X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=6c8cbc08979a4b30ac456795a0d4db232f107ba2;hb=6a951ef313becea88861eb3f48c244be82da1ca0;hp=9f65f71fea1acd6644e08766108bce20339054f3;hpb=d1aade87dce0266a471dfa1e96d5a94499d5d262;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9f65f71..6c8cbc0 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -219,6 +219,8 @@ public class Sequence extends ASequence implements SequenceI
     initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
+    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
+            seq.getSourceDBRef());
     if (seq.getSequenceFeatures() != null)
     {
       SequenceFeature[] sf = seq.getSequenceFeatures();
@@ -228,10 +230,10 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     setDatasetSequence(seq.getDatasetSequence());
-    if (datasetSequence == null && seq.getDBRef() != null)
+    if (datasetSequence == null && seq.getDBRefs() != null)
     {
       // only copy DBRefs if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRef();
+      DBRefEntry[] dbr = seq.getDBRefs();
       for (int i = 0; i < dbr.length; i++)
       {
         addDBRef(new DBRefEntry(dbr[i]));
@@ -264,11 +266,10 @@ 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 +289,7 @@ 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];
@@ -419,7 +421,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public Vector<PDBEntry> getAllPDBEntries()
   {
-    return pdbIds;
+    return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
   }
 
   /**
@@ -610,17 +612,15 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
+   * Returns the character of the aligned sequence at the given position (base
+   * zero), or space if the position is not within the sequence's bounds
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public char getCharAt(int i)
   {
-    if (i < sequence.length)
+    if (i >= 0 && i < sequence.length)
     {
       return sequence[i];
     }
@@ -911,18 +911,18 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void setDBRef(DBRefEntry[] dbref)
+  public void setDBRefs(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
   @Override
-  public DBRefEntry[] getDBRef()
+  public DBRefEntry[] getDBRefs()
   {
     if (dbrefs == null && datasetSequence != null
             && this != datasetSequence)
     {
-      return datasetSequence.getDBRef();
+      return datasetSequence.getDBRefs();
     }
     return dbrefs;
   }
@@ -930,6 +930,7 @@ 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 +964,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
+    // TODO check for circular reference before setting?
     datasetSequence = seq;
   }
 
@@ -1079,8 +1081,8 @@ public class Sequence extends ASequence implements SequenceI
       datasetSequence.setDescription(getDescription());
       setSequenceFeatures(null);
       // move database references onto dataset sequence
-      datasetSequence.setDBRef(getDBRef());
-      setDBRef(null);
+      datasetSequence.setDBRefs(getDBRefs());
+      setDBRefs(null);
       datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
       datasetSequence.updatePDBIds();
@@ -1255,7 +1257,7 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     // transfer database references
-    DBRefEntry[] entryRefs = entry.getDBRef();
+    DBRefEntry[] entryRefs = entry.getDBRefs();
     if (entryRefs != null)
     {
       for (int r = 0; r < entryRefs.length; r++)