Merge branch 'develop' into JAL-1705_trialMerge

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c8bd902..7b05649 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -219,6 +219,7 @@ public class Sequence extends ASequence implements SequenceI
     initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
+    sourceDBRef = seq.getSourceDBRef();
     if (seq.getSequenceFeatures() != null)
     {
       SequenceFeature[] sf = seq.getSequenceFeatures();
@@ -264,11 +265,10 @@ public class Sequence extends ASequence implements SequenceI
     }
     if (seq.getAllPDBEntries() != null)
     {
-      Vector ids = seq.getAllPDBEntries();
-      Enumeration e = ids.elements();
-      while (e.hasMoreElements())
+      Vector<PDBEntry> ids = seq.getAllPDBEntries();
+      for (PDBEntry pdb : ids)
       {
-        this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+        this.addPDBId(new PDBEntry(pdb));
       }
     }
   }
@@ -288,6 +288,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
+    // TODO add to dataset sequence instead if there is one?
     if (sequenceFeatures == null)
     {
       sequenceFeatures = new SequenceFeature[0];
@@ -911,7 +912,7 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void setDBRef(DBRefEntry[] dbref)
+  public void setDBRefs(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
@@ -930,6 +931,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO add to dataset sequence instead if there is one?
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -963,6 +965,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
+    // TODO check for circular reference before setting?
     datasetSequence = seq;
   }
 
@@ -1079,8 +1082,8 @@ public class Sequence extends ASequence implements SequenceI
       datasetSequence.setDescription(getDescription());
       setSequenceFeatures(null);
       // move database references onto dataset sequence
-      datasetSequence.setDBRef(getDBRefs());
-      setDBRef(null);
+      datasetSequence.setDBRefs(getDBRefs());
+      setDBRefs(null);
       datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();