X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=fba921158ebc20efe3f4ee077e412341cbfc46ad;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=b1824f7f342e1c75c6f3eb6a1f52bb10d797dafb;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b1824f7..fba9211 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -23,7 +23,10 @@ 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)
+ * jalview.ws.DbSourcProxy) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
  * 
  * @author JimP
  * 
@@ -38,12 +41,15 @@ public class DBRefSource
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME";
+  public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
 
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+  public static final String EMBLCDSProduct = "EMBLCDSProtein"
+          .toUpperCase();
 
   /**
    * PDB Entry Code
@@ -73,69 +79,23 @@ public class DBRefSource
   /**
    * 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, RFAM };
-
-  /**
-   * set of unique DBRefSource property constants. These could be used to
-   * reconstruct the above groupings
-   */
-  public static final Object SEQDB = "SQ";
+  public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
-   * database of nucleic acid sequences
+   * Ensembl
    */
-  public static final Object DNASEQDB = "NASQ";
+  public static final String ENSEMBL = "ENSEMBL";
 
-  /**
-   * database of amino acid sequences
-   */
-  public static final Object PROTSEQDB = "PROTSQ";
+  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
 
   /**
-   * 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/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
 }