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JAL-1551 spotlessApply
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
321eee3
..
514a326
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-2050,14
+2050,14
@@
public class Alignment implements AlignmentI, AutoCloseable
public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
{
ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
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);
}
{
cm = _aa.groupRef.getContactMatrixFor(_aa);
}
- if (cm==null && _aa.sequenceRef!=null)
+ if (cm == null && _aa.sequenceRef != null)
{
cm = _aa.sequenceRef.getContactMatrixFor(_aa);
{
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);
{
// TODO fix up this logic and unify with getContactListFor
cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@@
-2076,14
+2076,19
@@
public class Alignment implements AlignmentI, AutoCloseable
}
if (cl == null && _aa.sequenceRef != null)
{
}
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);
+ // sequence associated
+ cl = _aa.sequenceRef.getContactListFor(_aa, column);
if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
{
if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
{
- _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos);
+ 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());
+ }
}
}
}
}
}
}
@@
-2096,8
+2101,7
@@
public class Alignment implements AlignmentI, AutoCloseable
AlignmentAnnotation aa = cmholder.addContactList(cm);
Annotation _aa[] = new Annotation[getWidth()];
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))
{
;
}
{
;
}