X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=a2243be9f9389d67fccbd216056d2448b07b35aa;hb=c14d9e8c9ff59de1857d4834ee70e80abf623415;hp=aaf0ada5660c8bdca325b7196da995f1019241d3;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index aaf0ada..a2243be 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,47 +1,103 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 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";
+  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";
+
+  /**
+   * mmCIF Entry Code
+   */
+  public static String MMCIF = "mmCIF";
+
   /**
    * 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();
+
+  /**
+   * 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 };
+
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+  public static final String[] PROTEINDBS = { UNIPROT, PDB, UNIPROTKB,
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
 }