/*
- * 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 2.8.2)
+ * 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.
- *
- * 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 <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)
+ * 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.
+ * 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
*/
/**
* 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 };
+ 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
+ * 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
+ * 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.
+ * 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";
}