*/
package jalview.datamodel;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* 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
*
/**
* UNIPROT Accession Number
*/
- public static String UNIPROT = "UNIPROT";
+ public static final String UNIPROT = "UNIPROT";
/**
* UNIPROT Entry Name
*/
- public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
/**
* PDB Entry Code
*/
- public static String PDB = "PDB";
+ public static final String PDB = "PDB";
/**
* EMBL ID
*/
- public static String EMBL = "EMBL";
+ public static final String EMBL = "EMBL";
/**
* EMBLCDS ID
*/
- public static String EMBLCDS = "EMBLCDS";
+ public static final String EMBLCDS = "EMBLCDS";
/**
* PFAM ID
*/
- public static String PFAM = "PFAM";
+ public static final String PFAM = "PFAM";
/**
* RFAM ID
*/
- public static String RFAM = "RFAM";
+ public static final String RFAM = "RFAM";
/**
* GeneDB ID
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
- */
- public static final Object DOMAINDB = "DOMAIN";
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
/**
- * 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";
-
- /**
- * DB query returns an alignment for each accession provided.
+ * List of databases whose sequences might have coding regions annotated
*/
- public static final Object ALIGNMENTDB = "ALIGNMENTS";
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL, ENSEMBLGENOMES };
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+ public static String[] allSources()
+ {
+ List<String> src = new ArrayList<>();
+ for (Field f : DBRefSource.class.getFields())
+ {
+ if (String.class.equals(f.getType()))
+ {
+ try
+ {
+ src.add((String) f.get(null));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ }
+ }
+ return src.toArray(new String[0]);
+ }
}