X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=6a676cfb30d75a907595d857c02daa56922a86a5;hb=16359e92bebc20edafc4958b7b580c8ceedd4d37;hp=d13f9c8c77d742acaf42e22544af2a61cb4de15e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index d13f9c8..6a676cf 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
@@ -71,28 +76,24 @@ public class DBRefSource
/**
* GeneDB ID
*/
- public static final String GENEDB = "GeneDB";
+ 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[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB };
- public static final String[] CODINGDBS =
- { EMBLCDS, GENEDB };
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB };
- public static final String[] PROTEINDBS =
- { UNIPROT, PDB, UNIPROTKB };
+ public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+ EMBLCDSProduct };
- public static final String[] PROTEINSEQ =
- { UNIPROT, UNIPROTKB };
+ public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB,
+ EMBLCDSProduct };
- public static final String[] PROTEINSTR =
- { PDB };
+ public static final String[] PROTEINSTR = { PDB };
- public static final String[] DOMAINDBS =
- { PFAM, RFAM };
+ public static final String[] DOMAINDBS = { PFAM, RFAM };
/**
* set of unique DBRefSource property constants. These could be used to