X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=6982594f5623fb34e33e6a76458e2b71f218c6e8;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=0552b2ce675b391bc9a59f958b203a10c57f2e59;hpb=3448f766a6dfe127f1d01e533c14d10aede962fa;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0552b2c..6982594 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,28 +1,32 @@
 /*
- * 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)
+ * 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
 {
@@ -30,73 +34,111 @@ 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.
+   * 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
    */
   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";
+  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};
-  public static final String[] PROTEINSEQ = { UNIPROT, UNIPROTKB};
-  public static final String[] PROTEINSTR = { PDB };
-  public static final String[] DOMAINDBS = { PFAM };
+  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
+   * 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
+   * 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.
+   * 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";
 }