X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=64e0e15558178fbbe9439fd7f094dc7e0c3d8e7d;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=3803fa1b8fd58c710ed79606489e5dd0c7a58f48;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 3803fa1..64e0e15 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -20,17 +20,26 @@ */ 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; @@ -38,48 +47,62 @@ import java.io.FileOutputStream; import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; -import java.util.Hashtable; +import java.util.ArrayList; +import java.util.List; +import java.util.SortedMap; import java.util.StringTokenizer; -import java.util.Vector; +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; /** - * 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); + + 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 userColourSchemes; + AlignmentPanel ap; SequenceGroup seqGroup; - Vector selectedButtons; + List selectedButtons; ColourSchemeI oldColourScheme; JInternalFrame frame; - AppJmol jmol; + JalviewStructureDisplayI structureViewer; - Vector upperCaseButtons; + List upperCaseButtons; - Vector lowerCaseButtons; + List lowerCaseButtons; /** * Creates a new UserDefinedColours object. * * @param ap - * DOCUMENT ME! * @param sg - * DOCUMENT ME! */ public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) { @@ -101,7 +124,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (oldColourScheme instanceof UserColourScheme) { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); + schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName()); if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null) { caseSensitive.setSelected(true); @@ -121,10 +144,11 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs) + public UserDefinedColours(JalviewStructureDisplayI viewer, + ColourSchemeI oldcs) { super(); - this.jmol = jmol; + this.structureViewer = viewer; colorChooser.getSelectionModel().addChangeListener(this); @@ -132,7 +156,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (oldColourScheme instanceof UserColourScheme) { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); + schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName()); } resetButtonPanel(false); @@ -147,18 +171,13 @@ public class UserDefinedColours extends GUserDefinedColours implements 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) @@ -167,7 +186,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (upperCaseButtons == null) { - upperCaseButtons = new Vector(); + upperCaseButtons = new ArrayList(); } JButton button; @@ -208,7 +227,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (lowerCaseButtons == null) { - lowerCaseButtons = new Vector(); + lowerCaseButtons = new ArrayList(); } for (int i = 0; i < 20; i++) @@ -229,6 +248,15 @@ public class UserDefinedColours extends GUserDefinedColours implements 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 = caseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE + : MY_FRAME_WIDTH; + this.frame.setSize(newWidth, this.frame.getHeight()); + } + buttonPanel.validate(); validate(); } @@ -239,42 +267,55 @@ public class UserDefinedColours extends GUserDefinedColours implements * @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++) { - button = (JButton) selectedButtons.elementAt(i); - button.setBackground(colorChooser.getColor()); - button.setForeground(button.getBackground().brighter().brighter() - .brighter()); + button = selectedButtons.get(i); + button.setBackground(newColour); + button.setForeground(ColorUtils.brighterThan(newColour)); } if (button == lcaseColour) { 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). + *

+ * On select button(s) with Ctrl/click or Shift/click: set button foreground + * text to brighter than background. + *

+ * On unselect button(s) with Ctrl/click on selected, or click to release + * current selection: reset foreground text to darker than background. + *

+ * Simple click: clear selection (resetting foreground to darker); set clicked + * button foreground to brighter + *

+ * 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(); + selectedButtons = new ArrayList(); } JButton pressed = (JButton) e.getSource(); @@ -284,8 +325,7 @@ public class UserDefinedColours extends GUserDefinedColours implements JButton start, end = (JButton) e.getSource(); if (selectedButtons.size() > 0) { - start = (JButton) selectedButtons - .elementAt(selectedButtons.size() - 1); + start = selectedButtons.get(selectedButtons.size() - 1); } else { @@ -317,7 +357,8 @@ public class UserDefinedColours extends GUserDefinedColours implements 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); } } @@ -326,73 +367,81 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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, - int buttonIndex) + JButton makeButton(String label, String residue, + List 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); 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) { } @@ -401,47 +450,82 @@ public class UserDefinedColours extends GUserDefinedColours implements 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 void applyButton_actionPerformed(ActionEvent e) + 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() + { + 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()); @@ -454,9 +538,9 @@ public class UserDefinedColours extends GUserDefinedColours implements { ap.alignFrame.changeColour(ucs); } - else if (jmol != null) + else if (structureViewer != null) { - jmol.setJalviewColourScheme(ucs); + structureViewer.setJalviewColourScheme(ucs); } } @@ -465,10 +549,23 @@ public class UserDefinedColours extends GUserDefinedColours implements 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); @@ -476,17 +573,30 @@ public class UserDefinedColours extends GUserDefinedColours implements 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()); + ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } return ucs; @@ -498,66 +608,57 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void loadbutton_actionPerformed(ActionEvent e) { - upperCaseButtons = new Vector(); - lowerCaseButtons = new Vector(); + upperCaseButtons = new ArrayList(); + lowerCaseButtons = new ArrayList(); 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 = (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 = 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 = (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()); } /** @@ -569,7 +670,7 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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) @@ -629,8 +730,7 @@ public class UserDefinedColours extends GUserDefinedColours implements name = jucs.getColour(i).getName(); if (ResidueProperties.aa3Hash.containsKey(name)) { - index = ((Integer) ResidueProperties.aa3Hash.get(name)) - .intValue(); + index = ResidueProperties.aa3Hash.get(name).intValue(); } else { @@ -678,7 +778,7 @@ public class UserDefinedColours extends GUserDefinedColours implements jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours(); - jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in); + jucs = jucs.unmarshal(in); newColours = new Color[jucs.getColourCount()]; @@ -712,27 +812,28 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void savebutton_actionPerformed(ActionEvent e) { 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 String[] - { 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; } @@ -740,12 +841,12 @@ public class UserDefinedColours extends GUserDefinedColours implements 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("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); @@ -753,47 +854,82 @@ public class UserDefinedColours extends GUserDefinedColours implements 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(); } } @@ -803,6 +939,7 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param e * DOCUMENT ME! */ + @Override protected void cancelButton_actionPerformed(ActionEvent e) { if (ap != null) @@ -818,9 +955,9 @@ public class UserDefinedColours extends GUserDefinedColours implements ap.paintAlignment(true); } - if (jmol != null) + if (structureViewer != null) { - jmol.setJalviewColourScheme(oldColourScheme); + structureViewer.setJalviewColourScheme(oldColourScheme); } try @@ -831,16 +968,14 @@ public class UserDefinedColours extends GUserDefinedColours implements } } - static Hashtable userColourSchemes; - - public static Hashtable getUserColourSchemes() + public static SortedMap getUserColourSchemes() { return userColourSchemes; } public static void initUserColourSchemes(String files) { - userColourSchemes = new Hashtable(); + userColourSchemes = new TreeMap(); if (files == null || files.length() == 0) { @@ -864,7 +999,7 @@ public class UserDefinedColours extends GUserDefinedColours implements coloursFound.append("|"); } coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); + userColourSchemes.put(ucs.getSchemeName(), ucs); } } catch (Exception ex) { @@ -875,13 +1010,11 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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); } } } @@ -892,11 +1025,11 @@ public class UserDefinedColours extends GUserDefinedColours implements // In case colours can't be loaded, we'll remove them // from the default list here. - userColourSchemes = new Hashtable(); + userColourSchemes = new TreeMap(); StringBuffer coloursFound = new StringBuffer(); StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); + Cache.getProperty(USER_DEFINED_COLOURS), "|"); while (st.hasMoreElements()) { @@ -904,14 +1037,14 @@ public class UserDefinedColours extends GUserDefinedColours implements 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) { @@ -921,28 +1054,28 @@ public class UserDefinedColours extends GUserDefinedColours implements 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); } } + @Override public void caseSensitive_actionPerformed(ActionEvent e) { resetButtonPanel(caseSensitive.isSelected()); lcaseColour.setEnabled(caseSensitive.isSelected()); } + @Override public void lcaseColour_actionPerformed(ActionEvent e) { if (selectedButtons == null) { - selectedButtons = new Vector(); + selectedButtons = new ArrayList(); } else { @@ -950,5 +1083,4 @@ public class UserDefinedColours extends GUserDefinedColours implements } selectedButtons.add(lcaseColour); } - }