+ updateFromPreferences();\r
+\r
+ }\r
+\r
+ public void updateFromPreferences()\r
+ {\r
+ String string = Cache.getProperty("SHOW_FULL_ID");\r
+ if(string!=null)\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_ANNOTATIONS");\r
+ if(string!=null)\r
+ showAnnotation = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_CONSERVATION");\r
+ if(string!=null)\r
+ showConservation = Boolean.valueOf(string).booleanValue();\r
+ string = Cache.getProperty("SHOW_QUALITY");\r
+ if(string!=null)\r
+ showQuality = Boolean.valueOf(string).booleanValue();\r
+ string = Cache.getProperty("SHOW_IDENTITY");\r
+ if(string!=null)\r
+ showIdentity = Boolean.valueOf(string).booleanValue();\r
+\r
+ string = Cache.getProperty("SHOW_FULL_ID");\r
+ if(string!=null)\r
+ showFullId = Boolean.valueOf(string).booleanValue();\r
+\r
+ String fontName = Cache.getProperty("FONT_NAME");\r
+ String fontStyle= Cache.getProperty("FONT_STYLE");\r
+ String fontSize = Cache.getProperty("FONT_SIZE");\r
+ if(fontName!=null && fontStyle!=null && fontSize!=null)\r
+ setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
+ else\r
+ setFont( font );\r
+\r
+ string = Cache.getProperty("GAP_SYMBOL");\r
+ if(string!=null)\r
+ alignment.setGapCharacter( string.charAt(0) );\r
+\r
+\r
+ // We must set conservation and consensus before setting colour,\r
+ // as Blosum and Clustal require this to be done\r
+ updateConservation();\r
+ updateConsensus();\r
+ string = Cache.getProperty("DEFAULT_COLOUR");\r
+ if(string!=null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, string);\r
+ if(globalColourScheme!=null)\r
+ globalColourScheme.setConsensus( vconsensus );\r
+ }\r
+\r