+ if (seqs.size()>0)
+ {
+ // try to make annotation for a prediction only input (default if no alignment is given)
+ Alignment tal = new Alignment(this.getSeqsAsArray());
+ try {
+ JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, true);
+ } catch (Exception e)
+ {
+ tal = null;
+ IOException ex = new IOException("Couldn't parse concise annotation for prediction profile.\n"+e);
+ throw ex;
+ }
+ this.annotations = new Vector();
+ AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+ for (int aai = 0; aan!=null && aai<aan.length; aai++)
+ {
+ annotations.addElement(aan[aai]);
+ }
+ }