Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch

[jalview.git] / src / jalview / datamodel / DBRefSource.java

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b1824f7..7a30141 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -20,10 +20,17 @@
  */
 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)
+ * 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
  * 
@@ -33,109 +40,85 @@ 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";
+  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";
+  public static final String PFAM = "PFAM";
 
   /**
    * RFAM ID
    */
-  public static String RFAM = "RFAM";
+  public static final 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
+   * Ensembl
    */
-  public static final String[] DNACODINGDBS =
-  { EMBL, EMBLCDS, GENEDB };
-
-  public static final String[] CODINGDBS =
-  { EMBLCDS, GENEDB };
+  public static final String ENSEMBL = "ENSEMBL";
 
-  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, RFAM };
+  public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
 
   /**
-   * 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/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.
-   */
-  public static final Object MULTIACC = "MULTIACC";
-
-  /**
-   * DB query returns an alignment for each accession provided.
+   * List of databases whose sequences might have coding regions annotated
    */
-  public static final Object ALIGNMENTDB = "ALIGNMENTS";
+  public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
+      ENSEMBL, ENSEMBLGENOMES };
+
+  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<>();
+    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]);
+  }
 }