+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
+ Color [] newColors = new Color[24];\r
+ for(int i=0; i<24; i++)\r
+ newColors[i] = new Color(60,160,115);\r
+\r
+ ucs.setColourScheme(newColors);\r
+ String searchString = textfield.getText();\r
+\r
+ searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+\r
+ for(int i=0; i<searchResults.size(); i+=3)\r
+ {\r
+ // its possible edits may have occurred since search was performed\r
+ // account for this here\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
+ int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
+ int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+\r
+ SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );\r
+ sg.addSequence(seq);\r
+ av.alignment.addGroup(sg);\r
+ searchGroup.addGroup( sg );\r
+\r
+ }\r