develop merge

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

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index ae99766..91b49eb 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -84,62 +84,18 @@ public class DBRefSource
   public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
-   * 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,
-      EMBLCDSProduct };
-
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
-      EMBLCDSProduct };
-
-  public static final String[] PROTEINSTR = { PDB };
-
-  public static final String[] DOMAINDBS = { PFAM, RFAM };
-
-  /**
-   * 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
+   * Ensembl
    */
-  public static final Object DNACODINGSEQDB = "XONCODING";
+  public static final String ENSEMBL = "ENSEMBL";
 
   /**
-   * DB returns several sequences associated with a protein/nucleotide domain
+   * List of databases whose sequences might have coding regions annotated
    */
-  public static final Object DOMAINDB = "DOMAIN";
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL };
 
-  /**
-   * 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";
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
-  /**
-   * DB query returns an alignment for each accession provided.
-   */
-  public static final Object ALIGNMENTDB = "ALIGNMENTS";
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 }