JAL-1705 refactoring etc for fetching Ensembl --> Uniprot

[jalview.git] / src / jalview / ext / ensembl / EnsemblCdna.java

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 467fc6d..856be74 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -4,12 +4,24 @@ import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
+import java.util.Arrays;
 import java.util.List;
 
 import com.stevesoft.pat.Regex;
 
+/**
+ * A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
+ * sequence that is transcribed to RNA, but not necessarily translated to
+ * protein)
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblCdna extends EnsemblSeqProxy
 {
+  private static final List<String> CROSS_REFERENCES = Arrays
+          .asList(new String[] { "Uniprot/SWISSPROT", "Uniprot/SPTREMBL" });
+
   /*
    * accepts ENST or ENSTG with 11 digits
    * or ENSMUST or similar for other species
@@ -26,11 +38,24 @@ public class EnsemblCdna extends EnsemblSeqProxy
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
   public EnsemblCdna()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblCdna(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -92,7 +117,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   protected List<String> getCrossReferenceDatabases()
   {
-    return super.getCrossReferenceDatabases();
+    return CROSS_REFERENCES;
     // 30/01/16 also found Vega_transcript, OTTT, ENS_LRG_transcript, UCSC,
     // HGNC_trans_name, RefSeq_mRNA, RefSeq_mRNA_predicted
   }