debugging cross references and duplicate sequence db refs

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 8bbb5f7..b9a9b98 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -47,17 +47,37 @@ public class DBRefEntry
           return true;
       if (entry==null)
           return false;
-      if ((source!=null && entry.source!=null && source.equals(entry.source))
-          &&
-          (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId))
-          &&
-          (version!=null && entry.version!=null && version.equals(entry.version))
-          &&
+      if (equalRef(entry)
+              &&
           ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
               return true;
           }
       return false;
   }
+  /**
+   * test for similar DBRef attributes, except for the map object.
+   * @param entry 
+   * @return true if source, accession and version are equal with those of entry
+   */
+  public boolean equalRef(DBRefEntry entry)
+  {
+    if (entry==null)
+    {
+      return false;
+    }
+    if (entry==this)
+      return true;
+    if ((source!=null && entry.source!=null && source.equals(entry.source))
+            &&
+            (accessionId!=null && entry.accessionId!=null && accessionId.equals(entry.accessionId))
+            &&
+            (version!=null && entry.version!=null && version.equals(entry.version))
+            )
+    {
+      return true;
+    }
+    return false;
+  }
   public String getSource()
   {
     return source;