X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=151d8c4ce886748a3294b34278cfa050330e0d97;hb=1f959f4a5bc07769cde4c2577022ad64e55b4a1a;hp=5bfdb04946a25dfa30ad01c208c3c35bd16586d6;hpb=6819fa797b45769bb38a80230e5961e09582ed9e;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5bfdb04..151d8c4 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -312,7 +312,11 @@ 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 && datasetSequence != null)
+    {
+      datasetSequence.addSequenceFeature(sf);
+      return;
+    }
     if (sequenceFeatures == null)
     {
       sequenceFeatures = new SequenceFeature[0];
@@ -338,6 +342,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
+      if (datasetSequence!=null) {
+    	  datasetSequence.deleteFeature(sf);
+      }
       return;
     }
 
@@ -959,26 +966,25 @@ public class Sequence extends ASequence implements SequenceI
       dbrefs = new DBRefEntry[0];
     }
 
-    int i, iSize = dbrefs.length;
-
-    for (i = 0; i < iSize; i++)
+    for (DBRefEntryI dbr : dbrefs)
     {
-      if (dbrefs[i].equalRef(entry))
+      if (dbr.updateFrom(entry))
       {
-        if (entry.getMap() != null)
-        {
-          if (dbrefs[i].getMap() == null)
-          {
-            // overwrite with 'superior' entry that contains a mapping.
-            dbrefs[i] = entry;
-          }
-        }
+        /*
+         * found a dbref that either matched, or could be
+         * updated from, the new entry - no need to add it
+         */
         return;
       }
     }
 
-    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
-    System.arraycopy(dbrefs, 0, temp, 0, iSize);
+    /*
+     * extend the array to make room for one more
+     */
+    // TODO use an ArrayList instead
+    int j = dbrefs.length;
+    DBRefEntry[] temp = new DBRefEntry[j + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, j);
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;