X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=91b49ebef4b33ded9060d790cae8beec80f5bfc2;hb=6a951ef313becea88861eb3f48c244be82da1ca0;hp=d13f9c8c77d742acaf42e22544af2a61cb4de15e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index d13f9c8..91b49eb 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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;
@@ -36,12 +38,15 @@ public class DBRefSource
/**
* UNIPROT Entry Name
*/
- public static String UP_NAME = "UNIPROT_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";
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+
+ public static final String EMBLCDSProduct = "EMBLCDSProtein"
+ .toUpperCase();
/**
* PDB Entry Code
@@ -49,6 +54,11 @@ public class DBRefSource
public static String PDB = "PDB";
/**
+ * mmCIF Entry Code
+ */
+ public static String MMCIF = "mmCIF";
+
+ /**
* EMBL ID
*/
public static String EMBL = "EMBL";
@@ -71,69 +81,21 @@ public class DBRefSource
/**
* 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, 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";
+ public static final String GENEDB = "GeneDB".toUpperCase();
/**
- * database of amino acid sequences
+ * Ensembl
*/
- public static final Object PROTSEQDB = "PROTSQ";
+ public static final String ENSEMBL = "ENSEMBL";
/**
- * 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
+ * List of databases whose sequences might have coding regions annotated
*/
- public static final Object DOMAINDB = "DOMAIN";
+ public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+ ENSEMBL };
- /**
- * 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";
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
- /**
- * DB query returns an alignment for each accession provided.
- */
- public static final Object ALIGNMENTDB = "ALIGNMENTS";
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
}