X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=47d108219da87faafeaa324d95675396dc127336;hb=f0acc63819a07d769095ff0923102de00f669ffd;hp=8783e4f3a712ce7f61efe14a9c919c2da94522e0;hpb=36de360de19fa715542db1cebe98ab65b83db540;p=jalview.git diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index 8783e4f..47d1082 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -20,77 +20,143 @@ */ 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)
+ * 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 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; + } + } + + }