X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=b1f6d1b8d194996f65d9ccf41e787546707c0362;hb=9cd96dd3e43ae32814fa8c62df274ff9224bfdbc;hp=10a9687c465c54ba3ee8d54a6b521249d5390c29;hpb=599107bb6f835ae4dbc679cbff023800faba7992;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 10a9687..b1f6d1b 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,26 +20,25 @@ */ 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 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; @@ -53,6 +52,8 @@ 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 @@ -61,17 +62,17 @@ 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 Font VERDANA_BOLD_10 = new Font("Verdana", - Font.BOLD, 10); + private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, + 10); public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; private static final String LAST_DIRECTORY = "LAST_DIRECTORY"; - private static final int MY_FRAME_HEIGHT = 420; + private static final int MY_FRAME_HEIGHT = 440; private static final int MY_FRAME_WIDTH = 810; @@ -79,52 +80,47 @@ public class UserDefinedColours extends GUserDefinedColours implements 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 changed; - 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) { this(); lcaseColour.setEnabled(false); - this.ap = ap; - seqGroup = sg; + this.ap = alignPanel; - if (seqGroup != null) - { - oldColourScheme = seqGroup.getColourScheme(); - } - else - { - oldColourScheme = ap.av.getGlobalColourScheme(); - } + oldColourScheme = alignPanel.av.getGlobalColourScheme(); if (oldColourScheme instanceof UserColourScheme) { schemeName.setText(oldColourScheme.getSchemeName()); - if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null) + if (((UserColourScheme) oldColourScheme) + .getLowerCaseColours() != null) { caseSensitive.setSelected(true); lcaseColour.setEnabled(true); - lcaseColour.setForeground(Color.GRAY); resetButtonPanel(true); } else @@ -140,32 +136,10 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI viewer, - ColourSchemeI oldcs) - { - this(); - this.structureViewer = viewer; - - colorChooser.getSelectionModel().addChangeListener(this); - - oldColourScheme = oldcs; - - if (oldColourScheme instanceof UserColourScheme) - { - schemeName.setText(((UserColourScheme) oldColourScheme) - .getSchemeName()); - } - - resetButtonPanel(false); - - showFrame(); - - } - - public UserDefinedColours() + UserDefinedColours() { super(); - selectedButtons = new ArrayList(); + selectedButtons = new ArrayList<>(); } void showFrame() @@ -176,11 +150,6 @@ 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() + ")"); - } } /** @@ -197,7 +166,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (upperCaseButtons == null) { - upperCaseButtons = new ArrayList(); + upperCaseButtons = new ArrayList<>(); } for (int i = 0; i < 20; i++) @@ -228,7 +197,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (lowerCaseButtons == null) { - lowerCaseButtons = new ArrayList(); + lowerCaseButtons = new ArrayList<>(); } for (int i = 0; i < 20; i++) @@ -277,22 +246,25 @@ public class UserDefinedColours extends GUserDefinedColours implements { JButton button = null; final Color newColour = colorChooser.getColor(); - for (int i = 0; i < selectedButtons.size(); i++) + if (lcaseColour.isSelected()) { - button = selectedButtons.get(i); - button.setBackground(newColour); - button.setForeground(ColorUtils.brighterThan(newColour)); - } - if (button == lcaseColour) - { - button.setForeground(Color.black); + selectedButtons.clear(); 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; } /** @@ -354,8 +326,8 @@ 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); } } @@ -368,7 +340,8 @@ 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); } @@ -376,13 +349,14 @@ 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); } } @@ -473,15 +447,25 @@ 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); @@ -492,6 +476,57 @@ 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). * @@ -509,37 +544,31 @@ 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(); - if (seqGroup != null) - { - seqGroup.setColourScheme(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() { @@ -591,31 +620,28 @@ 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(); + 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); @@ -627,8 +653,8 @@ public class UserDefinedColours extends GUserDefinedColours implements File choice = chooser.getSelectedFile(); Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - UserColourScheme ucs = ColourSchemes.loadColourScheme(choice - .getAbsolutePath()); + UserColourScheme ucs = ColourSchemeLoader + .loadColourScheme(choice.getAbsolutePath()); Color[] colors = ucs.getColours(); schemeName.setText(ucs.getSchemeName()); @@ -636,7 +662,6 @@ public class UserDefinedColours extends GUserDefinedColours implements { caseSensitive.setSelected(true); lcaseColour.setEnabled(true); - lcaseColour.setForeground(Color.GRAY); resetButtonPanel(true); for (int i = 0; i < lowerCaseButtons.size(); i++) { @@ -677,7 +702,7 @@ public class UserDefinedColours extends GUserDefinedColours implements { colours = colours.substring(0, colours.indexOf("|")); } - ret = ColourSchemes.loadColourScheme(colours); + ret = ColourSchemeLoader.loadColourScheme(colours); } if (ret == null) @@ -689,55 +714,82 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * 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() { 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 (ColourSchemes.getInstance().nameExists(name)) { int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( - "label.colour_scheme_exists_overwrite", new Object[] { - name, name }), + "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; } - ColourSchemes.getInstance().removeColourScheme(name); } JalviewFileChooser chooser = new JalviewFileChooser("jc", "Jalview User Colours"); JalviewFileView fileView = new JalviewFileView(); chooser.setFileView(fileView); - chooser.setDialogTitle(MessageManager - .getString("label.save_colour_scheme")); + 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) { - File file = chooser.getSelectedFile(); - addNewColourScheme(file.getPath()); - saveToFile(file); + return false; + } + + File file = chooser.getSelectedFile(); + UserColourScheme updatedScheme = addNewColourScheme(file.getPath()); + saveToFile(file); + changed = 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(); } + return true; } /** @@ -747,15 +799,16 @@ 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) @@ -779,6 +832,8 @@ public class UserDefinedColours extends GUserDefinedColours implements { ap.alignFrame.buildColourMenu(); } + + return ucs; } /** @@ -793,7 +848,8 @@ public class UserDefinedColours extends GUserDefinedColours implements * 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( @@ -805,9 +861,14 @@ public class UserDefinedColours extends GUserDefinedColours implements Colour col = new Colour(); col.setName(button.getText()); col.setRGB(Format.getHexString(button.getBackground())); - ucs.addColour(col); + ucs.getColour().add(col); } - ucs.marshal(out); + 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) { @@ -816,30 +877,14 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * On cancel, restores the colour scheme before the dialogue was opened - * - * @param e + * 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.setColourScheme(oldColourScheme); - } - else - { - ap.alignFrame.changeColour(oldColourScheme); - } - ap.paintAlignment(true); - } - - if (structureViewer != null) - { - structureViewer.setJalviewColourScheme(oldColourScheme); - } + ap.alignFrame.changeColour(oldColourScheme); + ap.paintAlignment(true, true); try { @@ -849,35 +894,17 @@ public class UserDefinedColours extends GUserDefinedColours implements } } + /** + * 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 caseSensitive_actionPerformed(ActionEvent e) + public void caseSensitive_actionPerformed() { boolean selected = caseSensitive.isSelected(); resetButtonPanel(selected); lcaseColour.setEnabled(selected); - lcaseColour.setForeground(Color.GRAY); - } - - /** - * Action on clicking 'Lower case colour', which results in changing colour of - * all lower-case buttons when a colour is picked. A second click of the - * button turns off this behaviour. - */ - @Override - public void lcaseColour_actionPerformed(ActionEvent e) - { - boolean enable = !selectedButtons.contains(lcaseColour); - selectedButtons.clear(); - if (enable) - { - selectedButtons.add(lcaseColour); - lcaseColour.setForeground(lowerCaseButtons.get(0).getForeground()); - lcaseColour.setForeground(Color.black); - } - else - { - lcaseColour.setBackground(Color.white); - lcaseColour.setForeground(Color.gray); - } } }