X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=0ac14e54e8ebc38f8f1722df64abef6782335297;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e92b31ad3c408d814deb205295951df1c6dd8a6e;hpb=3aab6543bd51af64e17ff6950357112b5e0a5c33;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index e92b31a..0ac14e5 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,92 +1,124 @@
 /*
- * 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;
+
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.List;
+
 /**
- * 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) <br/>
+ * TODO: replace with ontology to allow recognition of particular attributes
+ * (e.g. protein coding, alignment (ortholog db, paralog db, domain db),
+ * genomic, transcriptomic, 3D structure providing (PDB, MODBASE, etc) ..).
+ * 
  * @author JimP
- *
+ * 
  */
 public class DBRefSource
 {
   /**
    * UNIPROT Accession Number
    */
-  public static String UNIPROT = "UNIPROT";
+  public static final String UNIPROT = "UNIPROT";
+
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME";
+  public static final 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";
+  public static final String PDB = "PDB";
+
   /**
    * EMBL ID
    */
-  public static String EMBL = "EMBL";
+  public static final String EMBL = "EMBL";
+
   /**
    * EMBLCDS ID
    */
-  public static String EMBLCDS = "EMBLCDS";
+  public static final String EMBLCDS = "EMBLCDS";
+
   /**
    * PFAM ID
    */
-  public static String PFAM = "PFAM";
-  /**
-   * List of databases whose sequences might have coding regions annotated
-   */
-  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS};
-  public static final String[] CODINGDBS = { EMBLCDS};
-  public static final String[] PROTEINDBS = { UNIPROT, PDB };
-  public static final String[] PROTEINSEQ = { UNIPROT };
-  public static final String[] PROTEINSTR = { PDB };
-  public static final String[] DOMAINDBS = { PFAM };
-  /**
-   * 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 PFAM = "PFAM";
+
   /**
-   * database of amino acid sequences
+   * RFAM ID
    */
-  public static final Object PROTSEQDB = "PROTSQ";
+  public static final String RFAM = "RFAM";
+
   /**
-   * database of cDNA sequences
+   * GeneDB ID
    */
-  public static final Object CODINGSEQDB = "CODING";
+  public static final String GENEDB = "GeneDB".toUpperCase();
+
   /**
-   * database of na sequences with exon annotation
+   * Ensembl
    */
-  public static final Object DNACODINGSEQDB = "XONCODING";
+  public static final String ENSEMBL = "ENSEMBL";
+
+  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
+
   /**
-   * DB returns several sequences associated with a protein domain
-   */
-  public static final Object DOMAINDB = "DOMAIN";
-  /**
-   * DB query can take multiple accession codes concatenated
-   * by a separator.
+   * List of databases whose sequences might have coding regions annotated
    */
-  public static final Object MULTIACC = "MULTIACC";
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL };
+
+  public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+  public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB,
+      EMBLCDSProduct, ENSEMBL }; // Ensembl ENSP* entries are protein
+
+  public static String[] allSources()
+  {
+    List<String> src = new ArrayList<String>();
+    for (Field f : DBRefSource.class.getFields())
+    {
+      if (String.class.equals(f.getType()))
+      {
+        try
+        {
+          src.add((String) f.get(null));
+        } catch (Exception x)
+        {
+          x.printStackTrace();
+        }
+      }
+    }
+    return src.toArray(new String[0]);
+  }
 }