From e95890efd0e212a000a688f02b6ac2fce6e43b09 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 21 Jul 2006 08:43:57 +0000
Subject: [PATCH] DBRef is an array, not vector

---
 src/jalview/datamodel/Sequence.java  |   16 +++++++++++-----
 src/jalview/datamodel/SequenceI.java |    4 ++--
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 615f670..562440f 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -40,7 +40,7 @@ public class Sequence implements SequenceI
     Color color = Color.white;
     Vector pdbIds;
     String vamsasId;
-    Vector dbrefs;
+    DBRefEntry [] dbrefs;
 
     /** This annotation is displayed below the alignment but the
      * positions are tied to the residues of this sequence */
@@ -560,11 +560,12 @@ public class Sequence implements SequenceI
       vamsasId = id;
     }
 
-    public void setDBRef(Vector dbref)
+    public void setDBRef(DBRefEntry [] dbref)
     {
       dbrefs = dbref;
     }
-    public Vector getDBRef()
+
+    public DBRefEntry [] getDBRef()
     {
       return dbrefs;
     }
@@ -572,9 +573,14 @@ public class Sequence implements SequenceI
     public void addDBRef(DBRefEntry entry)
     {
       if(dbrefs == null)
-        dbrefs = new Vector();
+        dbrefs = new DBRefEntry[0];
+
+      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
+      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+
+      temp[temp.length-1] = entry;
 
-      dbrefs.addElement(entry);
+      dbrefs = temp;
     }
 
     public void setDatasetSequence(SequenceI seq)
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index ea49f68..f822fe6 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -232,9 +232,9 @@ public interface SequenceI
 
     public void setVamsasId(String id);
 
-    public void setDBRef(Vector dbs);
+    public void setDBRef(DBRefEntry[] dbs);
 
-    public Vector getDBRef();
+    public DBRefEntry [] getDBRef();
 
     public void addDBRef(DBRefEntry entry);
 
-- 
1.7.10.2