+\r
+ public void colourByStructure(String pdbid)\r
+ {\r
+ Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
+ .colourSequenceFromStructure(sequence, pdbid);\r
+\r
+ AlignmentAnnotation an = new AlignmentAnnotation(\r
+ "Structure", "Coloured by "+pdbid, anots);\r
+\r
+ ap.av.alignment.addAnnotation(an);\r
+ an.createSequenceMapping(sequence, 0, true);\r
+ //an.adjustForAlignment();\r
+ ap.av.alignment.setAnnotationIndex(an,0);\r
+\r
+ ap.adjustAnnotationHeight();\r
+\r
+ sequence.addAlignmentAnnotation(an);\r
+\r
+ }\r