+ private AlignmentAnnotation parseAnnotationRow(String label, String annots)\r
+ {\r
+ String type = (label.indexOf("_cons")==label.length()-5) ? label.substring(0, label.length()-5)\r
+ : label;\r
+ boolean ss = false;\r
+ type = id2type(type);\r
+ if (type.equals("secondary structure"))\r
+ {\r
+ ss=true;\r
+ }\r
+ // decide on secondary structure or not.\r
+ Annotation[] els = new Annotation[annots.length()];\r
+ for (int i = 0; i<annots.length(); i++)\r
+ {\r
+ String pos = annots.substring(i,i+1);\r
+ Annotation ann;\r
+ ann = new Annotation(pos, "", ' ', Float.NaN);\r
+ if (ss)\r
+ {\r
+ ann.secondaryStructure = jalview.schemes.ResidueProperties.getDssp3state(pos).charAt(0);\r
+ if (ann.secondaryStructure == pos.charAt(0) || pos.charAt(0)=='C')\r
+ {\r
+ ann.displayCharacter = "";\r
+ } else {\r
+ ann.displayCharacter += " ";\r
+ }\r
+ }\r
+ \r
+ els[i] = ann;\r
+ }\r
+ return new AlignmentAnnotation(label, label, els);\r
+ }\r
+ \r