From 3aab6543bd51af64e17ff6950357112b5e0a5c33 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 15:05:17 +0000
Subject: [PATCH] more semantic groupings of dbs

---
 src/jalview/datamodel/DBRefSource.java |   43 +++++++++++++++++++++++++++++++-
 1 file changed, 42 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 9e394bb..e92b31a 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -17,7 +17,13 @@
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 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)
+ * @author JimP
+ *
+ */
 public class DBRefSource
 {
   /**
@@ -48,4 +54,39 @@ public class DBRefSource
    * List of databases whose sequences might have coding regions annotated
    */
   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[] PROTEINSTR = { PDB };
+  public static final String[] DOMAINDBS = { PFAM };
+  /**
+   * set of unique DBRefSource property constants.
+   * These could be used to reconstruct the above groupings
+   */
+  public static final Object SEQDB = "SQ";
+  /**
+   * database of nucleic acid sequences
+   */
+  public static final Object DNASEQDB = "NASQ";
+  /**
+   * database of amino acid sequences
+   */
+  public static final Object PROTSEQDB = "PROTSQ";
+  /**
+   * database of cDNA sequences
+   */
+  public static final Object CODINGSEQDB = "CODING";
+  /**
+   * database of na sequences with exon annotation
+   */
+  public static final Object DNACODINGSEQDB = "XONCODING";
+  /**
+   * DB returns several sequences associated with a protein domain
+   */
+  public static final Object DOMAINDB = "DOMAIN";
+  /**
+   * DB query can take multiple accession codes concatenated
+   * by a separator.
+   */
+  public static final Object MULTIACC = "MULTIACC";
 }
-- 
1.7.10.2