Merge branch 'develop' into bug/JAL-2154projectMappings

[jalview.git] / src / jalview / datamodel / DBRefSource.java

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 99c68ba..fba9211 100755 (executable)
--- 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
 }