-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * 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
- /**\r
- * DB query returns an alignment for each accession provided.\r
- */\r
- public static final Object ALIGNMENTDB = "ALIGNMENTS";\r
-}\r
+/*
+ * 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.
+ *
+ * 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;
+
+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) <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 final String UNIPROT = "UNIPROT";
+
+ /**
+ * UNIPROT Entry 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 final String PDB = "PDB";
+
+ /**
+ * EMBL ID
+ */
+ public static final String EMBL = "EMBL";
+
+ /**
+ * EMBLCDS ID
+ */
+ public static final String EMBLCDS = "EMBLCDS";
+
+ /**
+ * PFAM ID
+ */
+ 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 };
+
+ 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