+ AlignmentAnnotation lastssa=null;
+ if (pssecstr.length()==maxLength)
+ {
+ Vector ss=new Vector();
+ AlignmentAnnotation ssa=lastssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", pssecstr.toString());
+ ssa.label="Secondary Structure";
+ annotations.addElement(ssa);
+ }
+ if (consstr.length()==maxLength)
+ {
+ Vector ss=new Vector();
+ AlignmentAnnotation ssa=StockholmFile.parseAnnotationRow(ss, "secondary structure", consstr.toString());
+ ssa.label="Consensus Secondary Structure";
+ if (lastssa==null || !lastssa.getRNAStruc().equals(ssa.getRNAStruc().replace('-', '.')))
+ {
+ annotations.addElement(ssa);
+ }
+ }