From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Jan 2016 15:31:11 +0000 (+0000)
Subject: JAL-1705 ENSEMBL added, unused constants removed
X-Git-Tag: Release_2_10_0~296^2~73
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=inline;h=36de360de19fa715542db1cebe98ab65b83db540;p=jalview.git

JAL-1705 ENSEMBL added, unused constants removed
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 99c68ba..8783e4f 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -79,19 +79,18 @@ public class DBRefSource
   public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
+   * Ensembl
+   */
+  public static final String ENSEMBL = "ENSEMBL";
+
+  /**
    * List of databases whose sequences might have coding regions annotated
    */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL };
 
-  public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
   public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
-      EMBLCDSProduct };
-
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
-      EMBLCDSProduct };
-
-  public static final String[] PROTEINSTR = { PDB };
-
-  public static final String[] DOMAINDBS = { PFAM, RFAM };
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 }