/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.Locale; import jalview.bin.Cache; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.jbgui.GUserDefinedColours; 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.MouseAdapter; import java.awt.event.MouseEvent; import java.io.File; import java.io.FileOutputStream; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; 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 * save the colour scheme. * * @author Andrew Waterhouse * @author Mungo Carstairs */ public class UserDefinedColours extends GUserDefinedColours implements ChangeListener { private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10); 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; private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970; AlignmentPanel ap; /* * the colour scheme when the dialog was opened, or * the scheme last saved to file */ ColourSchemeI oldColourScheme; /* * flag is true if the colour scheme has been changed since the * dialog was opened, or the changes last saved to file */ boolean changedButNotSaved; JInternalFrame frame; List upperCaseButtons; List lowerCaseButtons; /** * Creates and displays a new UserDefinedColours panel * * @param alignPanel */ public UserDefinedColours(AlignmentPanel alignPanel) { this(); lcaseColour.setEnabled(false); this.ap = alignPanel; oldColourScheme = alignPanel.av.getGlobalColourScheme(); if (oldColourScheme instanceof UserColourScheme) { schemeName.setText(oldColourScheme.getSchemeName()); if (((UserColourScheme) oldColourScheme) .getLowerCaseColours() != null) { caseSensitive.setSelected(true); lcaseColour.setEnabled(true); resetButtonPanel(true); } else { resetButtonPanel(false); } } else { resetButtonPanel(false); } showFrame(); } UserDefinedColours() { super(); selectedButtons = new ArrayList<>(); } void showFrame() { colorChooser.getSelectionModel().addChangeListener(this); frame = new JInternalFrame(); frame.setContentPane(this); Desktop.addInternalFrame(frame, MessageManager.getString("label.user_defined_colours"), Desktop.FRAME_MAKE_VISIBLE, MY_FRAME_WIDTH, MY_FRAME_HEIGHT, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300); } /** * 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<>(); } for (int i = 0; i < 20; 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); } buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20)); buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21)); buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22)); buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23)); if (!isCaseSensitive) { gridLayout.setRows(6); gridLayout.setColumns(4); } else { gridLayout.setRows(7); int cols = 7; gridLayout.setColumns(cols + 1); if (lowerCaseButtons == null) { 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(Locale.ROOT), ResidueProperties.aa[i].toLowerCase(Locale.ROOT), lowerCaseButtons, i); buttonPanel.add(button, index); } } if (isCaseSensitive) { buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20)); buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21)); buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22)); } // JAL-1360 widen the frame dynamically to accommodate case-sensitive AA // codes if (this.frame != null) { int newWidth = isCaseSensitive ? MY_FRAME_WIDTH_CASE_SENSITIVE : MY_FRAME_WIDTH; this.frame.setSize(newWidth, this.frame.getHeight()); } buttonPanel.validate(); validate(); } /** * 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 */ @Override public void stateChanged(ChangeEvent evt) { JButton button = null; final Color newColour = colorChooser.getColor(); if (lcaseColour.isSelected()) { selectedButtons.clear(); for (int i = 0; i < lowerCaseButtons.size(); i++) { button = lowerCaseButtons.get(i); button.setBackground(newColour); 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; } /** * Performs actions when a residue button is clicked. This manages the button * selection set (highlighted by brighter foreground text). *

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

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

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

* Finally, synchronize the colour chooser to the colour of the first button * in the selected set. * * @param e */ public void colourButtonPressed(MouseEvent e) { JButton pressed = (JButton) e.getSource(); if (e.isShiftDown()) { JButton start, end = (JButton) e.getSource(); if (selectedButtons.size() > 0) { start = selectedButtons.get(selectedButtons.size() - 1); } else { start = (JButton) e.getSource(); } int startIndex = 0, endIndex = 0; for (int b = 0; b < buttonPanel.getComponentCount(); b++) { if (buttonPanel.getComponent(b) == start) { startIndex = b; } if (buttonPanel.getComponent(b) == end) { endIndex = b; } } if (startIndex > endIndex) { int temp = startIndex; startIndex = endIndex; endIndex = temp; } for (int b = startIndex; b <= endIndex; b++) { JButton button = (JButton) buttonPanel.getComponent(b); if (!selectedButtons.contains(button)) { button.setForeground( ColorUtils.brighterThan(button.getBackground())); selectedButtons.add(button); } } } else if (!e.isControlDown()) { for (int b = 0; b < selectedButtons.size(); b++) { JButton button = selectedButtons.get(b); button.setForeground(ColorUtils.darkerThan(button.getBackground())); } selectedButtons.clear(); pressed.setForeground( ColorUtils.brighterThan(pressed.getBackground())); selectedButtons.add(pressed); } else if (e.isControlDown()) { if (selectedButtons.contains(pressed)) { pressed.setForeground( ColorUtils.darkerThan(pressed.getBackground())); selectedButtons.remove(pressed); } else { pressed.setForeground( ColorUtils.brighterThan(pressed.getBackground())); selectedButtons.add(pressed); } } if (selectedButtons.size() > 0) { colorChooser.setColor((selectedButtons.get(0)).getBackground()); } } /** * 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 * @param residue * @param the * list of buttons * @param buttonIndex * the button's position in the list */ JButton makeButton(String label, String residue, List buttons, int buttonIndex) { final JButton button; Color col; if (buttonIndex < buttons.size()) { button = buttons.get(buttonIndex); col = button.getBackground(); } else { button = new JButton(); button.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) { colourButtonPressed(e); } }); 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 && oldColourScheme.isSimple()) { col = oldColourScheme.findColour(residue.charAt(0), 0, null, null, 0f); } } if (caseSensitive.isSelected()) { button.setMargin(new Insets(2, 2, 2, 2)); } else { 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(VERDANA_BOLD_10); return button; } /** * 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() { if (isNoSelectionMade()) { JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), 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); } catch (Exception ex) { } } } /** * 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.getDesktopPane(), 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). * * @return */ protected boolean isNoSelectionMade() { final boolean noUpperCaseSelected = upperCaseButtons == null || upperCaseButtons.isEmpty(); final boolean noLowerCaseSelected = caseSensitive.isSelected() && (lowerCaseButtons == null || lowerCaseButtons.isEmpty()); final boolean noSelectionMade = noUpperCaseSelected || noLowerCaseSelected; return noSelectionMade; } /** * Applies the current colour scheme to the alignment or sequence group */ @Override protected void applyButton_actionPerformed() { if (isNoSelectionMade()) { JvOptionPane.showMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.no_colour_selection_in_scheme"), MessageManager.getString("label.no_colour_selection_warn"), JvOptionPane.WARNING_MESSAGE); } UserColourScheme ucs = getSchemeFromButtons(); ap.alignFrame.changeColour(ucs); } /** * Constructs an instance of UserColourScheme with the residue colours * currently set on the buttons on the panel * * @return */ UserColourScheme getSchemeFromButtons() { Color[] newColours = new Color[24]; int length = upperCaseButtons.size(); if (length < 24) { int i = 0; for (JButton btn : upperCaseButtons) { newColours[i] = btn.getBackground(); i++; } } else { for (int i = 0; i < 24; i++) { JButton button = upperCaseButtons.get(i); newColours[i] = button.getBackground(); } } UserColourScheme ucs = new UserColourScheme(newColours); ucs.setName(schemeName.getText()); if (caseSensitive.isSelected()) { newColours = new Color[23]; length = lowerCaseButtons.size(); if (length < 23) { int i = 0; for (JButton btn : lowerCaseButtons) { newColours[i] = btn.getBackground(); i++; } } else { for (int i = 0; i < 23; i++) { JButton button = lowerCaseButtons.get(i); newColours[i] = button.getBackground(); } } ucs.setLowerCaseColours(newColours); } return ucs; } /** * 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() { 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.setToolTipText(MessageManager.getString("action.load")); 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); } /** * 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 */ public static UserColourScheme loadDefaultColours() { UserColourScheme ret = null; String colours = Cache.getProperty(USER_DEFINED_COLOURS); if (colours != null) { if (colours.indexOf("|") > -1) { colours = colours.substring(0, colours.indexOf("|")); } ret = ColourSchemeLoader.loadColourScheme(colours); } if (ret == null) { ret = new UserColourScheme("white"); } return ret; } /** * 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() { String name = schemeName.getText().trim(); if (name.length() < 1) { JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager .getString("label.user_colour_scheme_must_have_name"), MessageManager.getString("label.no_name_colour_scheme"), JvOptionPane.WARNING_MESSAGE); } if (!Platform.isJS() && ColourSchemes.getInstance().nameExists(name)) { /** * java only * * @j2sIgnore */ { int reply = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), 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; } } } JalviewFileChooser chooser = new JalviewFileChooser("jc", "Jalview User Colours"); JalviewFileView fileView = new JalviewFileView(); chooser.setFileView(fileView); chooser.setDialogTitle( MessageManager.getString("label.save_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.save")); int option = chooser.showSaveDialog(this); if (option == JalviewFileChooser.APPROVE_OPTION) { 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(); } } } /** * Adds the current colour scheme to the Jalview properties file so it is * loaded on next startup, and updates the Colour menu in the parent * AlignFrame (if there is one). Note this action does not including applying * the colour scheme. * * @param filePath * @return */ 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); if (defaultColours.indexOf(filePath) == -1) { if (defaultColours.length() > 0) { defaultColours = defaultColours.concat("|"); } defaultColours = defaultColours.concat(filePath); } Cache.setProperty(USER_DEFINED_COLOURS, defaultColours); /* * construct and register the colour scheme */ UserColourScheme ucs = getSchemeFromButtons(); ColourSchemes.getInstance().registerColourScheme(ucs); /* * update the Colour menu items */ if (ap != null) { ap.alignFrame.buildColourMenu(); } return ucs; } /** * Saves the colour scheme to file in XML format * * @param path */ protected void saveToFile(File toFile) { /* * 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 { PrintWriter out = new PrintWriter(new OutputStreamWriter( new FileOutputStream(toFile), "UTF-8")); for (int i = 0; i < buttonPanel.getComponentCount(); i++) { JButton button = (JButton) buttonPanel.getComponent(i); Colour col = new Colour(); col.setName(button.getText()); col.setRGB(Format.getHexString(button.getBackground())); 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) { ex.printStackTrace(); } } /** * On cancel, restores the colour scheme that was selected before the dialogue * was opened */ @Override protected void cancelButton_actionPerformed() { ap.alignFrame.changeColour(oldColourScheme); ap.paintAlignment(true, true); try { frame.setClosed(true); } catch (Exception ex) { } } /** * 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() { boolean selected = caseSensitive.isSelected(); resetButtonPanel(selected); lcaseColour.setEnabled(selected); } }