public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
{
ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
- if (cm==null && _aa.groupRef!=null)
+ if (cm == null && _aa.groupRef != null)
{
cm = _aa.groupRef.getContactMatrixFor(_aa);
}
- if (cm==null && _aa.sequenceRef!=null)
+ if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
- if (cm==null)
+ if (cm == null && _aa.sequenceRef.getDatasetSequence() != null)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
+ if (_aa.annotations == null || column >= _aa.annotations.length
+ || column < 0)
+ {
+ return null;
+ }
ContactListI cl = cmholder.getContactListFor(_aa, column);
if (cl == null && _aa.groupRef != null)
{
&& spos <= 1 + _aa.sequenceRef.getEnd())
{
cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
- spos-_aa.sequenceRef.getStart());
+ 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))
{
;
}