X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=b1824f7f342e1c75c6f3eb6a1f52bb10d797dafb;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=b9442df0828a95ba76b92a2fbf84f28a82e13395;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java index b9442df..b1824f7 100755 --- a/src/jalview/datamodel/DBRefSource.java +++ b/src/jalview/datamodel/DBRefSource.java @@ -1,128 +1,141 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * 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. - * - * 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 Jalview. If not, see . - */ -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"; - - /** - * 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, 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 }; - - /** - * 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 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"; -} +/* + * 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. + * + * 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 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, 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"; +}