
- }
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
+ new FileOutputStream(toFile), "UTF-8"));
- // 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)
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ JButton button = (JButton) buttonPanel.getComponent(i);
+ Colour col = new Colour();
+ col.setName(button.getText());
+ col.setRGB(Format.getHexString(button.getBackground()));
+ ucs.addColour(col);
}
- }
- if (!files.equals(coloursFound.toString()))
+ ucs.marshal(out);
+ out.close();
+ } catch (Exception ex)
{
- if (coloursFound.toString().length() > 1)
- {
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
- }
- else
- {
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
- }
+ ex.printStackTrace();
}
}
- public static void removeColourFromDefaults(String target)
+ /**
+ * On cancel, restores the colour scheme before the dialogue was opened
+ *
+ * @param e
+ */
+ @Override
+ protected void cancelButton_actionPerformed(ActionEvent e)
{
- // 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 Hashtable();
-
- StringBuffer coloursFound = new StringBuffer();
- StringTokenizer st = new StringTokenizer(
- jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
-
- while (st.hasMoreElements())
+ if (ap != null)
{
- String file = st.nextToken();
- try
+ if (seqGroup != null)
{
- 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)
+ seqGroup.setColourScheme(oldColourScheme);
+ }
+ else
{
- System.out.println("Error loading User ColourFile\n" + ex);
+ ap.alignFrame.changeColour(oldColourScheme);
}
+ ap.paintAlignment(true);
}
- if (coloursFound.toString().length() > 1)
+ if (structureViewer != null)
{
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
- coloursFound.toString());
+ structureViewer.setJalviewColourScheme(oldColourScheme);
}
- else
+
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
{
- jalview.bin.Cache.applicationProperties
- .remove("USER_DEFINED_COLOURS");
}
-
}
+ @Override
public void caseSensitive_actionPerformed(ActionEvent e)
{
- resetButtonPanel(caseSensitive.isSelected());
- lcaseColour.setEnabled(caseSensitive.isSelected());
+ boolean selected = caseSensitive.isSelected();
+ resetButtonPanel(selected);
+ lcaseColour.setEnabled(selected);
+ lcaseColour.setForeground(Color.GRAY);
}
+ /**
+ * Action on clicking 'Lower case colour', which results in changing colour of
+ * all lower-case buttons when a colour is picked. A second click of the
+ * button turns off this behaviour.
+ */
+ @Override
public void lcaseColour_actionPerformed(ActionEvent e)
{
- if (selectedButtons == null)
+ boolean enable = !selectedButtons.contains(lcaseColour);
+ selectedButtons.clear();
+ if (enable)
{
- selectedButtons = new Vector();
+ selectedButtons.add(lcaseColour);
+ lcaseColour.setForeground(lowerCaseButtons.get(0).getForeground());
+ lcaseColour.setForeground(Color.black);
}
else
{
- selectedButtons.clear();
+ lcaseColour.setBackground(Color.white);
+ lcaseColour.setForeground(Color.gray);
}
- selectedButtons.add(lcaseColour);
}
-
}
git://source.jalview.org / jalview.git / blobdiff