X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefSource.java;h=0ac14e54e8ebc38f8f1722df64abef6782335297;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=b9442df0828a95ba76b92a2fbf84f28a82e13395;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b9442df..0ac14e5 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -1,128 +1,124 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * 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.
- * 
- * 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/>.
- */
-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";
-
-  /**
-   * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
-   */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
-
-  /**
-   * 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";
-
-  /**
-   * GeneDB ID
-   */
-  public static final String GENEDB = "GeneDB";
-
-  /**
-   * 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 };
-
-  /**
-   * 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
-   */
-  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.
-   */
-  public static final Object MULTIACC = "MULTIACC";
-}
+/*
+ * 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.
+ *  
+ * 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/>.
+ * 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) <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 final String UNIPROT = "UNIPROT";
+
+  /**
+   * UNIPROT Entry 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 final String PDB = "PDB";
+
+  /**
+   * EMBL ID
+   */
+  public static final String EMBL = "EMBL";
+
+  /**
+   * EMBLCDS ID
+   */
+  public static final String EMBLCDS = "EMBLCDS";
+
+  /**
+   * PFAM ID
+   */
+  public static final String PFAM = "PFAM";
+
+  /**
+   * RFAM ID
+   */
+  public static final 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, 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]);
+  }
+}