X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=1ec702cf523b47413097c9d17e4bd2177f88a998;hb=9e40070f757fc662aba39ba6314be4937276ead4;hp=fe6582951e5df44bf76330c1f118b6ada51fe6a0;hpb=b197088233e07bcdbf41a12e975185aee3efe146;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index fe65829..1ec702c 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2047,9 +2047,23 @@ public class Alignment implements AlignmentI, AutoCloseable
   }
 
   @Override
-  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
   {
-    return cmholder.getContactMatrixFor(ann);
+    ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
+    if (cm==null && _aa.groupRef!=null)
+    {
+      cm = _aa.groupRef.getContactMatrixFor(_aa);
+    }
+    if (cm==null && _aa.sequenceRef!=null)
+    {
+      cm = _aa.sequenceRef.getContactMatrixFor(_aa);
+      if (cm==null)
+      {
+        // TODO fix up this logic and unify with getContactListFor
+        cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
+      }
+    }
+    return cm;
   }
 
   @Override
@@ -2062,14 +2076,19 @@ public class Alignment implements AlignmentI, AutoCloseable
     }
     if (cl == null && _aa.sequenceRef != null)
     {
-      int spos = _aa.sequenceRef.findPosition(column) - 1;
-      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)
         {
-          _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());
+          }
         }
       }
     }