X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=fba921158ebc20efe3f4ee077e412341cbfc46ad;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=99c68ba8a54d752bfd3b42f7bfb7e3d4699d361d;hpb=409fd993c6e32e999b24082aae107a043a590f8f;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 99c68ba..fba9211 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -23,7 +23,10 @@ package jalview.datamodel;
 /**
  * Defines internal constants for unambiguous annotation of DbRefEntry source
  * strings and describing the data retrieved from external database sources (see
- * jalview.ws.DbSourcProxy)
+ * jalview.ws.DbSourcProxy) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
  * 
  * @author JimP
  * 
@@ -79,19 +82,20 @@ public class DBRefSource
   public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
-   * List of databases whose sequences might have coding regions annotated
+   * Ensembl
    */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
-
-  public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
+  public static final String ENSEMBL = "ENSEMBL";
 
-  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
-      EMBLCDSProduct };
+  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
 
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
-      EMBLCDSProduct };
+  /**
+   * List of databases whose sequences might have coding regions annotated
+   */
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL };
 
-  public static final String[] PROTEINSTR = { PDB };
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
-  public static final String[] DOMAINDBS = { PFAM, RFAM };
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 }