X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=4a5c888330710c073d9fd635f43ba54907a999c9;hb=8f08ed712138cea8987594a62b6053a0bfdba327;hp=ae06650f2ce9914fdf49fa1b9355b38d0489c3a4;hpb=d0d660cab06c31659e7bb0a1780317b3d2231eb6;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index ae06650..4a5c888 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import java.util.Locale;
+
 import jalview.api.DBRefEntryI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -95,7 +97,7 @@ public class DBRefEntry implements DBRefEntryI
           Mapping map,boolean isCanonical)
   {
 	
-    this.source = source.toUpperCase();
+    this.source = source.toUpperCase(Locale.ROOT);
     setVersion(version);
     this.accessionId = accessionId;
     this.map = map;
@@ -113,7 +115,7 @@ public class DBRefEntry implements DBRefEntryI
                     : new String(entry.getVersion())),
             (entry.getAccessionId() == null ? ""
                     : new String(entry.getAccessionId())),
-            (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+            (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
   }
 
   @Override
@@ -172,6 +174,7 @@ public class DBRefEntry implements DBRefEntryI
       return true;
     }
 
+    boolean improved=false;
     /*
      * source must either match or be both null
      */
@@ -195,6 +198,19 @@ public class DBRefEntry implements DBRefEntryI
       return false;
     }
 
+    if (!isCanonicalAccession && other.isCanonical())
+    {
+      isCanonicalAccession = true;
+      improved = true;
+    }
+    else
+    {
+      if (isCanonicalAccession && !other.isCanonical())
+      {
+        // other is not an authoritative source of canonical accessions
+        return false;
+      }
+    }
     /*
      * if my version is null, "0" or "source:0" then replace with other version,
      * otherwise the versions have to match
@@ -211,12 +227,15 @@ public class DBRefEntry implements DBRefEntryI
       if (version != null && (otherVersion == null
               || !version.equalsIgnoreCase(otherVersion)))
       {
-        return false;
+        // FIXME: there may be a problem with old version strings not allowing
+        // updating of dbrefentries
+        return improved;
       }
     }
 
     /*
-     * if I have no mapping, take that of the other dbref
+     * if I have no mapping, take that of the other dbref 
+     * - providing it had a version and so do I
      */
     if (map == null)
     {
@@ -289,7 +308,7 @@ public class DBRefEntry implements DBRefEntryI
   public void setAccessionId(String accessionId)
   {
 	  this.accessionId = accessionId;
-//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase();
+//    this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
   }
 
   /**
@@ -300,7 +319,7 @@ public class DBRefEntry implements DBRefEntryI
   {
 	  this.source = source;
 	  
-//    this.source = (source == null ? "" : source).toUpperCase();
+//    this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
 //    this.canonicalSourceName = 	DBRefUtils.getCanonicalName(this.source);
 //    this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
   }
@@ -309,7 +328,7 @@ public class DBRefEntry implements DBRefEntryI
   public void setVersion(String version)
   {
     this.version = version;
-    this.ucversion = (version == null ? null : version.toUpperCase());
+    this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
   }
 
   @Override