JAL-2110 refactor + tests to allow a dbref version to update "0" or

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index a61f093..151d8c4 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -966,26 +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;