From: jprocter <Jim Procter>
Date: Wed, 25 Jul 2007 17:17:11 +0000 (+0000)
Subject: uniprot synonym
X-Git-Tag: Release_2_4~339
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a5a70dd1efb0b9fdb539dbf6016d97dd962f6d0a;p=jalview.git

uniprot synonym
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index e92b31a..7344c9e 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -35,6 +35,11 @@ public class DBRefSource
    */
   public static String UP_NAME = "UNIPROT_NAME";
   /**
+   * Uniprot Knowledgebase/TrEMBL
+   * as served from EMBL protein products.
+   */
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  /**
    * PDB Entry Code
    */
   public static String PDB = "PDB";
@@ -55,8 +60,8 @@ public class DBRefSource
    */
   public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
   public static final String[] CODINGDBS = { EMBLCDS};
-  public static final String[] PROTEINDBS = { UNIPROT, PDB };
-  public static final String[] PROTEINSEQ = { UNIPROT };
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
+  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
   public static final String[] PROTEINSTR = { PDB };
   public static final String[] DOMAINDBS = { PFAM };
   /**
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index f016fe6..3e0004e 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -117,6 +117,7 @@ public class DBRefUtils
     if (CanonicalSourceNameLookup==null) {
       CanonicalSourceNameLookup = new Hashtable();
       CanonicalSourceNameLookup.put("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
+      CanonicalSourceNameLookup.put("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
       CanonicalSourceNameLookup.put("pdb", jalview.datamodel.DBRefSource.PDB);
     }
     String canonical = (String) CanonicalSourceNameLookup.get(source.