X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=2f948841e7c05cff48b8cf977b1ea420f35bdf04;hb=339d1bf247a3b0d000044892bee3d5668a8d9b11;hp=f8039bb6341844f2a7a994845f913d67e45c7854;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index f8039bb..2f94884 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -20,10 +20,6 @@ */ 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. @@ -45,145 +41,124 @@ public class DBRefSource - /** - * UNIPROT Accession Number - */ public static final String UNIPROT = "UNIPROT"; - - /** - * UNIPROT Entry Name - */ 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(); - - - /** - * 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"; - + public static final String ENSEMBL = "ENSEMBL"; + public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES"; - /** - * PFAM ID - */ - public static final String PFAM = "PFAM"; - - /** - * RFAM ID - */ - public static final String RFAM = "RFAM"; + public static final String EMBL = "EMBL"; + public static final String EMBLCDS = "EMBLCDS"; + public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(); - /** - * GeneDB ID - */ + 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(); - - /** - * Ensembl - */ - public static final String ENSEMBL = "ENSEMBL"; + 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<= 0;) - s += PROTEINDBS[i] + ";"; - PROTEINDBSKEYS = s; - - s = ";"; - for (int i = DNACODINGDBS.length; --i >= 0;) - s += DNACODINGDBS[i] + ";"; - DNACODINGDBSKEYS = s; - - PROMTYPES = new String[] { null, ";" + UNIPROT + ";", ";" + ENSEMBL + ";" , ";" + UNIPROT + ";" + ENSEMBL + ";" }; -} - - public static String[] allSourcesFromReflection; - - public static String[] allSources() - - { - /** - * @j2sNative - * - * return C$.allTypes; - * - */ + public static final String[] PROTEINDBS = { + UNIPROT, UNIPROTKB, + ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein + + public static final int PROTEIN_MASK = + UNIPROT_MASK | UNIPROT_KB_MASK + | ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ; + + + // for SequenceAnnotationReport only + +// public static final String[][] PRIMARY_SOURCES = new String[][] { +// CODINGDBS, DNACODINGDBS, PROTEINDBS }; +// + public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK; + + public static boolean isPrimarySource(String source) + { + return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0); + } + 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 (allSourcesFromReflection == null) + if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources { - 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]); + // 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 allSourcesFromReflection; } - } - + return true; +} + + + }