*/
package jalview.datamodel;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
/**
+ * BH 2018 SwingJS note: If additional final static Strings are added to this
+ * file, they should be added to public static final String[] allTypes.
+ *
* 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
*
*/
public class DBRefSource
{
+
+
+
/**
* 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.
*/
public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
- public static final String EMBLCDSProduct = "EMBLCDSProtein"
- .toUpperCase();
+ public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
+
/**
* 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();
+
/**
* 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 };
+ ENSEMBL, ENSEMBLGENOMES };
public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
- public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+
+ public static final String[] allTypes = new String[] {
+ UNIPROT, UP_NAME, UNIPROTKB,
+ EMBLCDSProduct, PDB, EMBL,
+ EMBLCDS, PFAM, RFAM,
+ GENEDB, ENSEMBL, ENSEMBLGENOMES
+ };
+
+
+ public static String[] allSourcesFromReflection;
+
+ public static String[] allSources()
+
+ {
+ /**
+ * @j2sNative
+ *
+ * return C$.allTypes;
+ *
+ */
+
+ {
+ if (allSourcesFromReflection == null)
+ {
+ 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();
+ }
+ }
+ }
+ allSourcesFromReflection = src.toArray(new String[0]);
+ }
+ return allSourcesFromReflection;
+ }
+ }
+
+
}