X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=6982594f5623fb34e33e6a76458e2b71f218c6e8;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=e060b5431828e9f149f0f40ff7d2f957bfb64452;hpb=56d8f0b05df600ea54388d58cf505d911beb630a;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index e060b54..6982594 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,133 +1,144 @@
-/*
- * 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";
-
- /**
- * DB query returns an alignment for each accession provided.
- */
- public static final Object ALIGNMENTDB = "ALIGNMENTS";
-}
+/*
+ * 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;
+
+/**
+ * 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".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";
+
+ /**
+ * EMBL ID
+ */
+ public static String EMBL = "EMBL";
+
+ /**
+ * EMBLCDS ID
+ */
+ public static String EMBLCDS = "EMBLCDS";
+
+ /**
+ * PFAM ID
+ */
+ public static String PFAM = "PFAM";
+
+ /**
+ * RFAM ID
+ */
+ public static String RFAM = "RFAM";
+
+ /**
+ * GeneDB ID
+ */
+ public static final String GENEDB = "GeneDB".toUpperCase();
+
+ /**
+ * 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, EMBLCDSProduct };
+
+ public static final String[] PROTEINSEQ =
+ { UNIPROT, UNIPROTKB, EMBLCDSProduct };
+
+ public static final String[] PROTEINSTR =
+ { PDB };
+
+ public static final String[] DOMAINDBS =
+ { PFAM, RFAM };
+
+ /**
+ * 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/nucleotide 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";
+
+ /**
+ * DB query returns an alignment for each accession provided.
+ */
+ public static final Object ALIGNMENTDB = "ALIGNMENTS";
+}