// 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].getLength();
int[] gapmap = al.getSequenceAt(firstSeq).gapMap();
if ((delMap != null && delMap.length > width)
|| (delMap == null && gapmap.length != width))
MessageManager
.formatMessage(
"exception.number_of_residues_in_query_sequence_differ_from_prediction",
- new String[]
- {
+ new String[] {
(delMap == null ? "" : MessageManager
.getString("label.mapped")),
al.getSequenceAt(firstSeq).getName(),
for (int spos = 0; spos < width; spos++)
{
int sposw = (delMap == null) ? gapmap[spos]
- : delMap[gapmap[spos]];
+ : gapmap[delMap[spos]];
if (firstsol)
{
sol[sposw] = new Annotation(0f);
if (id.equals("JNETCONF"))
{
annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations, 0f, 10f,
+ "JPred Output", annotations, 0f, 10f,
AlignmentAnnotation.BAR_GRAPH);
}
else
{
annot = new AlignmentAnnotation(preds[i].getName(),
- "JNet Output", annotations);
+ "JPred Output", annotations);
}
if (seqRef != null)