X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=e92b31ad3c408d814deb205295951df1c6dd8a6e;hb=3aab6543bd51af64e17ff6950357112b5e0a5c33;hp=aaf0ada5660c8bdca325b7196da995f1019241d3;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aaf0ada..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
 {
   /**
@@ -44,4 +50,43 @@ public class DBRefSource
    * PFAM ID
    */
   public static String PFAM = "PFAM";
+  /**
+   * 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";
 }