/*\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
Vector selectedButtons;\r
ColourSchemeI oldColourScheme;\r
JInternalFrame frame;\r
+ MCview.PDBCanvas pdbcanvas;\r
+ Vector upperCaseButtons;\r
+ Vector lowerCaseButtons;\r
+\r
\r
/**\r
* Creates a new UserDefinedColours object.\r
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
{\r
super();\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\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
- }\r
+ //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+ casePanel.setVisible(false);\r
\r
- if (sg != null)\r
- {\r
- frame.setTitle(frame.getTitle() + " (" + sg.getName() + ")");\r
- }\r
\r
- colorChooser.getSelectionModel().addChangeListener(this);\r
+ lcaseColour.setEnabled(false);\r
\r
this.ap = ap;\r
seqGroup = sg;\r
\r
if (seqGroup != null)\r
- {\r
oldColourScheme = seqGroup.cs;\r
- }\r
else\r
- {\r
oldColourScheme = ap.av.getGlobalColourScheme();\r
- }\r
\r
if (oldColourScheme instanceof UserColourScheme)\r
{\r
- schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
+ if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)\r
+ {\r
+ caseSensitive.setSelected(true);\r
+ lcaseColour.setEnabled(true);\r
+ resetButtonPanel(true);\r
+ }\r
+ else\r
+ resetButtonPanel(false);\r
}\r
- for (int i = 0; i < 20; i++)\r
+ else\r
+ resetButtonPanel(false);\r
+\r
+ showFrame();\r
+ }\r
+\r
+ public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
+ {\r
+ super();\r
+ pdbcanvas = pdb;\r
+\r
+ colorChooser.getSelectionModel().addChangeListener(this);\r
+\r
+ oldColourScheme = oldcs;\r
+\r
+ if (oldColourScheme instanceof UserColourScheme)\r
{\r
- makeButton(ResidueProperties.aa2Triplet.get(ResidueProperties.aa[i]) +\r
- "", ResidueProperties.aa[i]);\r
+ schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
}\r
\r
- makeButton("B", "B");\r
- makeButton("Z", "Z");\r
- makeButton("X", "X");\r
- makeButton("Gap", "-");\r
+ resetButtonPanel(false);\r
+\r
+ showFrame();\r
+\r
+ }\r
+\r
+ void showFrame()\r
+ {\r
+ colorChooser.getSelectionModel().addChangeListener(this);\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
+\r
+ if (seqGroup != null)\r
+ frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");\r
+\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ {\r
+ frame.setSize(760, 370);\r
+ }\r
+ }\r
+\r
+ void resetButtonPanel(boolean caseSensitive)\r
+ {\r
+ //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+ caseSensitive = false;\r
+\r
+ buttonPanel.removeAll();\r
+\r
+\r
+ if(upperCaseButtons==null)\r
+ upperCaseButtons = new Vector();\r
+\r
+ JButton button;\r
+ String label;\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ if(caseSensitive)\r
+ label = ResidueProperties.aa[i];\r
+ else\r
+ label = ResidueProperties.aa2Triplet.get\r
+ (ResidueProperties.aa[i]).toString();\r
+\r
+ button = makeButton(label,\r
+ ResidueProperties.aa[i],\r
+ upperCaseButtons, i);\r
+\r
+ buttonPanel.add(button);\r
+ }\r
+\r
+ buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));\r
+ buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));\r
+ buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));\r
+ buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));\r
+\r
+ if(!caseSensitive)\r
+ {\r
+ gridLayout.setRows(6);\r
+ gridLayout.setColumns(4);\r
+ }\r
+ else\r
+ {\r
+ gridLayout.setRows(7);\r
+ int cols = 7;\r
+ gridLayout.setColumns(cols+1);\r
+\r
+ if(lowerCaseButtons==null)\r
+ lowerCaseButtons = new Vector();\r
+\r
+\r
+ for (int i = 0; i < 20; i++)\r
+ {\r
+ int row = i / cols + 1;\r
+ int index = (row * cols) + i;\r
+ button = makeButton(\r
+ ResidueProperties.aa[i].toLowerCase(),\r
+ ResidueProperties.aa[i].toLowerCase(),\r
+ lowerCaseButtons,\r
+ i);\r
+\r
+ buttonPanel.add(button, index);\r
+ }\r
+ }\r
+\r
+\r
+ if(caseSensitive)\r
+ {\r
+ buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));\r
+ buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));\r
+ buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));\r
+ }\r
+\r
+ buttonPanel.validate();\r
+ validate();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
if (selectedButtons != null)\r
{\r
- JButton button;\r
+ JButton button=null;\r
for(int i=0; i<selectedButtons.size(); i++)\r
{\r
button = (JButton)selectedButtons.elementAt(i);\r
button.setBackground(colorChooser.getColor());\r
button.setForeground( button.getBackground().brighter().brighter().brighter());\r
}\r
+ if(button==lcaseColour)\r
+ {\r
+ for(int i=0; i<lowerCaseButtons.size(); i++)\r
+ {\r
+ button = (JButton)lowerCaseButtons.elementAt(i);\r
+ button.setBackground(colorChooser.getColor());\r
+ button.setForeground( button.getBackground().brighter().brighter().brighter());\r
+ }\r
+ }\r
}\r
}\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
* @param label DOCUMENT ME!\r
* @param aa DOCUMENT ME!\r
*/\r
- void makeButton(String label, String aa)\r
+ JButton makeButton(String label,\r
+ String aa,\r
+ Vector caseSensitiveButtons,\r
+ int buttonIndex)\r
{\r
- final JButton button = new JButton();\r
- Color col = Color.white;\r
+ final JButton button;\r
+ Color col;\r
\r
- try\r
+ if(buttonIndex<caseSensitiveButtons.size())\r
{\r
- col = oldColourScheme.findColour(aa, -1);\r
+ button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);\r
+ col = button.getBackground();\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
- // ex.printStackTrace();\r
+ button = new JButton();\r
+ button.addMouseListener(new java.awt.event.MouseAdapter()\r
+ {\r
+ public void mouseClicked(MouseEvent e)\r
+ {\r
+ colourButtonPressed(e);\r
+ }\r
+ });\r
+\r
+ caseSensitiveButtons.addElement(button);\r
+\r
+ col = Color.white;\r
+\r
+ try\r
+ {\r
+ col = oldColourScheme.findColour(aa, -1);\r
+ }\r
+ catch (Exception ex)\r
+ { }\r
}\r
\r
+ /* //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
+ if(caseSensitive.isSelected())\r
+ button.setMargin(new java.awt.Insets(2,2,2,2));\r
+ else\r
+ button.setMargin(new java.awt.Insets(2,14,2,14));\r
+ */\r
+\r
button.setBackground(col);\r
button.setText(label);\r
button.setForeground(col.darker().darker().darker());\r
- button.setFont(new java.awt.Font("Verdana", 1, 10));\r
- button.addMouseListener(new java.awt.event.MouseAdapter()\r
- {\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- colourButtonPressed(e);\r
- }\r
- });\r
+ button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));\r
\r
- buttonPanel.add(button, null);\r
+ return button;\r
}\r
\r
/**\r
*/\r
protected void applyButton_actionPerformed(ActionEvent e)\r
{\r
- UserColourScheme ucs = getSchemeFromGUI();\r
+ UserColourScheme ucs = getSchemeFromButtons();\r
ucs.setName(schemeName.getText());\r
\r
if (seqGroup != null)\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
+ UserColourScheme getSchemeFromButtons()\r
{\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
+ JButton button = (JButton) upperCaseButtons.elementAt(i);\r
newColours[i] = button.getBackground();\r
}\r
\r
UserColourScheme ucs = new UserColourScheme(newColours);\r
- ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\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
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
Color[] colors = ucs.getColours();\r
schemeName.setText(ucs.getName());\r
\r
- for (int i = 0; i < colors.length; i++)\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) buttonPanel.getComponent(i);\r
+ JButton button = (JButton) upperCaseButtons.elementAt(i);\r
button.setBackground(colors[i]);\r
}\r
+\r
}\r
}\r
\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
+ if ( colours != null )\r
{\r
if(colours.indexOf("|")>-1)\r
colours = colours.substring(0, colours.indexOf("|"));\r
\r
- return loadColours(colours);\r
+ ret = loadColours(colours);\r
}\r
- else\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
- return new UserColourScheme(newColours);\r
+ ret = new UserColourScheme(newColours);\r
}\r
+\r
+ return ret;\r
}\r
\r
/**\r
{\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 jucs = new jalview.binding.JalviewUserColours();\r
- jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\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
- newColours = new Color[jucs.getColourCount()];\r
+ Color [] lowerCase = null;\r
+ boolean caseSensitive = false;\r
\r
- for (int i = 0; i < 24; i++)\r
+\r
+ String name;\r
+ int index;\r
+ for (int i = 0; i < jucs.getColourCount(); i++)\r
{\r
- newColours[i] = new Color(Integer.parseInt(\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 = ((Integer)ResidueProperties.aaHash.get(name)).intValue();\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
- System.out.println("Error loading User ColourFile\n"+ex);\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
-\r
return ucs;\r
}\r
\r
defaultColours = defaultColours.concat(choice);\r
}\r
\r
- userColourSchemes.put(schemeName.getText(), getSchemeFromGUI());\r
+ userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());\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
+ 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 < 24; i++)\r
+ for (int i = 0; i < buttonPanel.getComponentCount(); i++)\r
{\r
JButton button = (JButton) buttonPanel.getComponent(i);\r
- jalview.binding.Colour col = new jalview.binding.Colour();\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
*/\r
protected void cancelButton_actionPerformed(ActionEvent e)\r
{\r
+ if (ap != null)\r
+ {\r
if (seqGroup != null)\r
{\r
- seqGroup.cs = oldColourScheme;\r
+ seqGroup.cs = oldColourScheme;\r
}\r
- else\r
+ else if (ap != null)\r
{\r
- ap.av.setGlobalColourScheme(oldColourScheme);\r
+ ap.av.setGlobalColourScheme(oldColourScheme);\r
}\r
-\r
ap.repaint();\r
+ }\r
+\r
+ if(pdbcanvas!=null)\r
+ {\r
+ pdbcanvas.pdb.setColours(oldColourScheme);\r
+ }\r
\r
try\r
{\r
{\r
userColourSchemes = new Hashtable();\r
\r
- if(files==null)\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
}\r
if (!files.equals(coloursFound.toString()))\r
{\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\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
+ 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
+ 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
+ public void caseSensitive_actionPerformed(ActionEvent e)\r
+ {\r
+ resetButtonPanel(caseSensitive.isSelected());\r
+ lcaseColour.setEnabled(caseSensitive.isSelected());\r
+ }\r
+\r
+ public void lcaseColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if(selectedButtons==null)\r
+ selectedButtons = new Vector();\r
+ else\r
+ selectedButtons.clear();\r
+ selectedButtons.add(lcaseColour);\r
}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff