}
}
// this will overwrite any existing t-coffee scores for the alignment
- AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,false,s,null);
+ AlignmentAnnotation aa=al.findOrCreateAnnotation(TCOFFEE_SCORE,TCOFFEE_SCORE,false,s, null);
if (s!=null)
{
aa.label="T-COFFEE";