+\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\r
+\r
+\r
+ if(caseSensitive.isSelected())\r
+ {\r
+ newColours = new Color[23];\r
+ for (int i = 0; i < 23; i++)\r
+ {\r
+ JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
+ newColours[i] = button.getBackground();\r
+ }\r
+ ucs.setLowerCaseColours(newColours);\r
+ }\r
+\r
+ if(ap!=null)\r
+ ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+\r
+\r
+ return ucs;\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void loadbutton_actionPerformed(ActionEvent e)\r
+ {\r
+ upperCaseButtons = new Vector();\r
+ lowerCaseButtons = new Vector();\r
+\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "jc" },\r
+ new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Load colour scheme");\r
+ chooser.setToolTipText("Load");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ File choice = chooser.getSelectedFile();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",\r
+ choice.getPath());\r
+ if (defaultColours.indexOf(choice.getPath()) == -1)\r
+ defaultColours = defaultColours.concat("|").concat(choice.getPath());\r
+\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+\r
+\r
+ UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
+ Color[] colors = ucs.getColours();\r
+ schemeName.setText(ucs.getName());\r
+\r
+ if(ucs.getLowerCaseColours()!=null)\r
+ {\r
+ caseSensitive.setSelected(true);\r
+ lcaseColour.setEnabled(true);\r
+ resetButtonPanel(true);\r
+ for (int i = 0; i < lowerCaseButtons.size(); i++)\r
+ {\r
+ JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
+ button.setBackground(ucs.getLowerCaseColours()[i]);\r
+ }\r
+\r
+ }\r
+ else\r
+ {\r
+ caseSensitive.setSelected(false);\r
+ lcaseColour.setEnabled(false);\r
+ resetButtonPanel(false);\r
+ }\r
+\r
+ for (int i = 0; i < upperCaseButtons.size(); i++)\r
+ {\r
+ JButton button = (JButton) upperCaseButtons.elementAt(i);\r
+ button.setBackground(colors[i]);\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static UserColourScheme loadDefaultColours()\r
+ {\r
+ UserColourScheme ret = null;\r
+\r
+ String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
+ if ( colours != null )\r
+ {\r
+ if(colours.indexOf("|")>-1)\r
+ colours = colours.substring(0, colours.indexOf("|"));\r
+\r
+ ret = loadColours(colours);\r
+ }\r
+\r
+ if(ret == null)\r
+ {\r
+ Color[] newColours = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColours[i] = Color.white;\r
+ }\r
+ ret = new UserColourScheme(newColours);\r
+ }\r
+\r
+ return ret;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ static UserColourScheme loadColours(String file)\r
+ {\r
+ UserColourScheme ucs = null;\r
+ Color[] newColours = null;\r
+ try\r
+ {\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
+\r
+ jalview.schemabinding.version2.JalviewUserColours jucs\r
+ = new jalview.schemabinding.version2.JalviewUserColours();\r
+\r
+ org.exolab.castor.xml.Unmarshaller unmar\r
+ = new org.exolab.castor.xml.Unmarshaller(jucs);\r
+ jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );\r
+\r
+ newColours = new Color[24];\r
+\r
+ Color [] lowerCase = null;\r
+ boolean caseSensitive = false;\r
+\r
+\r
+ String name;\r
+ int index;\r
+ for (int i = 0; i < jucs.getColourCount(); i++)\r
+ {\r
+ name = jucs.getColour(i).getName();\r
+ if(ResidueProperties.aa3Hash.containsKey(name))\r
+ {\r
+ index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();\r
+ }\r
+ else\r
+ {\r
+ index = ResidueProperties.aaIndex[name.charAt(0)];\r
+ }\r
+ if(index == -1)\r
+ continue;\r
+\r
+ if(name.toLowerCase().equals(name))\r
+ {\r
+ if(lowerCase==null)\r
+ lowerCase = new Color[23];\r
+ caseSensitive = true;\r
+ lowerCase[index] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
+ }\r
+ else\r
+ {\r
+ newColours[index] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
+ }\r
+ }\r
+\r
+ if (newColours != null)\r
+ {\r
+ ucs = new UserColourScheme(newColours);\r
+ ucs.setName( jucs.getSchemeName() );\r
+ if(caseSensitive)\r
+ {\r
+ ucs.setLowerCaseColours(lowerCase);\r
+ }\r
+ }\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ //Could be Archive Jalview format\r
+ try{\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
+\r
+ jalview.binding.JalviewUserColours jucs\r
+ = new jalview.binding.JalviewUserColours();\r
+\r
+ jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
+\r
+ newColours = new Color[jucs.getColourCount()];\r
+\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ newColours[i] = new Color(Integer.parseInt(\r
+ jucs.getColour(i).getRGB(), 16));\r
+ }\r
+ if (newColours != null)\r
+ {\r
+ ucs = new UserColourScheme(newColours);\r
+ ucs.setName(jucs.getSchemeName());\r
+ }\r
+ }catch(Exception ex2)\r
+ { ex2.printStackTrace(); }\r
+\r
+ if(newColours==null)\r
+ System.out.println("Error loading User ColourFile\n"+ex);\r
+ }\r
+\r
+ return ucs;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void savebutton_actionPerformed(ActionEvent e)\r
+ {\r
+ if(schemeName.getText().trim().length()<1)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "User colour scheme must have a name!",\r
+ "No name for colour scheme",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
+ if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )\r
+ {\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."\r
+ +"\nContinue saving colour scheme as "+schemeName.getText()+"?",\r
+ "Duplicate scheme name", JOptionPane.YES_NO_OPTION);\r
+ if(reply != JOptionPane.YES_OPTION)\r
+ return;\r
+\r
+ userColourSchemes.remove(schemeName.getText());\r
+ }\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "jc" },\r
+ new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
+\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Save colour scheme");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);\r
+ if(defaultColours.indexOf(choice)==-1)\r
+ {\r
+ if(defaultColours.length()>0)\r
+ defaultColours = defaultColours.concat("|");\r
+ defaultColours = defaultColours.concat(choice);\r
+ }\r
+\r
+ userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());\r
+\r
+ ap.alignFrame.updateUserColourMenu();\r
+\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+\r
+ jalview.schemabinding.version2.JalviewUserColours ucs\r
+ = new jalview.schemabinding.version2.JalviewUserColours();\r
+\r
+ ucs.setSchemeName(schemeName.getText());\r
+ try\r
+ {\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
+ new FileOutputStream(choice), "UTF-8"));\r
+\r
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)\r
+ {\r
+ JButton button = (JButton) buttonPanel.getComponent(i);\r
+ jalview.schemabinding.version2.Colour col\r
+ = new jalview.schemabinding.version2.Colour();\r
+ col.setName(button.getText());\r
+ col.setRGB(jalview.util.Format.getHexString(\r
+ button.getBackground()));\r
+ ucs.addColour(col);\r
+ }\r
+\r
+ ucs.marshal(out);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void cancelButton_actionPerformed(ActionEvent e)\r
+ {\r
+ if (ap != null)\r
+ {\r
+ if (seqGroup != null)\r
+ {\r
+ seqGroup.cs = oldColourScheme;\r
+ }\r
+ else if (ap != null)\r
+ {\r
+ ap.av.setGlobalColourScheme(oldColourScheme);\r
+ }\r
+ ap.repaint();\r
+ }\r
+\r
+ if(pdbcanvas!=null)\r
+ {\r
+ pdbcanvas.pdb.setColours(oldColourScheme);\r
+ }\r
+\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r