X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=2f948841e7c05cff48b8cf977b1ea420f35bdf04;hb=afffa24481a7d3cb65ae41e0948c16a5f490f302;hp=e92b31ad3c408d814deb205295951df1c6dd8a6e;hpb=3aab6543bd51af64e17ff6950357112b5e0a5c33;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index e92b31a..2f94884 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,92 +1,164 @@
/*
- * 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 .
+ * 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)
+ * 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)
+ * 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
{
+
+
+
+ public static final String UNIPROT = "UNIPROT";
+ public static final String UP_NAME = "UNIPROT_NAME".toUpperCase();
/**
- * UNIPROT Accession Number
+ * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static String UNIPROT = "UNIPROT";
- /**
- * UNIPROT Entry Name
- */
- public static String UP_NAME = "UNIPROT_NAME";
- /**
- * 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";
- /**
- * 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";
- /**
- * 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
- */
- public static final Object DOMAINDB = "DOMAIN";
- /**
- * DB query can take multiple accession codes concatenated
- * by a separator.
- */
- public static final Object MULTIACC = "MULTIACC";
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+ public static final String ENSEMBL = "ENSEMBL";
+ public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
+ public static final String EMBL = "EMBL";
+ public static final String EMBLCDS = "EMBLCDS";
+ public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase();
+
+ public static final String PDB = "PDB";
+ public static final String PFAM = "PFAM";
+ public static final String RFAM = "RFAM";
+ public static final String GENEDB = "GeneDB".toUpperCase();
+
+ public static final String PDB_CANONICAL_NAME = PDB;
+
+
+ public static final String[] allSources = new String[] {
+ UNIPROT,
+ UP_NAME, UNIPROTKB,
+ ENSEMBL, ENSEMBLGENOMES,
+ EMBL, EMBLCDS, EMBLCDSProduct,
+ PDB, PFAM, RFAM, GENEDB
+ };
+
+ public static final int UNIPROT_MASK = 1<<0;
+ public static final int UP_NAME_MASK = 1<<1;
+ public static final int UNIPROT_KB_MASK = 1<<2;
+ public static final int ENSEMBL_MASK = 1<<3;
+ public static final int ENSEMBL_GENOMES_MASK = 1<<4;
+ public static final int EMBL_MASK = 1<<5;
+ public static final int EMBL_CDS_MASK = 1<<6;
+ public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
+ public static final int PDB_MASK = 1<<8;
+ public static final int PFAM_MASK = 1<<9;
+ public static final int RFAM_MASK = 1<<10;
+ public static final int GENE_DB_MASK = 1<<11;
+
+ public static final int MASK_COUNT = 12;
+
+ public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
+
+ public static int getSourceKey(String name) {
+ for (int i = 0; i < MASK_COUNT; i++) {
+ if (name.equals(allSources[i]))
+ {
+ return 1<= 0;)
+ {
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase() unnecessary here for allSources
+ {
+ // by convention, many secondary references inherit the primary
+ // reference's
+ // source string as a prefix for any version information from the
+ // secondary reference.
+ return false;
+ }
+ }
+ return true;
+}
+
+
+
+
}