// 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))
{
- throw (new Exception(MessageManager.formatMessage("exception.number_of_residues_in_query_sequence_differ_from_prediction", new String[]{
- (delMap == null ? "" : MessageManager.getString("label.mapped")),
- al.getSequenceAt(firstSeq).getName(),
- al.getSequenceAt(firstSeq).getSequenceAsString(),
- Integer.valueOf(width).toString()
- })));
+ throw (new Exception(
+ MessageManager
+ .formatMessage(
+ "exception.number_of_residues_in_query_sequence_differ_from_prediction",
+ new String[] {
+ (delMap == null ? "" : MessageManager
+ .getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq)
+ .getSequenceAsString(),
+ Integer.valueOf(width).toString() })));
}
AlignmentAnnotation annot;
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 (preds[i].getCharAt(spos) == 'B'
- && (sol[spos].value == 0f || sol[spos].value < amnt))
+ && (sol[sposw].value == 0f || sol[sposw].value < amnt))
{
sol[sposw].value = amnt;
}
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)