-/*
- * 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
- * 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.
- *
- * 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
- */
-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";
- /**
- * List of databases whose sequences might have coding regions annotated
- */
- public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
- public static final String[] CODINGDBS = { EMBLCDS};
- 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.
- */
- public static final Object MULTIACC = "MULTIACC";
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.datamodel;\r
+\r
+/**\r
+ * Defines internal constants for unambiguous annotation of DbRefEntry source\r
+ * strings and describing the data retrieved from external database sources (see\r
+ * jalview.ws.DbSourcProxy)\r
+ * \r
+ * @author JimP\r
+ * \r
+ */\r
+public class DBRefSource\r
+{\r
+ /**\r
+ * UNIPROT Accession Number\r
+ */\r
+ public static String UNIPROT = "UNIPROT";\r
+\r
+ /**\r
+ * UNIPROT Entry Name\r
+ */\r
+ public static String UP_NAME = "UNIPROT_NAME";\r
+\r
+ /**\r
+ * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.\r
+ */\r
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL";\r
+\r
+ /**\r
+ * PDB Entry Code\r
+ */\r
+ public static String PDB = "PDB";\r
+\r
+ /**\r
+ * EMBL ID\r
+ */\r
+ public static String EMBL = "EMBL";\r
+\r
+ /**\r
+ * EMBLCDS ID\r
+ */\r
+ public static String EMBLCDS = "EMBLCDS";\r
+\r
+ /**\r
+ * PFAM ID\r
+ */\r
+ public static String PFAM = "PFAM";\r
+ \r
+ /**\r
+ * RFAM ID\r
+ */\r
+ public static String RFAM = "RFAM";\r
+\r
+ /**\r
+ * GeneDB ID\r
+ */\r
+ public static final String GENEDB = "GeneDB";\r
+\r
+ /**\r
+ * List of databases whose sequences might have coding regions annotated\r
+ */\r
+ public static final String[] DNACODINGDBS =\r
+ { EMBL, EMBLCDS, GENEDB };\r
+\r
+ public static final String[] CODINGDBS =\r
+ { EMBLCDS, GENEDB };\r
+\r
+ public static final String[] PROTEINDBS =\r
+ { UNIPROT, PDB, UNIPROTKB };\r
+\r
+ public static final String[] PROTEINSEQ =\r
+ { UNIPROT, UNIPROTKB };\r
+\r
+ public static final String[] PROTEINSTR =\r
+ { PDB };\r
+\r
+ public static final String[] DOMAINDBS =\r
+ { PFAM, RFAM };\r
+\r
+ /**\r
+ * set of unique DBRefSource property constants. These could be used to\r
+ * reconstruct the above groupings\r
+ */\r
+ public static final Object SEQDB = "SQ";\r
+\r
+ /**\r
+ * database of nucleic acid sequences\r
+ */\r
+ public static final Object DNASEQDB = "NASQ";\r
+\r
+ /**\r
+ * database of amino acid sequences\r
+ */\r
+ public static final Object PROTSEQDB = "PROTSQ";\r
+\r
+ /**\r
+ * database of cDNA sequences\r
+ */\r
+ public static final Object CODINGSEQDB = "CODING";\r
+\r
+ /**\r
+ * database of na sequences with exon annotation\r
+ */\r
+ public static final Object DNACODINGSEQDB = "XONCODING";\r
+\r
+ /**\r
+ * DB returns several sequences associated with a protein/nucleotide domain\r
+ */\r
+ public static final Object DOMAINDB = "DOMAIN";\r
+\r
+ /**\r
+ * DB query can take multiple accession codes concatenated by a separator.\r
+ * Value of property indicates maximum number of accession codes to send at a\r
+ * time.\r
+ */\r
+ public static final Object MULTIACC = "MULTIACC";\r
+\r
+ /**\r
+ * DB query returns an alignment for each accession provided.\r
+ */\r
+ public static final Object ALIGNMENTDB = "ALIGNMENTS";\r
+}\r
git://source.jalview.org / jalview.git / blobdiff