From 202c28a9c7cdcb1ffe878627bf8d2d3f98fafbb6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 31 Jul 2007 17:02:48 +0000
Subject: [PATCH] debugging cross references and duplicate sequence db refs

---
 src/jalview/datamodel/DBRefEntry.java         |   32 ++++++++++++++++++++-----
 src/jalview/datamodel/Sequence.java           |   10 +++++++-
 src/jalview/datamodel/SequenceI.java          |    6 +++++
 src/jalview/datamodel/xdb/embl/EmblEntry.java |    8 +++----
 4 files changed, 45 insertions(+), 11 deletions(-)

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 8bbb5f7..b9a9b98 100755
--- 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;
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0e72690..ec135d0 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -760,8 +760,16 @@ public class Sequence
 
     for(i=0; i<iSize; i++)
     {
-      if(dbrefs[i].equals(entry))
+      if(dbrefs[i].equalRef(entry))
       {
+        if (entry.getMap()!=null)
+        {
+          if (dbrefs[i].getMap()==null)
+          {
+            // overwrite with 'superior' entry that contains a mapping.
+            dbrefs[i] = entry;
+          }
+        }
         return;
       }
     }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 731b646..5c15108 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -244,6 +244,12 @@ public interface SequenceI
 
   public DBRefEntry[] getDBRef();
 
+  /**
+   * add the given entry to the list of DBRefs for this sequence, 
+   * or replace a similar one if entry contains a map object 
+   * and the existing one doesnt. 
+   * @param entry
+   */
   public void addDBRef(DBRefEntry entry);
 
   public void addSequenceFeature(SequenceFeature sf);
diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 906122d..a1c4c3c 100644
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -642,15 +642,15 @@ public class EmblEntry
                 jalview.datamodel.DBRefSource.UNIPROT))
         {
           ref.setMap(map);
-          /*if (map.getTo()!=null)
+          if (map!=null && map.getTo()!=null)
           {
-            map.getTo().setName(map.getTo().getName()+"|"+ref.getSource()+"|"+ref.getAccessionId());
-          }*/
+            map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
+          }
         }
         if (product != null)
         {
           DBRefEntry pref = new DBRefEntry(ref.getSource(), ref
-                  .getVersion(), ref.getAccessionId());
+                .getVersion(), ref.getAccessionId());
           pref.setMap(null); // reference is direct
           product.addDBRef(pref);
           // Add converse mapping reference
-- 
1.7.10.2