/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
/**
* 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
/**
* 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