/*
- * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
+
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
/**
- * 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) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
+ *
* @author JimP
- *
+ *
*/
public class DBRefSource
{
/**
* UNIPROT Accession Number
*/
- public static String UNIPROT = "UNIPROT";
+ public static final String UNIPROT = "UNIPROT";
+
/**
* UNIPROT Entry Name
*/
- public static String UP_NAME = "UNIPROT_NAME";
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
+
+ /**
+ * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
+ */
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+ public static final String EMBLCDSProduct = "EMBLCDSProtein"
+ .toUpperCase();
+
/**
* PDB Entry Code
*/
- public static String PDB = "PDB";
+ public static final String PDB = "PDB";
+
/**
* EMBL ID
*/
- public static String EMBL = "EMBL";
+ public static final String EMBL = "EMBL";
+
/**
* EMBLCDS ID
*/
- public static String EMBLCDS = "EMBLCDS";
+ public static final 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 };
- public static final String[] PROTEINSEQ = { UNIPROT };
- 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";
+ public static final String PFAM = "PFAM";
+
/**
- * database of amino acid sequences
+ * RFAM ID
*/
- public static final Object PROTSEQDB = "PROTSQ";
+ public static final String RFAM = "RFAM";
+
/**
- * database of cDNA sequences
+ * GeneDB ID
*/
- public static final Object CODINGSEQDB = "CODING";
+ public static final String GENEDB = "GeneDB".toUpperCase();
+
/**
- * database of na sequences with exon annotation
+ * Ensembl
*/
- public static final Object DNACODINGSEQDB = "XONCODING";
+ public static final String ENSEMBL = "ENSEMBL";
+
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
/**
- * 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.
+ * List of databases whose sequences might have coding regions annotated
*/
- public static final Object MULTIACC = "MULTIACC";
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+ public static String[] allSources()
+ {
+ List<String> src = new ArrayList<String>();
+ for (Field f : DBRefSource.class.getFields())
+ {
+ if (String.class.equals(f.getType()))
+ {
+ try
+ {
+ src.add((String) f.get(null));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ }
+ }
+ return src.toArray(new String[0]);
+ }
}
git://source.jalview.org / jalview.git / blobdiff