X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=2d2ae4ff582c24e59cabafade39de76660b9a353;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=58c63ad8e43bedad182c0f20fa2bb3b759fd32c8;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index 58c63ad..2d2ae4f 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,11 +20,10 @@ */ 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)
@@ -32,93 +31,136 @@ import java.util.List; * (e.g. protein coding, alignment (ortholog db, paralog db, domain db), * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..). * + * + * * @author JimP * */ +import java.util.Locale; + public class DBRefSource { - /** - * UNIPROT Accession Number - */ + + + public static final String UNIPROT = "UNIPROT"; - - /** - * UNIPROT Entry Name - */ - public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(); - + public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT); /** * 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 final String PDB = "PDB"; - - /** - * EMBL ID - */ - public static final String EMBL = "EMBL"; - - /** - * EMBLCDS ID - */ - public static final String EMBLCDS = "EMBLCDS"; - - /** - * PFAM ID - */ - public static final String PFAM = "PFAM"; - - /** - * RFAM ID - */ - 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 UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT); + public static final String ENSEMBL = "ENSEMBL"; public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES"; + + public static final String EMBL = "EMBL"; + public static final String EMBLCDS = "EMBLCDS"; + public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT); + + public static final String PDB = "PDB"; + public static final String PFAM = "PFAM"; + public static final String RFAM = "RFAM"; + public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT); + + public static final String PDB_CANONICAL_NAME = PDB; + + + public static final String[] allSources = new String[] { + UNIPROT, + UP_NAME, UNIPROTKB, + ENSEMBL, ENSEMBLGENOMES, + EMBL, EMBLCDS, EMBLCDSProduct, + PDB, PFAM, RFAM, GENEDB + }; + + public static final int UNIPROT_MASK = 1<<0; + public static final int UP_NAME_MASK = 1<<1; + public static final int UNIPROT_KB_MASK = 1<<2; + public static final int ENSEMBL_MASK = 1<<3; + public static final int ENSEMBL_GENOMES_MASK = 1<<4; + public static final int EMBL_MASK = 1<<5; + public static final int EMBL_CDS_MASK = 1<<6; + public static final int EMBL_CDS_PRODUCT_MASK = 1<<7; + public static final int PDB_MASK = 1<<8; + public static final int PFAM_MASK = 1<<9; + public static final int RFAM_MASK = 1<<10; + public static final int GENE_DB_MASK = 1<<11; + + public static final int MASK_COUNT = 12; + + public static final int ALL_MASKS = (1 << MASK_COUNT) - 1; + + public static int getSourceKey(String name) { + for (int i = 0; i < MASK_COUNT; i++) { + if (name.equals(allSources[i])) + { + return 1< src = new ArrayList(); - for (Field f : DBRefSource.class.getFields()) + public static boolean isPrimaryCandidate(String ucversion) { + // tricky - this test really needs to search the sequence's set of dbrefs to + // see if there is a primary reference that derived this reference. + for (int i = allSources.length; --i >= 0;) { - if (String.class.equals(f.getType())) + if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources { - try - { - src.add((String) f.get(null)); - } catch (Exception x) - { - x.printStackTrace(); - } + // by convention, many secondary references inherit the primary + // reference's + // source string as a prefix for any version information from the + // secondary reference. + return false; } } - return src.toArray(new String[0]); - } + return true; +} + + + + }