X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=b1824f7f342e1c75c6f3eb6a1f52bb10d797dafb;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=9e394bb1d277c6a32dd73c76c7d22a29037712d3;hpb=3bf07ba3afb39cea37a1e3eb32da7d498a1fd901;p=jalview.git diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index 9e394bb..b1824f7 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -1,51 +1,141 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; +/** + * Defines internal constants for unambiguous annotation of DbRefEntry source + * strings and describing the data retrieved from external database sources (see + * jalview.ws.DbSourcProxy) + * + * @author JimP + * + */ public class DBRefSource { /** * UNIPROT Accession Number */ public static String UNIPROT = "UNIPROT"; + /** * UNIPROT Entry Name */ public static String UP_NAME = "UNIPROT_NAME"; + + /** + * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products. + */ + public static final String UNIPROTKB = "UniProtKB/TrEMBL"; + /** * PDB Entry Code */ public static String PDB = "PDB"; + /** * EMBL ID */ public static String EMBL = "EMBL"; + /** * EMBLCDS ID */ public static String EMBLCDS = "EMBLCDS"; + /** * PFAM ID */ public static String PFAM = "PFAM"; + + /** + * RFAM ID + */ + public static String RFAM = "RFAM"; + + /** + * GeneDB ID + */ + public static final String GENEDB = "GeneDB"; + /** * List of databases whose sequences might have coding regions annotated */ - public static final String[] DNACODINGDBS = { EMBL, EMBLCDS}; + public static final String[] DNACODINGDBS = + { EMBL, EMBLCDS, GENEDB }; + + public static final String[] CODINGDBS = + { EMBLCDS, GENEDB }; + + public static final String[] PROTEINDBS = + { UNIPROT, PDB, UNIPROTKB }; + + public static final String[] PROTEINSEQ = + { UNIPROT, UNIPROTKB }; + + public static final String[] PROTEINSTR = + { PDB }; + + public static final String[] DOMAINDBS = + { PFAM, RFAM }; + + /** + * set of unique DBRefSource property constants. These could be used to + * reconstruct the above groupings + */ + public static final Object SEQDB = "SQ"; + + /** + * database of nucleic acid sequences + */ + public static final Object DNASEQDB = "NASQ"; + + /** + * database of amino acid sequences + */ + public static final Object PROTSEQDB = "PROTSQ"; + + /** + * database of cDNA sequences + */ + public static final Object CODINGSEQDB = "CODING"; + + /** + * database of na sequences with exon annotation + */ + public static final Object DNACODINGSEQDB = "XONCODING"; + + /** + * DB returns several sequences associated with a protein/nucleotide domain + */ + public static final Object DOMAINDB = "DOMAIN"; + + /** + * 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"; + + /** + * DB query returns an alignment for each accession provided. + */ + public static final Object ALIGNMENTDB = "ALIGNMENTS"; }