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JAL-3855 JAL-2349 AlignmentI.getContactList takes care of mapping columns to sequence...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
3ae6831
..
fe65829
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-2062,10
+2062,15
@@
public class Alignment implements AlignmentI, AutoCloseable
}
if (cl == null && _aa.sequenceRef != null)
{
}
if (cl == null && _aa.sequenceRef != null)
{
- cl = _aa.sequenceRef.getContactListFor(_aa, column);
- if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+ int spos = _aa.sequenceRef.findPosition(column) - 1;
+ if (spos >= _aa.sequenceRef.getStart()
+ && spos <= 1 + _aa.sequenceRef.getEnd())
{
{
- _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, column);
+ cl = _aa.sequenceRef.getContactListFor(_aa, spos);
+ if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
+ {
+ _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos);
+ }
}
}
return cl;
}
}
return cl;