Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / datamodel / ContactMapHolder.java

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
index 296feaf..af083dd 100644 (file)
--- a/src/jalview/datamodel/ContactMapHolder.java
+++ b/src/jalview/datamodel/ContactMapHolder.java
@@ -5,6 +5,8 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 
+import jalview.ws.datamodel.MappableContactMatrixI;
+
 public class ContactMapHolder implements ContactMapHolderI
 {
 
@@ -28,6 +30,14 @@ public class ContactMapHolder implements ContactMapHolderI
     {
       return null;
     }
+    if (cm instanceof MappableContactMatrixI)
+    {
+      if (_aa.sequenceRef != null)
+      {
+        return ((MappableContactMatrixI) cm)
+                .getMappableContactList(_aa.sequenceRef, column);
+      }
+    }
     // TODO: could resolve sequence position to column position here
     // TODO: what about for complexes - where contactMatrix may involve two or
     // more sequences
@@ -49,9 +59,9 @@ public class ContactMapHolder implements ContactMapHolderI
     contactmaps.put(aa.annotationId, cm);
     // TODO: contact matrices could be intra or inter - more than one refseq
     // possible!
-    if (cm.hasReferenceSeq())
+    if (cm instanceof MappableContactMatrixI)
     {
-      aa.setSequenceRef(cm.getReferenceSeq());
+      aa.setSequenceRef(((MappableContactMatrixI) cm).getReferenceSeq());
     }
     return aa;
   }