* Automagic translation happens for annotation called 'JNETPRED' (translated to Secondary Structure Prediction), or 'JNETCONF' (translates to 'Prediction Confidence').
* Numeric scores are differentiated from symbolic by being parseable into a float vector. They are put in Scores.
* Symscores gets the others.
- * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment.
- *
+ * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment. It is automatically called
+ * but can be used to transfer the annotation onto a sequence in another alignment (and insert gaps where necessary)
* @author jprocter
* @version $Revision$
*/
seqs.addElement(newSeq);
}
+ 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. ("+e.getMessage()+")");
+ ex.setStackTrace(e.getStackTrace());
+ throw ex;
+ }
+ this.annotations = new Vector();
+ AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+ for (int aai = 0; aan!=null && aai<aan.length; aai++)
+ {
+ annotations.addElement(aan[aai]);
+ }
+ }
}
/**