X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=4d3d5787566a502bd9d0dbe1c2edecfcd13cebef;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=321eee3c5ab502839122a17286318fec97d94c6d;hpb=7420ce36f2b43280ef610e3743960207e4c2dbe3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 321eee3..4d3d578 100755
--- 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);
-    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);
@@ -2080,10 +2080,12 @@ public class Alignment implements AlignmentI, AutoCloseable
       if (spos >= _aa.sequenceRef.getStart()
               && spos <= 1 + _aa.sequenceRef.getEnd())
       {
-        cl = _aa.sequenceRef.getContactListFor(_aa, spos);
+        cl = _aa.sequenceRef.getContactListFor(_aa,
+                spos - _aa.sequenceRef.getStart());
         if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
         {
-          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos);
+          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+                  spos - _aa.sequenceRef.getStart());
         }
       }
     }