develop merge

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 99c68ba..91b49eb 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -54,6 +54,11 @@ public class DBRefSource
   public static String PDB = "PDB";
 
   /**
+   * mmCIF Entry Code
+   */
+  public static String MMCIF = "mmCIF";
+
+  /**
    * EMBL ID
    */
   public static String EMBL = "EMBL";
@@ -79,19 +84,18 @@ 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
 }