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)
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
if (spos >= _aa.sequenceRef.getStart()
&& spos <= 1 + _aa.sequenceRef.getEnd())
{
- cl = _aa.sequenceRef.getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
+ cl = _aa.sequenceRef.getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
{
- _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
+ _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+ spos - _aa.sequenceRef.getStart());
}
}
}