/*
- * 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;
+
+/**
+ * BH 2018 SwingJS note: If additional final static Strings are added to this
+ * file, they should be added to public static final String[] allTypes.
+ *
+ * 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";
+ public static final String PFAM = "PFAM";
+
+ /**
+ * RFAM ID
+ */
+ public static final String RFAM = "RFAM";
+
+ /**
+ * GeneDB ID
+ */
+ public static final String GENEDB = "GeneDB".toUpperCase();
+
+
+ /**
+ * Ensembl
+ */
+ public static final String ENSEMBL = "ENSEMBL";
+
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
+
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL, ENSEMBLGENOMES };
+
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+
+ public static final String[] allTypes = new String[] {
+ UNIPROT, UP_NAME, UNIPROTKB,
+ EMBLCDSProduct, PDB, EMBL,
+ EMBLCDS, PFAM, RFAM,
+ GENEDB, ENSEMBL, ENSEMBLGENOMES
+ };
+
+public static final String PROTEINDBSKEYS, DNACODINGDBSKEYS;
+
+public static final String[] PROMTYPES;
+
+
+public static final int UNIPROT_MASK = 1;
+
+public static final int ENSEMBL_MASK = 2;
+
+public static final int ALL_MASKS = UNIPROT_MASK | ENSEMBL_MASK;
+
+public static final String PDB_CANONICAL_NAME = PDB;
+
+static {
+ // BH 2019.01.25 trying to speed this up
+ String s = ";";
+ for (int i = PROTEINDBS.length; --i >= 0;)
+ s += PROTEINDBS[i] + ";";
+ PROTEINDBSKEYS = s;
+
+ s = ";";
+ for (int i = DNACODINGDBS.length; --i >= 0;)
+ s += DNACODINGDBS[i] + ";";
+ DNACODINGDBSKEYS = s;
+
+ PROMTYPES = new String[] { null, ";" + UNIPROT + ";", ";" + ENSEMBL + ";" , ";" + UNIPROT + ";" + ENSEMBL + ";" };
+}
+
+ public static String[] allSourcesFromReflection;
+
+ public static String[] allSources()
+
+ {
+ /**
+ * @j2sNative
+ *
+ * return C$.allTypes;
+ *
+ */
+
+ {
+ if (allSourcesFromReflection == null)
+ {
+ List<String> src = new ArrayList<>();
+ for (Field f : DBRefSource.class.getFields())
+ {
+ if (String.class.equals(f.getType()))
+ {
+ try
+ {
+ src.add((String) f.get(null));
+ } catch (Exception x)
+ {
+ x.printStackTrace();
+ }
+ }
+ }
+ allSourcesFromReflection = src.toArray(new String[0]);
+ }
+ return allSourcesFromReflection;
+ }
+ }
+
+
}
git://source.jalview.org / jalview.git / blobdiff