-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\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
- * 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 };\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 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * 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";
+}
git://source.jalview.org / jalview.git / blobdiff