JAL-2154 simplify expression

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index ed6d860..a1f06e5 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -31,6 +31,7 @@ import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import com.stevesoft.pat.Regex;
 
@@ -59,6 +60,18 @@ public class DBRefUtils
 
     canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
     canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+    // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+    // from ENA.
+    canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+    canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
+    // Make sure we have lowercase entries for all canonical string lookups
+    Set<String> keys = canonicalSourceNameLookup.keySet();
+    for (String k : keys)
+    {
+      canonicalSourceNameLookup.put(k.toLowerCase(),
+              canonicalSourceNameLookup.get(k));
+    }
 
     dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
     dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
@@ -521,7 +534,7 @@ public class DBRefUtils
     {
       return true;
     }
-    return (o1 == null ? o2.equals(o1) : o1.equals(o2));
+    return o1.equals(o2);
   }
 
   /**
@@ -546,7 +559,7 @@ public class DBRefUtils
 
   /**
    * Returns the (possibly empty) list of those supplied dbrefs which have the
-   * specified source databse
+   * specified source database, with a case-insensitive match of source name
    * 
    * @param dbRefs
    * @param source
@@ -560,7 +573,7 @@ public class DBRefUtils
     {
       for (DBRefEntry dbref : dbRefs)
       {
-        if (source.equals(dbref.getSource()))
+        if (source.equalsIgnoreCase(dbref.getSource()))
         {
           matches.add(dbref);
         }