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

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

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index aa5e0ab..3b32797 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -29,6 +29,9 @@ import com.stevesoft.pat.Regex;
  */
 public class EnsemblGene extends EnsemblSeqProxy
 {
+  private static final List<String> CROSS_REFERENCES = Arrays
+          .asList(new String[] { "CCDS" });
+
   private static final String GENE_PREFIX = "gene:";
 
   /*
@@ -332,7 +335,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     /*
      * fetch and save cross-references
      */
-    super.getCrossReferences(transcript);
+    new EnsemblCdna(getDomain()).getCrossReferences(transcript);
 
     /*
      * and finally fetch the protein product and save as a cross-reference
@@ -468,7 +471,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     // found these for ENSG00000157764 on 30/01/2016:
     // return new String[] {"Vega_gene", "OTTG", "ENS_LRG_gene", "ArrayExpress",
     // "EntrezGene", "HGNC", "MIM_GENE", "MIM_MORBID", "WikiGene"};
-    return super.getCrossReferenceDatabases();
+    return CROSS_REFERENCES;
   }
 
   /**