X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;fp=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=8b45c409e8afb7dcc01be9f9e9d6f09eb3778bcb;hb=9f70ff4b6d193b340031997634c9e3602486bc8e;hp=c38004900fc145d196ab1c1e458a618b1e431754;hpb=76844c43faeeeba369deaf42f1998ca0fb33d956;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index c380049..8b45c40 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,34 +20,35 @@ */ 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.ColourSchemeLoader; +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.event.ActionEvent; +import java.awt.Insets; +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.Hashtable; -import java.util.StringTokenizer; +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; @@ -58,10 +59,17 @@ import javax.swing.event.ChangeListener; * @author Andrew Waterhouse * @author Mungo Carstairs */ -public class UserDefinedColours extends GUserDefinedColours implements - ChangeListener +public class UserDefinedColours extends GUserDefinedColours + implements ChangeListener { - private static final int MY_FRAME_HEIGHT = 420; + 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 = 440; private static final int MY_FRAME_WIDTH = 810; @@ -69,50 +77,44 @@ public class UserDefinedColours extends GUserDefinedColours implements AlignmentPanel ap; - SequenceGroup seqGroup; - - ArrayList selectedButtons; - + /* + * the colour scheme when the dialog was opened, or + * the scheme last saved to file + */ ColourSchemeI oldColourScheme; - JInternalFrame frame; + /* + * flag is true if the colour scheme has been changed since the + * dialog was opened, or the changes last saved to file + */ + boolean changed; - JalviewStructureDisplayI jmol; + JInternalFrame frame; - ArrayList upperCaseButtons; + List upperCaseButtons; - ArrayList lowerCaseButtons; + List lowerCaseButtons; /** - * Creates a new UserDefinedColours object. + * Creates and displays a new UserDefinedColours panel * - * @param ap - * DOCUMENT ME! - * @param sg - * DOCUMENT ME! + * @param alignPanel */ - public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) + public UserDefinedColours(AlignmentPanel alignPanel) { - super(); + this(); lcaseColour.setEnabled(false); - this.ap = ap; - seqGroup = sg; + this.ap = alignPanel; - if (seqGroup != null) - { - oldColourScheme = seqGroup.cs; - } - else - { - oldColourScheme = ap.av.getGlobalColourScheme(); - } + oldColourScheme = alignPanel.av.getGlobalColourScheme(); if (oldColourScheme instanceof UserColourScheme) { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); - if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null) + schemeName.setText(oldColourScheme.getSchemeName()); + if (((UserColourScheme) oldColourScheme) + .getLowerCaseColours() != null) { caseSensitive.setSelected(true); lcaseColour.setEnabled(true); @@ -131,25 +133,10 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI jmol, - ColourSchemeI oldcs) + UserDefinedColours() { super(); - this.jmol = jmol; - - colorChooser.getSelectionModel().addChangeListener(this); - - oldColourScheme = oldcs; - - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); - } - - resetButtonPanel(false); - - showFrame(); - + selectedButtons = new ArrayList(); } void showFrame() @@ -160,14 +147,17 @@ public class UserDefinedColours extends GUserDefinedColours implements Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true); - - if (seqGroup != null) - { - frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")"); - } } - 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(); @@ -176,23 +166,13 @@ public class UserDefinedColours extends GUserDefinedColours implements upperCaseButtons = new ArrayList(); } - 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); } @@ -201,7 +181,7 @@ public class UserDefinedColours extends GUserDefinedColours implements buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22)); buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23)); - if (!caseSensitive) + if (!isCaseSensitive) { gridLayout.setRows(6); gridLayout.setColumns(4); @@ -221,14 +201,14 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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)); @@ -239,7 +219,7 @@ public class UserDefinedColours extends GUserDefinedColours implements // 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()); } @@ -249,35 +229,39 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * 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(); + if (lcaseColour.isSelected()) { - JButton button = null; - final Color newColour = colorChooser.getColor(); - for (int i = 0; i < selectedButtons.size(); i++) + selectedButtons.clear(); + for (int i = 0; i < lowerCaseButtons.size(); i++) { - button = selectedButtons.get(i); + button = lowerCaseButtons.get(i); button.setBackground(newColour); - button.setForeground(ColorUtils.brighterThan(newColour)); - } - if (button == lcaseColour) - { - for (int i = 0; i < lowerCaseButtons.size(); i++) - { - button = lowerCaseButtons.get(i); - button.setBackground(newColour); - button.setForeground(ColorUtils.brighterThan(button - .getBackground())); - } + button.setForeground( + ColorUtils.brighterThan(button.getBackground())); } } + for (int i = 0; i < selectedButtons.size(); i++) + { + button = selectedButtons.get(i); + button.setBackground(newColour); + button.setForeground(ColorUtils.brighterThan(newColour)); + } + + changed = true; } /** @@ -300,11 +284,6 @@ public class UserDefinedColours extends GUserDefinedColours implements */ public void colourButtonPressed(MouseEvent e) { - if (selectedButtons == null) - { - selectedButtons = new ArrayList(); - } - JButton pressed = (JButton) e.getSource(); if (e.isShiftDown()) @@ -344,8 +323,8 @@ public class UserDefinedColours extends GUserDefinedColours implements JButton button = (JButton) buttonPanel.getComponent(b); if (!selectedButtons.contains(button)) { - button.setForeground(ColorUtils.brighterThan(button - .getBackground())); + button.setForeground( + ColorUtils.brighterThan(button.getBackground())); selectedButtons.add(button); } } @@ -358,7 +337,8 @@ public class UserDefinedColours extends GUserDefinedColours implements button.setForeground(ColorUtils.darkerThan(button.getBackground())); } selectedButtons.clear(); - pressed.setForeground(ColorUtils.brighterThan(pressed.getBackground())); + pressed.setForeground( + ColorUtils.brighterThan(pressed.getBackground())); selectedButtons.add(pressed); } @@ -366,13 +346,14 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (selectedButtons.contains(pressed)) { - pressed.setForeground(ColorUtils.darkerThan(pressed.getBackground())); + pressed.setForeground( + ColorUtils.darkerThan(pressed.getBackground())); selectedButtons.remove(pressed); } else { - pressed.setForeground(ColorUtils.brighterThan(pressed - .getBackground())); + pressed.setForeground( + ColorUtils.brighterThan(pressed.getBackground())); selectedButtons.add(pressed); } } @@ -384,28 +365,35 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * 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 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 = 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) @@ -414,57 +402,66 @@ public class UserDefinedColours extends GUserDefinedColours implements } }); - caseSensitiveButtons.add(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(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() { if (isNoSelectionMade()) { - JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager - .getString("label.no_colour_selection_in_scheme"), + 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(null); + /* + * OK is treated as 'apply colours and close' + */ + applyButton_actionPerformed(); + + /* + * If editing a named colour scheme, warn if changes + * have not been saved + */ + warnIfUnsavedChanges(); try { @@ -476,6 +473,57 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** + * If we have made changes to an existing user defined colour scheme but not + * saved them, show a dialog with the option to save. If the user chooses to + * save, do so, else clear the colour scheme name to indicate a new colour + * scheme. + */ + protected void warnIfUnsavedChanges() + { + if (!changed) + { + return; + } + + String name = schemeName.getText().trim(); + if (oldColourScheme != null && !"".equals(name) + && name.equals(oldColourScheme.getSchemeName())) + { + String message = MessageManager.formatMessage("label.scheme_changed", + name); + String title = MessageManager.getString("label.save_changes"); + String[] options = new String[] { title, + MessageManager.getString("label.dont_save_changes"), }; + final String question = JvSwingUtils.wrapTooltip(true, message); + int response = JvOptionPane.showOptionDialog(Desktop.desktop, + question, title, JvOptionPane.DEFAULT_OPTION, + JvOptionPane.PLAIN_MESSAGE, null, options, options[0]); + + boolean saved = false; + if (response == 0) + { + /* + * prompt to save changes to file + */ + saved = savebutton_actionPerformed(); + } + + /* + * if user chooses not to save (either in this dialog or in the + * save as dialogs), treat this as a new user defined colour scheme + */ + if (!saved) + { + /* + * clear scheme name and re-apply as an anonymous scheme + */ + schemeName.setText(""); + applyButton_actionPerformed(); + } + } + } + + /** * Returns true if the user has not made any colour selection (including if * 'case-sensitive' selected and no lower-case colour chosen). * @@ -493,40 +541,31 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Applies the current colour scheme to the alignment or sequence group */ @Override - protected void applyButton_actionPerformed(ActionEvent e) + protected void applyButton_actionPerformed() { if (isNoSelectionMade()) { - JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager - .getString("label.no_colour_selection_in_scheme"), + 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; - ap.paintAlignment(true); - } - else if (ap != null) - { - ap.alignFrame.changeColour(ucs); - } - else if (jmol != null) - { - jmol.setJalviewColourScheme(ucs); - } + ap.alignFrame.changeColour(ucs); } + /** + * Constructs an instance of UserColourScheme with the residue colours + * currently set on the buttons on the panel + * + * @return + */ UserColourScheme getSchemeFromButtons() { @@ -552,6 +591,7 @@ public class UserDefinedColours extends GUserDefinedColours implements } UserColourScheme ucs = new UserColourScheme(newColours); + ucs.setName(schemeName.getText()); if (caseSensitive.isSelected()) { @@ -577,473 +617,286 @@ public class UserDefinedColours extends GUserDefinedColours implements ucs.setLowerCaseColours(newColours); } - if (ap != null) - { - ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); - } - return ucs; } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Action on clicking Load scheme button. + *
    + *
  • Open a file chooser to browse for files with extension .jc
    • + *
  • Load in the colour scheme and transfer it to this panel's buttons
    • + *
  • Register the loaded colour scheme
    • + *
*/ @Override - protected void loadbutton_actionPerformed(ActionEvent e) + protected void loadbutton_actionPerformed() { upperCaseButtons = new ArrayList(); lowerCaseButtons = new ArrayList(); - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "jc", - "Jalview User Colours", "Jalview User Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.load_colour_scheme")); + 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 = 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 = ColourSchemeLoader + .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 = 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()); } /** - * 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 = ColourSchemeLoader.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! + * Action on pressing the Save button. + *
    + *
  • Check a name has been entered
    • + *
  • Warn if the name already exists, remove any existing scheme of the same + * name if overwriting
    • + *
  • Do the standard file chooser thing to write with extension .jc
    • + *
  • If saving changes (possibly not yet applied) to the currently selected + * colour scheme, then apply the changes, as it is too late to back out + * now
    • + *
  • Don't apply the changes if the currently selected scheme is different, + * to allow a new scheme to be configured and saved but not applied
    • + *
+ * Returns true if the scheme is saved to file, false if it is not * - * @param e - * DOCUMENT ME! + * @return */ @Override - protected void savebutton_actionPerformed(ActionEvent e) + protected boolean savebutton_actionPerformed() { - 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"), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager + .getString("label.user_colour_scheme_must_have_name"), MessageManager.getString("label.no_name_colour_scheme"), JvOptionPane.WARNING_MESSAGE); - return; + return false; } - 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() }), + "label.colour_scheme_exists_overwrite", new Object[] + { name, name }), MessageManager.getString("label.duplicate_scheme_name"), JvOptionPane.YES_NO_OPTION); if (reply != JvOptionPane.YES_OPTION) { - return; + return false; } - - userColourSchemes.remove(schemeName.getText()); } - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "jc", - "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) + 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); + return false; + } - jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours(); + File file = chooser.getSelectedFile(); + UserColourScheme updatedScheme = addNewColourScheme(file.getPath()); + saveToFile(file); + changed = false; - 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(); - } + /* + * changes saved - apply to alignment if we are changing + * the currently selected colour scheme; also make the updated + * colours the 'backout' scheme on Cancel + */ + if (oldColourScheme != null + && name.equals(oldColourScheme.getSchemeName())) + { + oldColourScheme = updatedScheme; + applyButton_actionPerformed(); } + return true; } /** - * 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 + * @return */ - @Override - protected void cancelButton_actionPerformed(ActionEvent e) + protected UserColourScheme 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) - { - seqGroup.cs = oldColourScheme; - } - else if (ap != null) + if (defaultColours.length() > 0) { - ap.av.setGlobalColourScheme(oldColourScheme); + defaultColours = defaultColours.concat("|"); } - 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; + return ucs; } - 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(); + String name = schemeName.getText(); + ucs.setSchemeName(name); + 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 + for (int i = 0; i < buttonPanel.getComponentCount(); i++) { - UserColourScheme ucs = loadColours(file); - if (ucs != null) - { - if (coloursFound.length() > 0) - { - coloursFound.append("|"); - } - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); - } - } catch (Exception ex) - { - 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 that was selected before the dialogue + * was opened + */ + @Override + protected void cancelButton_actionPerformed() { - // 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(); + ap.alignFrame.changeColour(oldColourScheme); + ap.paintAlignment(true); - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); - - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - 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) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } - - if (coloursFound.toString().length() > 1) + try { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); - } - else + 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()); } + /** + * Action on selecting or deselecting the Case Sensitive option. When + * selected, separate buttons are shown for lower case residues, and the panel + * is resized to accommodate them. Also, the checkbox for 'apply colour to all + * lower case' is enabled. + */ @Override - public void lcaseColour_actionPerformed(ActionEvent e) + public void caseSensitive_actionPerformed() { - if (selectedButtons == null) - { - selectedButtons = new ArrayList(); - } - else - { - selectedButtons.clear(); - } - selectedButtons.add(lcaseColour); + boolean selected = caseSensitive.isSelected(); + resetButtonPanel(selected); + lcaseColour.setEnabled(selected); } }