// in the future we could search for the query
// sequence in the alignment before calling this function.
SequenceI seqRef = al.getSequenceAt(firstSeq);
- int width = preds[0].getSequence().length();
+ int width = preds[0].getSequence().length;
int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
- if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width))
+ if ((delMap!=null && delMap.length > width) || (delMap==null && gapmap.length!=width))
{
throw (new Exception(
"Number of residues in "+(delMap==null ? "" : " mapped ")+"supposed query sequence ('" +
for (int j = 0; j < width; j++)
{
annotations[gapmap[delMap[j]]] = new Annotation(preds[i].getCharAt(
- j) + "", "", ' ', 0);
+ j) + "", "", ' ', 0);
}
}
}
*/
}
-}
\ No newline at end of file
+}