}
if (cl == null && _aa.sequenceRef != null)
{
- int spos = _aa.sequenceRef.findPosition(column);
- if (spos >= _aa.sequenceRef.getStart()
- && spos <= 1 + _aa.sequenceRef.getEnd())
+ if (_aa.annotations[column] != null)
{
- cl = _aa.sequenceRef.getContactListFor(_aa,
- spos - _aa.sequenceRef.getStart());
+ // sequence associated
+ cl = _aa.sequenceRef.getContactListFor(_aa, column);
if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
{
- _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
- spos - _aa.sequenceRef.getStart());
+ int spos = _aa.sequenceRef.findPosition(column);
+ if (spos >= _aa.sequenceRef.getStart()
+ && spos <= 1 + _aa.sequenceRef.getEnd())
+ {
+ cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
+ }
}
}
}
AlignmentAnnotation aa = cmholder.addContactList(cm);
Annotation _aa[] = new Annotation[getWidth()];
- Annotation dummy = new Annotation(0.0f);
- for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+ for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
{
;
}