X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=3b6ebfa2e665c1f250228f012cab2e11da27fce1;hb=36c0eac11fb0d0ac6df2d971fabf524325db5e97;hp=0df23e08e41bf513557157724478fc26b68ff7f3;hpb=90add82a33c05e218a92eb1cdb2c345da05465f8;p=jalview.git diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 0df23e0..3b6ebfa 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -26,15 +26,20 @@ 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.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; @@ -43,8 +48,10 @@ import java.io.InputStreamReader; import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.util.ArrayList; -import java.util.Hashtable; +import java.util.List; +import java.util.SortedMap; import java.util.StringTokenizer; +import java.util.TreeMap; import javax.swing.JButton; import javax.swing.JInternalFrame; @@ -61,35 +68,41 @@ import javax.swing.event.ChangeListener; public class UserDefinedColours extends GUserDefinedColours implements ChangeListener { + private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10); + + private 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_WIDTH = 810; private static final int MY_FRAME_WIDTH_CASE_SENSITIVE = 970; + static SortedMap userColourSchemes; + AlignmentPanel ap; 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) { @@ -131,11 +144,11 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(JalviewStructureDisplayI jmol, + public UserDefinedColours(JalviewStructureDisplayI viewer, ColourSchemeI oldcs) { super(); - this.jmol = jmol; + this.structureViewer = viewer; colorChooser.getSelectionModel().addChangeListener(this); @@ -384,28 +397,35 @@ 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) @@ -414,14 +434,14 @@ public class UserDefinedColours extends GUserDefinedColours implements } }); - caseSensitiveButtons.add(button); + buttons.add(button); col = Color.white; if (oldColourScheme != null) { try { - col = oldColourScheme.findColour(aa.charAt(0), -1, null); + col = oldColourScheme.findColour(residue.charAt(0), -1, null); } catch (Exception ex) { } @@ -430,30 +450,29 @@ public class UserDefinedColours extends GUserDefinedColours implements 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()) { @@ -464,7 +483,7 @@ public class UserDefinedColours extends GUserDefinedColours implements } else { - applyButton_actionPerformed(null); + applyButton_actionPerformed(); try { @@ -493,13 +512,11 @@ 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()) { @@ -521,9 +538,9 @@ public class UserDefinedColours extends GUserDefinedColours implements { ap.alignFrame.changeColour(ucs); } - else if (jmol != null) + else if (structureViewer != null) { - jmol.setJalviewColourScheme(ucs); + structureViewer.setJalviewColourScheme(ucs); } } @@ -598,8 +615,7 @@ public class UserDefinedColours extends GUserDefinedColours implements lowerCaseButtons = new ArrayList(); JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "jc", - "Jalview User Colours"); + Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager .getString("label.load_colour_scheme")); @@ -607,50 +623,42 @@ public class UserDefinedColours extends GUserDefinedColours implements 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 = loadColours(choice.getAbsolutePath()); + Color[] colors = ucs.getColours(); + schemeName.setText(ucs.getName()); - 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()); } /** @@ -662,7 +670,7 @@ public class UserDefinedColours extends GUserDefinedColours implements { 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) @@ -833,7 +841,7 @@ public class UserDefinedColours extends GUserDefinedColours implements userColourSchemes.remove(schemeName.getText()); } JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), "jc", + Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours"); chooser.setFileView(new JalviewFileView()); @@ -846,47 +854,82 @@ 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) + addNewColourScheme(choice); + saveToFile(choice); + } + } + + /** + * 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 + */ + protected void 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) { - if (defaultColours.length() > 0) - { - defaultColours = defaultColours.concat("|"); - } - defaultColours = defaultColours.concat(choice); + defaultColours = defaultColours.concat("|"); } + defaultColours = defaultColours.concat(filePath); + } + Cache.setProperty(USER_DEFINED_COLOURS, defaultColours); - 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(); + /* + * add to the cache in this object + */ + userColourSchemes.put(schemeName.getText(), getSchemeFromButtons()); - ucs.setSchemeName(schemeName.getText()); - try - { - PrintWriter out = new PrintWriter(new OutputStreamWriter( - new FileOutputStream(choice), "UTF-8")); + /* + * update the Colour menu items + */ + if (ap != null) + { + ap.alignFrame.buildColourMenu();// updateUserColourMenu(); + } + } - 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); - } + /** + * Saves the colour scheme to file in XML format + * + * @param filePath + */ + protected void saveToFile(String filePath) + { + /* + * build a Java model of colour scheme as XML, and + * marshal to file + */ + JalviewUserColours ucs = new JalviewUserColours(); + ucs.setSchemeName(schemeName.getText()); + try + { + PrintWriter out = new PrintWriter(new OutputStreamWriter( + new FileOutputStream(filePath), "UTF-8")); - ucs.marshal(out); - out.close(); - } catch (Exception ex) + for (int i = 0; i < buttonPanel.getComponentCount(); i++) { - ex.printStackTrace(); + JButton button = (JButton) buttonPanel.getComponent(i); + Colour col = new Colour(); + col.setName(button.getText()); + col.setRGB(Format.getHexString(button.getBackground())); + ucs.addColour(col); } + ucs.marshal(out); + out.close(); + } catch (Exception ex) + { + ex.printStackTrace(); } } @@ -912,9 +955,9 @@ public class UserDefinedColours extends GUserDefinedColours implements ap.paintAlignment(true); } - if (jmol != null) + if (structureViewer != null) { - jmol.setJalviewColourScheme(oldColourScheme); + structureViewer.setJalviewColourScheme(oldColourScheme); } try @@ -925,16 +968,14 @@ public class UserDefinedColours extends GUserDefinedColours implements } } - static Hashtable userColourSchemes; - - public static Hashtable getUserColourSchemes() + public static SortedMap getUserColourSchemes() { return userColourSchemes; } public static void initUserColourSchemes(String files) { - userColourSchemes = new Hashtable(); + userColourSchemes = new TreeMap(); if (files == null || files.length() == 0) { @@ -969,13 +1010,11 @@ public class UserDefinedColours extends GUserDefinedColours implements { if (coloursFound.toString().length() > 1) { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); + Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString()); } else { - jalview.bin.Cache.applicationProperties - .remove("USER_DEFINED_COLOURS"); + Cache.applicationProperties.remove(USER_DEFINED_COLOURS); } } } @@ -986,11 +1025,11 @@ public class UserDefinedColours extends GUserDefinedColours implements // In case colours can't be loaded, we'll remove them // from the default list here. - userColourSchemes = new Hashtable(); + userColourSchemes = new TreeMap(); StringBuffer coloursFound = new StringBuffer(); StringTokenizer st = new StringTokenizer( - jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|"); + Cache.getProperty(USER_DEFINED_COLOURS), "|"); while (st.hasMoreElements()) { @@ -1015,13 +1054,11 @@ public class UserDefinedColours extends GUserDefinedColours implements if (coloursFound.toString().length() > 1) { - jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", - coloursFound.toString()); + Cache.setProperty(USER_DEFINED_COLOURS, coloursFound.toString()); } else { - jalview.bin.Cache.applicationProperties - .remove("USER_DEFINED_COLOURS"); + Cache.applicationProperties.remove(USER_DEFINED_COLOURS); } }