/*
- * 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.
*
package jalview.datamodel;
/**
+ * 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
*
*/
+import java.util.Locale;
+
public class DBRefSource
{
- /**
- * UNIPROT Accession Number
- */
- public static String UNIPROT = "UNIPROT";
- /**
- * UNIPROT Entry Name
- */
- public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
+ public static final String UNIPROT = "UNIPROT";
+
+ 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 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();
+ .toUpperCase(Locale.ROOT);
- /**
- * 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 PFAM = "PFAM";
- /**
- * EMBLCDS ID
- */
- public static String EMBLCDS = "EMBLCDS";
+ public static final String RFAM = "RFAM";
- /**
- * PFAM ID
- */
- public static String PFAM = "PFAM";
+ public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
- /**
- * RFAM ID
- */
- public static String RFAM = "RFAM";
+ public static final String PDB_CANONICAL_NAME = PDB;
- /**
- * GeneDB ID
- */
- public static final String GENEDB = "GeneDB".toUpperCase();
+ public static final String[] allSources = new String[] { UNIPROT, UP_NAME,
+ UNIPROTKB, ENSEMBL, ENSEMBLGENOMES, EMBL, EMBLCDS, EMBLCDSProduct,
+ PDB, PFAM, RFAM, GENEDB };
- /**
- * List of databases whose sequences might have coding regions annotated
- */
- public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
+ public static final int UNIPROT_MASK = 1 << 0;
- public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
+ public static final int UP_NAME_MASK = 1 << 1;
- public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
- EMBLCDSProduct };
+ public static final int UNIPROT_KB_MASK = 1 << 2;
- public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
- EMBLCDSProduct };
+ public static final int ENSEMBL_MASK = 1 << 3;
- public static final String[] PROTEINSTR = { PDB };
+ public static final int ENSEMBL_GENOMES_MASK = 1 << 4;
- public static final String[] DOMAINDBS = { PFAM, RFAM };
+ public static final int EMBL_MASK = 1 << 5;
- /**
- * set of unique DBRefSource property constants. These could be used to
- * reconstruct the above groupings
- */
- public static final Object SEQDB = "SQ";
+ public static final int EMBL_CDS_MASK = 1 << 6;
- /**
- * database of nucleic acid sequences
- */
- public static final Object DNASEQDB = "NASQ";
+ public static final int EMBL_CDS_PRODUCT_MASK = 1 << 7;
- /**
- * database of amino acid sequences
- */
- public static final Object PROTSEQDB = "PROTSQ";
+ public static final int PDB_MASK = 1 << 8;
- /**
- * database of cDNA sequences
- */
- public static final Object CODINGSEQDB = "CODING";
+ public static final int PFAM_MASK = 1 << 9;
- /**
- * database of na sequences with exon annotation
- */
- public static final Object DNACODINGSEQDB = "XONCODING";
+ public static final int RFAM_MASK = 1 << 10;
- /**
- * DB returns several sequences associated with a protein/nucleotide domain
- */
- public static final Object DOMAINDB = "DOMAIN";
+ public static final int GENE_DB_MASK = 1 << 11;
- /**
- * 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";
+ 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 << i;
+ }
+ }
+ return 0;
+ }
+
+ public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
/**
- * 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 = { ENSEMBL, ENSEMBLGENOMES,
+ EMBL, EMBLCDS, GENEDB };
+
+ public static final int DNA_CODING_MASK = ENSEMBL_MASK
+ | ENSEMBL_GENOMES_MASK | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK
+ | ENSEMBL_MASK;
+
+ 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)
+ {
+ if (ucversion == null)
+ {
+ // Null/empty version is not a real reference ?
+ return false;
+ }
+ // 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 (ucversion.startsWith(allSources[i])) // BH 2019.01.25
+ // .toUpperCase(Locale.ROOT)
+ // unnecessary here for
+ // allSources
+ {
+ // 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 true;
+ }
+
}
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