bugfix to avoid null pointer exceptions being raised for groups with no colourscheme...

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aaf0ada..0552b2c 100755 (executable)
--- 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
 {
   /**
@@ -29,6 +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";
@@ -44,4 +55,48 @@ public class DBRefSource
    * PFAM ID
    */
   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, 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 };
+  /**
+   * 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. Value of property indicates maximum number of accession codes to send at a time.
+   */
+  public static final Object MULTIACC = "MULTIACC";
 }