X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;fp=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=9ab43278b94218c17552be163ff38bf8190c84a8;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=c9c1531512d1f616fe79b8d7d2dde49b48b2cd2b;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index c9c1531..9ab4327 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -21,32 +21,37 @@ package jalview.gui; import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; import jalview.datamodel.SequenceGroup; import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; import jalview.jbgui.GUserDefinedColours; +import jalview.schemabinding.version2.Colour; +import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeLoader; +import jalview.schemes.ColourSchemes; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.util.ColorUtils; +import jalview.util.Format; import jalview.util.MessageManager; import java.awt.Color; import java.awt.Font; +import java.awt.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.Hashtable; -import java.util.StringTokenizer; +import java.util.List; import javax.swing.JButton; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; @@ -60,7 +65,14 @@ import javax.swing.event.ChangeListener; public class UserDefinedColours extends GUserDefinedColours implements ChangeListener { - private static final int MY_FRAME_HEIGHT = 420; + private static final Font VERDANA_BOLD_10 = new Font("Verdana", + Font.BOLD, 10); + + public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS"; + + private static final String LAST_DIRECTORY = "LAST_DIRECTORY"; + + private static final int MY_FRAME_HEIGHT = 440; private static final int MY_FRAME_WIDTH = 810; @@ -70,29 +82,27 @@ public class UserDefinedColours extends GUserDefinedColours implements SequenceGroup seqGroup; - ArrayList selectedButtons; + List selectedButtons; ColourSchemeI oldColourScheme; JInternalFrame frame; - JalviewStructureDisplayI jmol; + JalviewStructureDisplayI structureViewer; - ArrayList upperCaseButtons; + List upperCaseButtons; - ArrayList lowerCaseButtons; + List lowerCaseButtons; /** * Creates a new UserDefinedColours object. * * @param ap - * DOCUMENT ME! * @param sg - * DOCUMENT ME! */ public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg) { - super(); + this(); lcaseColour.setEnabled(false); @@ -101,7 +111,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (seqGroup != null) { - oldColourScheme = seqGroup.cs; + oldColourScheme = seqGroup.getColourScheme(); } else { @@ -110,7 +120,7 @@ public class UserDefinedColours extends GUserDefinedColours implements if (oldColourScheme instanceof UserColourScheme) { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); + schemeName.setText(oldColourScheme.getSchemeName()); if (((UserColourScheme) oldColourScheme).getLowerCaseColours() != null) { caseSensitive.setSelected(true); @@ -130,11 +140,11 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI jmol, + public UserDefinedColours(JalviewStructureDisplayI viewer, ColourSchemeI oldcs) { - super(); - this.jmol = jmol; + this(); + this.structureViewer = viewer; colorChooser.getSelectionModel().addChangeListener(this); @@ -142,7 +152,8 @@ public class UserDefinedColours extends GUserDefinedColours implements if (oldColourScheme instanceof UserColourScheme) { - schemeName.setText(((UserColourScheme) oldColourScheme).getName()); + schemeName.setText(((UserColourScheme) oldColourScheme) + .getSchemeName()); } resetButtonPanel(false); @@ -151,6 +162,12 @@ public class UserDefinedColours extends GUserDefinedColours implements } + public UserDefinedColours() + { + super(); + selectedButtons = new ArrayList(); + } + void showFrame() { colorChooser.getSelectionModel().addChangeListener(this); @@ -166,7 +183,15 @@ public class UserDefinedColours extends GUserDefinedColours implements } } - 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(); @@ -175,23 +200,13 @@ public class UserDefinedColours extends GUserDefinedColours implements upperCaseButtons = new ArrayList(); } - JButton button; - String label; for (int i = 0; i < 20; i++) { - if (caseSensitive) - { - label = ResidueProperties.aa[i]; - } - else - { - label = ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) - .toString(); - } - - button = makeButton(label, ResidueProperties.aa[i], upperCaseButtons, - i); - + String label = isCaseSensitive ? ResidueProperties.aa[i] + : ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) + .toString(); + JButton button = makeButton(label, ResidueProperties.aa[i], + upperCaseButtons, i); buttonPanel.add(button); } @@ -200,7 +215,7 @@ 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); @@ -220,14 +235,14 @@ public class UserDefinedColours extends GUserDefinedColours implements { int row = i / cols + 1; int index = (row * cols) + i; - button = makeButton(ResidueProperties.aa[i].toLowerCase(), + JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(), ResidueProperties.aa[i].toLowerCase(), lowerCaseButtons, i); buttonPanel.add(button, index); } } - if (caseSensitive) + if (isCaseSensitive) { buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20)); buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21)); @@ -238,7 +253,7 @@ 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()); } @@ -248,35 +263,36 @@ 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)); + } } /** @@ -299,11 +315,6 @@ 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()) @@ -383,28 +394,35 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * DOCUMENT ME! + * A helper method to update or make a colour button, whose background colour + * is the associated colour, and text colour a darker shade of the same. If + * the button is already in the list, then its text and margins are updated, + * if not then it is created and added. This method supports toggling between + * case-sensitive and case-insensitive button panels. The case-sensitive + * version has abbreviated button text in order to fit in more buttons. * * @param label - * DOCUMENT ME! - * @param aa - * DOCUMENT ME! + * @param residue + * @param the + * list of buttons + * @param buttonIndex + * the button's position in the list */ - JButton makeButton(String label, String aa, - ArrayList caseSensitiveButtons, int buttonIndex) + JButton makeButton(String label, String residue, List buttons, + int buttonIndex) { final JButton button; Color col; - if (buttonIndex < caseSensitiveButtons.size()) + if (buttonIndex < buttons.size()) { - button = caseSensitiveButtons.get(buttonIndex); + button = buttons.get(buttonIndex); col = button.getBackground(); } else { button = new JButton(); - button.addMouseListener(new java.awt.event.MouseAdapter() + button.addMouseListener(new MouseAdapter() { @Override public void mouseClicked(MouseEvent e) @@ -413,57 +431,56 @@ public class UserDefinedColours extends GUserDefinedColours implements } }); - caseSensitiveButtons.add(button); + buttons.add(button); + /* + * make initial button colour that of the current colour scheme, + * if it is a simple per-residue colouring, else white + */ col = Color.white; - if (oldColourScheme != null) + if (oldColourScheme != null && oldColourScheme.isSimple()) { - try - { - col = oldColourScheme.findColour(aa.charAt(0), -1, null); - } catch (Exception ex) - { - } + col = oldColourScheme.findColour(residue.charAt(0), 0, null, null, + 0f); } } if (caseSensitive.isSelected()) { - button.setMargin(new java.awt.Insets(2, 2, 2, 2)); + button.setMargin(new Insets(2, 2, 2, 2)); } else { - button.setMargin(new java.awt.Insets(2, 14, 2, 14)); + button.setMargin(new Insets(2, 14, 2, 14)); } button.setOpaque(true); // required for the next line to have effect button.setBackground(col); button.setText(label); button.setForeground(ColorUtils.darkerThan(col)); - button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10)); + button.setFont(VERDANA_BOLD_10); return button; } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * On 'OK', check that at least one colour has been assigned to a residue (and + * if not issue a warning), and apply the chosen colour scheme and close the + * panel. */ @Override - protected void okButton_actionPerformed(ActionEvent e) + protected void okButton_actionPerformed() { if (isNoSelectionMade()) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .getString("label.no_colour_selection_in_scheme"), MessageManager.getString("label.no_colour_selection_warn"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } else { - applyButton_actionPerformed(null); + applyButton_actionPerformed(); try { @@ -492,37 +509,34 @@ public class UserDefinedColours extends GUserDefinedColours implements } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Applies the current colour scheme to the alignment, sequence group or + * structure view. */ @Override - protected void applyButton_actionPerformed(ActionEvent e) + protected void applyButton_actionPerformed() { if (isNoSelectionMade()) { - JOptionPane.showMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .getString("label.no_colour_selection_in_scheme"), MessageManager.getString("label.no_colour_selection_warn"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } UserColourScheme ucs = getSchemeFromButtons(); - ucs.setName(schemeName.getText()); if (seqGroup != null) { - seqGroup.cs = ucs; + seqGroup.setColourScheme(ucs); ap.paintAlignment(true); } else if (ap != null) { ap.alignFrame.changeColour(ucs); } - else if (jmol != null) + else if (structureViewer != null) { - jmol.setJalviewColourScheme(ucs); + structureViewer.setJalviewColourScheme(ucs); } } @@ -551,6 +565,7 @@ public class UserDefinedColours extends GUserDefinedColours implements } UserColourScheme ucs = new UserColourScheme(newColours); + ucs.setName(schemeName.getText()); if (caseSensitive.isSelected()) { @@ -576,11 +591,6 @@ public class UserDefinedColours extends GUserDefinedColours implements ucs.setLowerCaseColours(newColours); } - if (ap != null) - { - ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); - } - return ucs; } @@ -596,91 +606,77 @@ public class UserDefinedColours extends GUserDefinedColours implements upperCaseButtons = new ArrayList(); lowerCaseButtons = new ArrayList(); - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "jc" }, new String[] { "Jalview User Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("jc", "Jalview User Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.load_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.load")); int value = chooser.showOpenDialog(this); - if (value == JalviewFileChooser.APPROVE_OPTION) + if (value != JalviewFileChooser.APPROVE_OPTION) { - File choice = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - String defaultColours = jalview.bin.Cache.getDefault( - "USER_DEFINED_COLOURS", choice.getPath()); - if (defaultColours.indexOf(choice.getPath()) == -1) - { - defaultColours = defaultColours.concat("|") - .concat(choice.getPath()); - } - - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours); - - UserColourScheme ucs = loadColours(choice.getAbsolutePath()); - Color[] colors = ucs.getColours(); - schemeName.setText(ucs.getName()); - - if (ucs.getLowerCaseColours() != null) - { - caseSensitive.setSelected(true); - lcaseColour.setEnabled(true); - resetButtonPanel(true); - for (int i = 0; i < lowerCaseButtons.size(); i++) - { - JButton button = lowerCaseButtons.get(i); - button.setBackground(ucs.getLowerCaseColours()[i]); - } + return; + } + File choice = chooser.getSelectedFile(); + Cache.setProperty(LAST_DIRECTORY, choice.getParent()); - } - else - { - caseSensitive.setSelected(false); - lcaseColour.setEnabled(false); - resetButtonPanel(false); - } + UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice + .getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getSchemeName()); - for (int i = 0; i < upperCaseButtons.size(); i++) + if (ucs.getLowerCaseColours() != null) + { + caseSensitive.setSelected(true); + lcaseColour.setEnabled(true); + resetButtonPanel(true); + for (int i = 0; i < lowerCaseButtons.size(); i++) { - JButton button = upperCaseButtons.get(i); - button.setBackground(colors[i]); + JButton button = lowerCaseButtons.get(i); + button.setBackground(ucs.getLowerCaseColours()[i]); } + } + else + { + caseSensitive.setSelected(false); + lcaseColour.setEnabled(false); + resetButtonPanel(false); + } + for (int i = 0; i < upperCaseButtons.size(); i++) + { + JButton button = upperCaseButtons.get(i); + button.setBackground(colors[i]); } + + addNewColourScheme(choice.getPath()); } /** - * DOCUMENT ME! + * Loads the user-defined colour scheme from the first file listed in property + * "USER_DEFINED_COLOURS". If this fails, returns an all-white colour scheme. * - * @return DOCUMENT ME! + * @return */ public static UserColourScheme loadDefaultColours() { UserColourScheme ret = null; - String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"); + String colours = Cache.getProperty(USER_DEFINED_COLOURS); if (colours != null) { if (colours.indexOf("|") > -1) { colours = colours.substring(0, colours.indexOf("|")); } - - ret = loadColours(colours); + ret = ColourSchemeLoader.loadColourScheme(colours); } if (ret == null) { - Color[] newColours = new Color[24]; - for (int i = 0; i < 24; i++) - { - newColours[i] = Color.white; - } - ret = new UserColourScheme(newColours); + ret = new UserColourScheme("white"); } return ret; @@ -689,155 +685,41 @@ public class UserDefinedColours extends GUserDefinedColours implements /** * 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! */ @Override protected void savebutton_actionPerformed(ActionEvent e) { - if (schemeName.getText().trim().length() < 1) + String name = schemeName.getText().trim(); + if (name.length() < 1) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.user_colour_scheme_must_have_name"), MessageManager.getString("label.no_name_colour_scheme"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } - if (userColourSchemes != null - && userColourSchemes.containsKey(schemeName.getText())) + if (ColourSchemes.getInstance().nameExists(name)) { - int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + int reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop, MessageManager.formatMessage( "label.colour_scheme_exists_overwrite", new Object[] { - schemeName.getText(), schemeName.getText() }), + name, name }), MessageManager.getString("label.duplicate_scheme_name"), - JOptionPane.YES_NO_OPTION); - if (reply != JOptionPane.YES_OPTION) + JvOptionPane.YES_NO_OPTION); + if (reply != JvOptionPane.YES_OPTION) { return; } - - userColourSchemes.remove(schemeName.getText()); + ColourSchemes.getInstance().removeColourScheme(name); } - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - new String[] { "jc" }, new String[] { "Jalview User Colours" }, + JalviewFileChooser chooser = new JalviewFileChooser("jc", "Jalview User Colours"); - chooser.setFileView(new jalview.io.JalviewFileView()); + JalviewFileView fileView = new JalviewFileView(); + chooser.setFileView(fileView); chooser.setDialogTitle(MessageManager .getString("label.save_colour_scheme")); chooser.setToolTipText(MessageManager.getString("action.save")); @@ -846,205 +728,126 @@ public class UserDefinedColours extends GUserDefinedColours implements if (value == JalviewFileChooser.APPROVE_OPTION) { - String choice = chooser.getSelectedFile().getPath(); - String defaultColours = jalview.bin.Cache.getDefault( - "USER_DEFINED_COLOURS", choice); - if (defaultColours.indexOf(choice) == -1) - { - if (defaultColours.length() > 0) - { - defaultColours = defaultColours.concat("|"); - } - defaultColours = defaultColours.concat(choice); - } - - userColourSchemes.put(schemeName.getText(), getSchemeFromButtons()); - - ap.alignFrame.updateUserColourMenu(); - - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours); - - jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours(); - - ucs.setSchemeName(schemeName.getText()); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); - - for (int i = 0; i < buttonPanel.getComponentCount(); i++) - { - JButton button = (JButton) buttonPanel.getComponent(i); - jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); - col.setName(button.getText()); - col.setRGB(jalview.util.Format.getHexString(button - .getBackground())); - ucs.addColour(col); - } - - ucs.marshal(out); - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } + File file = chooser.getSelectedFile(); + addNewColourScheme(file.getPath()); + saveToFile(file); } } /** - * DOCUMENT ME! + * Adds the current colour scheme to the Jalview properties file so it is + * loaded on next startup, and updates the Colour menu in the parent + * AlignFrame (if there is one). Note this action does not including applying + * the colour scheme. * - * @param e - * DOCUMENT ME! + * @param filePath */ - @Override - protected void cancelButton_actionPerformed(ActionEvent e) + protected void addNewColourScheme(String filePath) { - if (ap != null) + /* + * update the delimited list of user defined colour files in + * Jalview property USER_DEFINED_COLOURS + */ + String defaultColours = Cache + .getDefault(USER_DEFINED_COLOURS, filePath); + if (defaultColours.indexOf(filePath) == -1) { - if (seqGroup != null) - { - seqGroup.cs = oldColourScheme; - } - else if (ap != null) + if (defaultColours.length() > 0) { - ap.av.setGlobalColourScheme(oldColourScheme); + defaultColours = defaultColours.concat("|"); } - ap.paintAlignment(true); + defaultColours = defaultColours.concat(filePath); } + Cache.setProperty(USER_DEFINED_COLOURS, defaultColours); - if (jmol != null) - { - jmol.setJalviewColourScheme(oldColourScheme); - } + /* + * construct and register the colour scheme + */ + UserColourScheme ucs = getSchemeFromButtons(); + ColourSchemes.getInstance().registerColourScheme(ucs); - try - { - frame.setClosed(true); - } catch (Exception ex) + /* + * update the Colour menu items + */ + if (ap != null) { + ap.alignFrame.buildColourMenu(); } } - static Hashtable userColourSchemes; - - public static Hashtable getUserColourSchemes() - { - return userColourSchemes; - } - - public static void initUserColourSchemes(String files) + /** + * Saves the colour scheme to file in XML format + * + * @param path + */ + protected void saveToFile(File toFile) { - userColourSchemes = new Hashtable(); - - if (files == null || files.length() == 0) + /* + * build a Java model of colour scheme as XML, and + * marshal to file + */ + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName(schemeName.getText()); + try { - return; - } + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(toFile), "UTF-8")); - // In case colours can't be loaded, we'll remove them - // from the default list here. - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer(files, "|"); - while (st.hasMoreElements()) - { - String file = st.nextToken(); - try - { - UserColourScheme ucs = loadColours(file); - if (ucs != null) - { - if (coloursFound.length() > 0) - { - coloursFound.append("|"); - } - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); - } - } catch (Exception ex) + for (int i = 0; i < buttonPanel.getComponentCount(); i++) { - System.out.println("Error loading User ColourFile\n" + ex); + JButton button = (JButton) buttonPanel.getComponent(i); + Colour col = new Colour(); + col.setName(button.getText()); + col.setRGB(Format.getHexString(button.getBackground())); + ucs.addColour(col); } - } - if (!files.equals(coloursFound.toString())) + ucs.marshal(out); + out.close(); + } catch (Exception ex) { - if (coloursFound.toString().length() > 1) - { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); - } - else - { - jalview.bin.Cache.applicationProperties - .remove("USER_DEFINED_COLOURS"); - } + ex.printStackTrace(); } } - public static void removeColourFromDefaults(String target) + /** + * On cancel, restores the colour scheme before the dialogue was opened + * + * @param e + */ + @Override + protected void cancelButton_actionPerformed(ActionEvent e) { - // The only way to find colours by name is to load them in - // In case colours can't be loaded, we'll remove them - // from the default list here. - - userColourSchemes = new Hashtable(); - - StringBuffer coloursFound = new StringBuffer(); - StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); - - while (st.hasMoreElements()) + if (ap != null) { - String file = st.nextToken(); - try + if (seqGroup != null) { - UserColourScheme ucs = loadColours(file); - if (ucs != null && !ucs.getName().equals(target)) - { - if (coloursFound.length() > 0) - { - coloursFound.append("|"); - } - coloursFound.append(file); - userColourSchemes.put(ucs.getName(), ucs); - } - } catch (Exception ex) + seqGroup.setColourScheme(oldColourScheme); + } + else { - System.out.println("Error loading User ColourFile\n" + ex); + ap.alignFrame.changeColour(oldColourScheme); } + ap.paintAlignment(true); } - if (coloursFound.toString().length() > 1) + if (structureViewer != null) { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); + structureViewer.setJalviewColourScheme(oldColourScheme); } - else + + try + { + frame.setClosed(true); + } catch (Exception ex) { - jalview.bin.Cache.applicationProperties - .remove("USER_DEFINED_COLOURS"); } - } @Override public void caseSensitive_actionPerformed(ActionEvent e) { - resetButtonPanel(caseSensitive.isSelected()); - lcaseColour.setEnabled(caseSensitive.isSelected()); - } - - @Override - public void lcaseColour_actionPerformed(ActionEvent e) - { - if (selectedButtons == null) - { - selectedButtons = new ArrayList(); - } - else - { - selectedButtons.clear(); - } - selectedButtons.add(lcaseColour); + boolean selected = caseSensitive.isSelected(); + resetButtonPanel(selected); + lcaseColour.setEnabled(selected); } }