X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=c3f132baa467eafd1e0e2544b5c8a8279a3bc66d;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=5cfff8685d11451e9ad74f1dfa48e2d50d0e7a8d;hpb=92d5aeaf6d48b15a8122060f7dd32f16d2f552dc;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 5cfff86..c3f132b 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,43 +20,43 @@ */ package jalview.gui; -import jalview.api.structures.JalviewStructureDisplayI; +import java.util.Locale; + 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 jalview.util.Platform; +import jalview.xml.binding.jalview.JalviewUserColours; +import jalview.xml.binding.jalview.JalviewUserColours.Colour; +import jalview.xml.binding.jalview.ObjectFactory; 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.ArrayList; import java.util.List; -import java.util.SortedMap; -import java.util.StringTokenizer; -import java.util.TreeMap; import javax.swing.JButton; import javax.swing.JInternalFrame; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.Marshaller; /** * This panel allows the user to assign colours to Amino Acid residue codes, and @@ -65,67 +65,62 @@ 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 Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10); + private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, + 10); - private static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; + public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; private static final String LAST_DIRECTORY = "LAST_DIRECTORY"; - private static final int MY_FRAME_HEIGHT = 420; + private static final int MY_FRAME_HEIGHT = 440; 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; - - List 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 changedButNotSaved; - JalviewStructureDisplayI structureViewer; + JInternalFrame frame; List upperCaseButtons; List lowerCaseButtons; /** - * Creates a new UserDefinedColours object. + * Creates and displays a new UserDefinedColours panel * - * @param ap - * @param sg + * @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).getSchemeName()); - if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null) + schemeName.setText(oldColourScheme.getSchemeName()); + if (((UserColourScheme) oldColourScheme) + .getLowerCaseColours() != null) { caseSensitive.setSelected(true); lcaseColour.setEnabled(true); @@ -144,25 +139,10 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI viewer, - ColourSchemeI oldcs) + UserDefinedColours() { super(); - this.structureViewer = viewer; - - colorChooser.getSelectionModel().addChangeListener(this); - - oldColourScheme = oldcs; - - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName()); - } - - resetButtonPanel(false); - - showFrame(); - + selectedButtons = new ArrayList<>(); } void showFrame() @@ -173,39 +153,32 @@ 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(); if (upperCaseButtons == null) { - upperCaseButtons = new ArrayList(); + 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); } @@ -214,7 +187,7 @@ 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); @@ -227,21 +200,21 @@ public class UserDefinedColours extends GUserDefinedColours implements if (lowerCaseButtons == null) { - lowerCaseButtons = new ArrayList(); + lowerCaseButtons = new ArrayList<>(); } for (int i = 0; i < 20; i++) { int row = i / cols + 1; int index = (row * cols) + i; - button = makeButton(ResidueProperties.aa[i].toLowerCase(), - ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i); + JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(Locale.ROOT), + ResidueProperties.aa[i].toLowerCase(Locale.ROOT), lowerCaseButtons, i); buttonPanel.add(button, index); } } - if (caseSensitive) + if (isCaseSensitive) { buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20)); buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21)); @@ -252,7 +225,7 @@ 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()); } @@ -262,35 +235,39 @@ 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)); + } + + changedButNotSaved = true; } /** @@ -313,11 +290,6 @@ 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()) @@ -357,8 +329,8 @@ 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); } } @@ -371,7 +343,8 @@ 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); } @@ -379,13 +352,14 @@ 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); } } @@ -411,8 +385,8 @@ public class UserDefinedColours extends GUserDefinedColours implements * @param buttonIndex * the button's position in the list */ - JButton makeButton(String label, String residue, - List buttons, int buttonIndex) + JButton makeButton(String label, String residue, List buttons, + int buttonIndex) { final JButton button; Color col; @@ -436,15 +410,15 @@ public class UserDefinedColours extends GUserDefinedColours implements buttons.add(button); + /* + * make initial button colour that of the current colour scheme, + * if it is a simple per-residue colouring, else white + */ col = Color.white; - if (oldColourScheme != null) + if (oldColourScheme != null && oldColourScheme.isSimple()) { - try - { - col = oldColourScheme.findColour(residue.charAt(0), -1, null); - } catch (Exception ex) - { - } + col = oldColourScheme.findColour(residue.charAt(0), 0, null, null, + 0f); } } @@ -476,15 +450,25 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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 { + /* + * 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 { frame.setClosed(true); @@ -495,6 +479,62 @@ 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() + { + // BH 2018 no warning in JavaScript TODO + + if (!Platform.isJS() && changedButNotSaved) + /** + * Java only + * + * @j2sIgnore + */ + { + 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]); + + if (response == 0) + { + /* + * prompt to save changes to file; if done, + * resets 'changed' flag to false + */ + 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 (changedButNotSaved) + { + /* + * 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). * @@ -512,38 +552,31 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * Applies the current colour scheme to the alignment, sequence group or - * structure view. + * Applies the current colour scheme to the alignment or sequence group */ @Override 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 (structureViewer != null) - { - structureViewer.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() { @@ -569,6 +602,7 @@ public class UserDefinedColours extends GUserDefinedColours implements } UserColourScheme ucs = new UserColourScheme(newColours); + ucs.setName(schemeName.getText()); if (caseSensitive.isSelected()) { @@ -594,77 +628,77 @@ 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"); + upperCaseButtons = new ArrayList<>(); + lowerCaseButtons = new ArrayList<>(); + JalviewFileChooser chooser = new JalviewFileChooser("jc", + "Jalview User Colours"); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager - .getString("label.load_colour_scheme")); + chooser.setDialogTitle( + MessageManager.getString("label.load_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.load")); - - int value = chooser.showOpenDialog(this); - - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } - File choice = chooser.getSelectedFile(); - Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - - UserColourScheme ucs = loadColours(choice.getAbsolutePath()); - Color[] colors = ucs.getColours(); - schemeName.setText(ucs.getSchemeName()); - - 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]); - } - } - 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()); + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + File choice = chooser.getSelectedFile(); + Cache.setProperty(LAST_DIRECTORY, choice.getParent()); + + UserColourScheme ucs = ColourSchemeLoader + .loadColourScheme(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getSchemeName()); + + 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]); + } + } + 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()); + } + }); + + chooser.showOpenDialog(this); } /** - * 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() { @@ -677,185 +711,93 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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! - * - * @param e - * 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
    • + *
+ * If the scheme is saved to file, the 'changed' flag field is reset to false. */ @Override - protected void savebutton_actionPerformed(ActionEvent e) + protected void 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; } - if (userColourSchemes != null - && userColourSchemes.containsKey(schemeName.getText())) + if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name)) { - int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "label.colour_scheme_exists_overwrite", new Object[] { - schemeName.getText(), schemeName.getText() }), - MessageManager.getString("label.duplicate_scheme_name"), - JvOptionPane.YES_NO_OPTION); - if (reply != JvOptionPane.YES_OPTION) + /** + * java only + * + * @j2sIgnore + */ { - return; + int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage( + "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; + } } - - userColourSchemes.remove(schemeName.getText()); } - JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty(LAST_DIRECTORY), "jc", + + JalviewFileChooser chooser = new JalviewFileChooser("jc", "Jalview User Colours"); - chooser.setFileView(new 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) + int option = chooser.showSaveDialog(this); + if (option == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - addNewColourScheme(choice); - saveToFile(choice); + File file = chooser.getSelectedFile(); + UserColourScheme updatedScheme = addNewColourScheme(file.getPath()); + saveToFile(file); + changedButNotSaved = false; + + /* + * 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(); + } } } @@ -866,15 +808,16 @@ public class UserDefinedColours extends GUserDefinedColours implements * the colour scheme. * * @param filePath + * @return */ - protected void addNewColourScheme(String filePath) + protected UserColourScheme 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); + String defaultColours = Cache.getDefault(USER_DEFINED_COLOURS, + filePath); if (defaultColours.indexOf(filePath) == -1) { if (defaultColours.length() > 0) @@ -886,9 +829,10 @@ public class UserDefinedColours extends GUserDefinedColours implements Cache.setProperty(USER_DEFINED_COLOURS, defaultColours); /* - * add to the cache in this object + * construct and register the colour scheme */ - userColourSchemes.put(schemeName.getText(), getSchemeFromButtons()); + UserColourScheme ucs = getSchemeFromButtons(); + ColourSchemes.getInstance().registerColourScheme(ucs); /* * update the Colour menu items @@ -897,25 +841,28 @@ public class UserDefinedColours extends GUserDefinedColours implements { ap.alignFrame.buildColourMenu(); } + + return ucs; } /** * Saves the colour scheme to file in XML format * - * @param filePath + * @param path */ - protected void saveToFile(String filePath) + protected void saveToFile(File toFile) { /* * build a Java model of colour scheme as XML, and * marshal to file */ JalviewUserColours ucs = new JalviewUserColours(); - ucs.setSchemeName(schemeName.getText()); + String name = schemeName.getText(); + ucs.setSchemeName(name); try { PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(filePath), "UTF-8")); + new FileOutputStream(toFile), "UTF-8")); for (int i = 0; i < buttonPanel.getComponentCount(); i++) { @@ -923,9 +870,14 @@ public class UserDefinedColours extends GUserDefinedColours implements Colour col = new Colour(); col.setName(button.getText()); col.setRGB(Format.getHexString(button.getBackground())); - ucs.addColour(col); - } - ucs.marshal(out); + ucs.getColour().add(col); + } + JAXBContext jaxbContext = JAXBContext + .newInstance(JalviewUserColours.class); + Marshaller jaxbMarshaller = jaxbContext.createMarshaller(); + jaxbMarshaller.marshal( + new ObjectFactory().createJalviewUserColours(ucs), out); + // ucs.marshal(out); out.close(); } catch (Exception ex) { @@ -934,32 +886,14 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * On cancel, restores the colour scheme that was selected before the dialogue + * was opened */ @Override - protected void cancelButton_actionPerformed(ActionEvent e) + protected void cancelButton_actionPerformed() { - if (ap != null) - { - if (seqGroup != null) - { - seqGroup.cs = oldColourScheme; - } - else - { - ap.av.setGlobalColourScheme(oldColourScheme); - } - ap.alignFrame.changeColour(oldColourScheme); - ap.paintAlignment(true); - } - - if (structureViewer != null) - { - structureViewer.setJalviewColourScheme(oldColourScheme); - } + ap.alignFrame.changeColour(oldColourScheme); + ap.paintAlignment(true, true); try { @@ -969,119 +903,17 @@ public class UserDefinedColours extends GUserDefinedColours implements } } - public static SortedMap getUserColourSchemes() - { - return userColourSchemes; - } - - public static void initUserColourSchemes(String files) - { - userColourSchemes = new TreeMap(); - - if (files == null || files.length() == 0) - { - return; - } - - // In case colours can't be loaded, we'll remove them - // from the default list here. - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer(files, "|"); - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - UserColourScheme ucs = loadColours(file); - if (ucs != null) - { - if (coloursFound.length() > 0) - { - coloursFound.append("|"); - } - coloursFound.append(file); - userColourSchemes.put(ucs.getSchemeName(), ucs); - } - } catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } - if (!files.equals(coloursFound.toString())) - { - if (coloursFound.toString().length() > 1) - { - Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString()); - } - else - { - Cache.applicationProperties.remove(USER_DEFINED_COLOURS); - } - } - } - - public static void removeColourFromDefaults(String target) - { - // The only way to find colours by name is to load them in - // In case colours can't be loaded, we'll remove them - // from the default list here. - - userColourSchemes = new TreeMap(); - - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer( - Cache.getProperty(USER_DEFINED_COLOURS), "|"); - - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - UserColourScheme ucs = loadColours(file); - if (ucs != null && !ucs.getSchemeName().equals(target)) - { - if (coloursFound.length() > 0) - { - coloursFound.append("|"); - } - coloursFound.append(file); - userColourSchemes.put(ucs.getSchemeName(), ucs); - } - } catch (Exception ex) - { - System.out.println("Error loading User ColourFile\n" + ex); - } - } - - if (coloursFound.toString().length() > 1) - { - Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString()); - } - else - { - Cache.applicationProperties.remove(USER_DEFINED_COLOURS); - } - - } - - @Override - public void caseSensitive_actionPerformed(ActionEvent e) - { - 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); } }