- /**
- * UNIPROT Accession Number
- */
- public static String UNIPROT="UNIPROT";
- /**
- * UNIPROT Entry Name
- */
- public static String UP_NAME="UNIPROT_NAME";
- /**
- * PDB Entry Code
- */
- public static String PDB="PDB";
- /**
- * EMBL ID
- */
- public static String EMBL="EMBL";
- /**
- * EMBLCDS ID
- */
- public static String EMBLCDS="EMBLCDS";
- /**
- * PFAM ID
- */
- public static String PFAM="PFAM";
- }
+ /**
+ * UNIPROT Accession Number
+ */
+ public static String UNIPROT = "UNIPROT";
+
+ /**
+ * UNIPROT Entry 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".toUpperCase();
+
+ public static final String EMBLCDSProduct = "EMBLCDSProtein"
+ .toUpperCase();
+
+ /**
+ * PDB Entry Code
+ */
+ public static String PDB = "PDB";
+
+ /**
+ * EMBL ID
+ */
+ public static String EMBL = "EMBL";
+
+ /**
+ * EMBLCDS ID
+ */
+ public static String EMBLCDS = "EMBLCDS";
+
+ /**
+ * PFAM ID
+ */
+ public static String PFAM = "PFAM";
+
+ /**
+ * RFAM ID
+ */
+ public static String RFAM = "RFAM";
+
+ /**
+ * GeneDB ID
+ */
+ public static final String GENEDB = "GeneDB".toUpperCase();
+
+ /**
+ * Ensembl
+ */
+ public static final String ENSEMBL = "ENSEMBL";
+
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+}