X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=1836e33b3d35d70ee0f1b783ba785f840bb4603d;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=6e9a12169066690430a9bcc40b9b41adeee4a5bf;hpb=bbad0d026977fa78805e90e7c90521db9d7536c2;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 6e9a121..1836e33 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,14 +20,12 @@ */ 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; @@ -36,11 +34,14 @@ 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; @@ -54,6 +55,8 @@ 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 @@ -62,11 +65,11 @@ 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"; @@ -80,48 +83,44 @@ 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 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) { 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); @@ -140,32 +139,10 @@ 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 +153,6 @@ 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 +169,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (upperCaseButtons == null) { - upperCaseButtons = new ArrayList(); + upperCaseButtons = new ArrayList<>(); } for (int i = 0; i < 20; i++) @@ -228,15 +200,17 @@ 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; - JButton 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); } @@ -284,7 +258,8 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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++) @@ -293,6 +268,8 @@ public class UserDefinedColours extends GUserDefinedColours implements button.setBackground(newColour); button.setForeground(ColorUtils.brighterThan(newColour)); } + + changedButNotSaved = true; } /** @@ -354,8 +331,8 @@ 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 +345,8 @@ 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 +354,14 @@ 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 +452,25 @@ 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 +481,62 @@ 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). * @@ -509,37 +554,31 @@ 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() { @@ -591,72 +630,70 @@ 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")); + chooser.setResponseHandler(0, new Runnable() + { + @Override + public void run() + { + File choice = chooser.getSelectedFile(); + Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - int value = chooser.showOpenDialog(this); + UserColourScheme ucs = ColourSchemeLoader + .loadColourScheme(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getSchemeName()); - if (value != JalviewFileChooser.APPROVE_OPTION) - { - return; - } - File choice = chooser.getSelectedFile(); - Cache.setProperty(LAST_DIRECTORY, choice.getParent()); + 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); + } - UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice - .getAbsolutePath()); - Color[] colors = ucs.getColours(); - schemeName.setText(ucs.getSchemeName()); + for (int i = 0; i < upperCaseButtons.size(); i++) + { + JButton button = upperCaseButtons.get(i); + button.setBackground(colors[i]); + } - 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]); + addNewColourScheme(choice.getPath()); } - } - 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); } /** @@ -688,54 +725,81 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * 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() { 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 (ColourSchemes.getInstance().nameExists(name)) + if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name)) { - 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) + /** + * 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; + } } - 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) + int option = chooser.showSaveDialog(this); + if (option == JalviewFileChooser.APPROVE_OPTION) { File file = chooser.getSelectedFile(); - addNewColourScheme(file.getPath()); + 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(); + } } } @@ -746,15 +810,16 @@ 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) @@ -778,6 +843,8 @@ public class UserDefinedColours extends GUserDefinedColours implements { ap.alignFrame.buildColourMenu(); } + + return ucs; } /** @@ -792,7 +859,8 @@ 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( @@ -804,9 +872,14 @@ 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) { @@ -815,30 +888,14 @@ 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 { @@ -848,8 +905,14 @@ 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);