X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=7a301413aabc04a50e636325a7588295187c110b;hb=052b4c8f68f726eb02d69ce28c61f5b9dd05e54d;hp=b9442df0828a95ba76b92a2fbf84f28a82e13395;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b9442df..7a30141 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,128 +1,124 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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)
- *
- * @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.
- */
- 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";
-
- /**
- * GeneDB ID
- */
- public static final String GENEDB = "GeneDB";
-
- /**
- * 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 };
-
- /**
- * 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.
- * Value of property indicates maximum number of accession codes to send at a
- * time.
- */
- public static final Object MULTIACC = "MULTIACC";
-}
+/*
+ * 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 .
+ * 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)
+ * 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, 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 String[] allSources()
+ {
+ List 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();
+ }
+ }
+ }
+ return src.toArray(new String[0]);
+ }
+}