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JAL-4090 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
89ec5ad
..
73ccdc5
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 && _aa.sequenceRef.getDatasetSequence() != 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);
@@
-2069,6
+2069,11
@@
public class Alignment implements AlignmentI, AutoCloseable
@Override
public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
{
@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)
{
ContactListI cl = cmholder.getContactListFor(_aa, column);
if (cl == null && _aa.groupRef != null)
{
@@
-2087,7
+2092,7
@@
public class Alignment implements AlignmentI, AutoCloseable
&& spos <= 1 + _aa.sequenceRef.getEnd())
{
cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
&& spos <= 1 + _aa.sequenceRef.getEnd())
{
cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
- spos-_aa.sequenceRef.getStart());
+ spos - _aa.sequenceRef.getStart());
}
}
}
}
}
}