- 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
+ //Could be Archive Jalview format\r
+ try\r
+ {\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
+\r
+ jalview.binding.JalviewUserColours jucs\r
+ = new jalview.binding.JalviewUserColours();\r