X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=7e53c46229629db5c7532baab9032245d3616ff4;hb=a3f65dbb5ba8bd470a31ba2af72db6d8ddf60546;hp=6a0e64c100f373b8b8bdda467100458aaff9a135;hpb=0eda79421bb03c19e3b74c4b83b1644ca12ea66c;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6a0e64c..7e53c46 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -274,14 +274,6 @@ public class SequenceGroup implements AnnotatedCollectionI
               endRes + 1);
       if (seqipos != null)
       {
-        seqipos.setDescription(seq.getDescription());
-        seqipos.setDBRefs(seq.getDBRefs());
-        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
-        if (seq.getDatasetSequence() != null)
-        {
-          seqipos.setDatasetSequence(seq.getDatasetSequence());
-        }
-
         if (seq.getAnnotation() != null)
         {
           AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
@@ -311,6 +303,12 @@ public class SequenceGroup implements AnnotatedCollectionI
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
+            ContactMatrixI cm = seq
+                    .getContactMatrixFor(seq.getAnnotation()[a]);
+            if (cm != null)
+            {
+              seqs[ipos].addContactListFor(newannot, cm);
+            }
             seqipos.addAlignmentAnnotation(newannot);
           }
         }
@@ -647,7 +645,8 @@ public class SequenceGroup implements AnnotatedCollectionI
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
-      System.out.println("Out of memory loading groups: " + err);
+      jalview.bin.Console
+              .outPrintln("Out of memory loading groups: " + err);
     }
     return upd;
   }
@@ -1499,6 +1498,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  {
+    return cmholder.getContactMatrixFor(ann);
+  }
+
+  @Override
   public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
   {
     return cmholder.getContactListFor(_aa, column);
@@ -1519,4 +1524,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     // TODO passing annotations back to context to be added
     return aa;
   }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    cmholder.addContactListFor(annotation, cm);
+  }
+
 }