java 1.1 compatibility

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index e92b31a..0552b2c 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -35,6 +35,11 @@ public class DBRefSource
    */
   public static String UP_NAME = "UNIPROT_NAME";
   /**
+   * Uniprot Knowledgebase/TrEMBL
+   * as served from EMBL protein products.
+   */
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  /**
    * PDB Entry Code
    */
   public static String PDB = "PDB";
@@ -51,12 +56,17 @@ public class DBRefSource
    */
   public static String PFAM = "PFAM";
   /**
+   * GeneDB ID
+   */
+  public static final String GENEDB = "GeneDB";
+
+  /**
    * 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[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB};
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB};
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB};
+  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
   public static final String[] PROTEINSTR = { PDB };
   public static final String[] DOMAINDBS = { PFAM };
   /**
@@ -86,7 +96,7 @@ public class DBRefSource
   public static final Object DOMAINDB = "DOMAIN";
   /**
    * DB query can take multiple accession codes concatenated
-   * by a separator.
+   * by a separator. Value of property indicates maximum number of accession codes to send at a time.
    */
   public static final Object MULTIACC = "MULTIACC";
 }