Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 81f8664..7e53c46 100755 (executable)
--- 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();
@@ -311,8 +303,9 @@ 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)
+            ContactMatrixI cm = seq
+                    .getContactMatrixFor(seq.getAnnotation()[a]);
+            if (cm != null)
             {
               seqs[ipos].addContactListFor(newannot, cm);
             }
@@ -652,7 +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;
   }