/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
import javax.swing.event.*;\r
\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
AlignmentPanel ap;\r
SequenceGroup seqGroup;\r
Vector selectedButtons;\r
- Vector oldColours = new Vector();\r
ColourSchemeI oldColourScheme;\r
JInternalFrame frame;\r
+ MCview.PDBCanvas pdbcanvas;\r
\r
/**\r
* Creates a new UserDefinedColours object.\r
super();\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "User Defined Colours", 450, 530, false);\r
+ Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
\r
if (System.getProperty("os.name").startsWith("Mac"))\r
{\r
- frame.setSize(450, 560);\r
+ frame.setSize(760, 370);\r
}\r
\r
if (sg != null)\r
oldColourScheme = ap.av.getGlobalColourScheme();\r
}\r
\r
+ if (oldColourScheme instanceof UserColourScheme)\r
+ {\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+ }\r
for (int i = 0; i < 20; i++)\r
{\r
makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
makeButton("B", "B");\r
makeButton("Z", "Z");\r
makeButton("X", "X");\r
- makeButton("Gap", "'.','-',' '");\r
+ makeButton("Gap", "-");\r
+ }\r
+\r
+ public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
+ {\r
+ super();\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
+ pdbcanvas = pdb;\r
\r
- if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
{\r
- loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
+ frame.setSize(760, 370);\r
}\r
+\r
+ colorChooser.getSelectionModel().addChangeListener(this);\r
+\r
+ oldColourScheme = oldcs;\r
+\r
+ if (oldColourScheme instanceof UserColourScheme)\r
+ {\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+ }\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
+ "", ResidueProperties.aa[i]);\r
+ }\r
+\r
+ makeButton("B", "B");\r
+ makeButton("Z", "Z");\r
+ makeButton("X", "X");\r
+ makeButton("Gap", "-");\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
if(e.isShiftDown())\r
{\r
- JButton start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
- JButton end = (JButton) e.getSource();\r
+ JButton start, end = (JButton) e.getSource();\r
+ if(selectedButtons.size()>0)\r
+ start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
+ else\r
+ start = (JButton) e.getSource();\r
+\r
int startIndex=0, endIndex=0;\r
for(int b=0; b<buttonPanel.getComponentCount(); b++)\r
{\r
}\r
catch (Exception ex)\r
{\r
+ // ex.printStackTrace();\r
}\r
\r
button.setBackground(col);\r
- oldColours.addElement(col);\r
button.setText(label);\r
button.setForeground(col.darker().darker().darker());\r
button.setFont(new java.awt.Font("Verdana", 1, 10));\r
*/\r
protected void applyButton_actionPerformed(ActionEvent e)\r
{\r
- Color[] newColours = new Color[24];\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- JButton button = (JButton) buttonPanel.getComponent(i);\r
- newColours[i] = button.getBackground();\r
- }\r
-\r
- UserColourScheme ucs = new UserColourScheme(newColours);\r
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
+ UserColourScheme ucs = getSchemeFromGUI();\r
+ ucs.setName(schemeName.getText());\r
\r
if (seqGroup != null)\r
{\r
seqGroup.cs = ucs;\r
ap.repaint();\r
}\r
- else\r
+ else if(ap!=null)\r
{\r
ap.alignFrame.changeColour(ucs);\r
}\r
+ else if(pdbcanvas!=null)\r
+ {\r
+ pdbcanvas.pdb.setColours(ucs);\r
+ pdbcanvas.updateSeqColours();\r
+ }\r
}\r
\r
+ UserColourScheme getSchemeFromGUI()\r
+ {\r
+ Color[] newColours = new Color[24];\r
+\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ JButton button = (JButton) buttonPanel.getComponent(i);\r
+ newColours[i] = button.getBackground();\r
+ }\r
+\r
+ UserColourScheme ucs = new UserColourScheme(newColours);\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
{\r
File choice = chooser.getSelectedFile();\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR",\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
- Color[] colors = loadColours(choice.getAbsolutePath());\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
for (int i = 0; i < colors.length; i++)\r
{\r
*/\r
public static UserColourScheme loadDefaultColours()\r
{\r
- if (jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR") != null)\r
+ UserColourScheme ret = null;\r
+\r
+ String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
+ if ( colours != null )\r
{\r
- return loadDefaultColours(jalview.bin.Cache.getProperty(\r
- "USER_DEFINED_COLOUR"));\r
+ if(colours.indexOf("|")>-1)\r
+ colours = colours.substring(0, colours.indexOf("|"));\r
+\r
+ ret = loadColours(colours);\r
}\r
- else\r
+\r
+ if(ret == null)\r
{\r
- return null;\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
*\r
* @return DOCUMENT ME!\r
*/\r
- public static UserColourScheme loadDefaultColours(String file)\r
+ static UserColourScheme loadColours(String file)\r
{\r
- UserColourScheme ucs = null;\r
- Color[] cols = loadColours(file);\r
-\r
- if (cols != null)\r
- {\r
- ucs = new UserColourScheme(cols);\r
- }\r
-\r
- return ucs;\r
- }\r
-\r
- static Color[] loadColours(String file)\r
- {\r
- Color[] newColours = null;\r
+ UserColourScheme ucs = null;\r
+ Color[] newColours = null;\r
\r
try\r
{\r
InputStreamReader in = new InputStreamReader(new FileInputStream(\r
file), "UTF-8");\r
\r
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
- ucs = (jalview.binding.JalviewUserColours) ucs.unmarshal(in);\r
+ jalview.schemabinding.version2.JalviewUserColours jucs\r
+ = new jalview.schemabinding.version2.JalviewUserColours();\r
\r
- newColours = new Color[ucs.getColourCount()];\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[jucs.getColourCount()];\r
\r
for (int i = 0; i < 24; i++)\r
{\r
- newColours[i] = new Color(Integer.parseInt(\r
- ucs.getColour(i).getRGB(), 16));\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
+\r
}\r
catch (Exception ex)\r
{\r
- System.out.println("Error loading UserColourFile " + file);\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 newColours;\r
+ return ucs;\r
}\r
\r
/**\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
if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);\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
- jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
+ userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());\r
+\r
+ ap.alignFrame.updateUserColourMenu();\r
\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
+\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
+ ucs.setSchemeName(schemeName.getText());\r
try\r
{\r
PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
*/\r
protected void cancelButton_actionPerformed(ActionEvent e)\r
{\r
- Color[] newColours = new Color[24];\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
- for (int i = 0; i < 24; i++)\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
{\r
- newColours[i] = (Color) oldColours.elementAt(i);\r
- buttonPanel.getComponent(i).setBackground(newColours[i]);\r
}\r
+ }\r
\r
- UserColourScheme ucs = new UserColourScheme(newColours);\r
\r
- if (seqGroup != null)\r
+ static Hashtable userColourSchemes;\r
+\r
+ public static Hashtable getUserColourSchemes()\r
+ {\r
+ return userColourSchemes;\r
+ }\r
+\r
+ public static void initUserColourSchemes(String files)\r
+ {\r
+ userColourSchemes = new Hashtable();\r
+\r
+ if(files==null || files.length()==0)\r
+ return;\r
+\r
+\r
+ // In case colours can't be loaded, we'll remove them\r
+ // from the default list here.\r
+ StringBuffer coloursFound = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(files, "|");\r
+ while (st.hasMoreElements())\r
+ {\r
+ String file = st.nextToken();\r
+ try\r
{\r
- seqGroup.cs = ucs;\r
+ UserColourScheme ucs = loadColours(file);\r
+ if (ucs != null)\r
+ {\r
+ if (coloursFound.length() > 0)\r
+ coloursFound.append("|");\r
+ coloursFound.append(file);\r
+ userColourSchemes.put(ucs.getName(), ucs);\r
+ }\r
}\r
- else\r
+ catch (Exception ex)\r
{\r
- ap.av.setGlobalColourScheme(ucs);\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
}\r
+ }\r
+ if (!files.equals(coloursFound.toString()))\r
+ {\r
+ if (coloursFound.toString().length() > 1)\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
+ coloursFound.toString());\r
+ else\r
+ jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
+ }\r
+ }\r
\r
- ap.repaint();\r
+ public static void removeColourFromDefaults(String target)\r
+ {\r
+ // The only way to find colours by name is to load them in\r
+ // In case colours can't be loaded, we'll remove them\r
+ // from the default list here.\r
+\r
+ userColourSchemes = new Hashtable();\r
\r
+ StringBuffer coloursFound = new StringBuffer();\r
+ StringTokenizer st = new StringTokenizer(\r
+ jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ String file = st.nextToken();\r
try\r
{\r
- frame.setClosed(true);\r
+ UserColourScheme ucs = loadColours(file);\r
+ if (ucs != null && !ucs.getName().equals(target))\r
+ {\r
+ if (coloursFound.length() > 0)\r
+ coloursFound.append("|");\r
+ coloursFound.append(file);\r
+ userColourSchemes.put(ucs.getName(), ucs);\r
+ }\r
}\r
catch (Exception ex)\r
{\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
}\r
+ }\r
+\r
+ if (coloursFound.toString().length() > 1)\r
+ jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
+ else\r
+ jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
+\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff