JAL-1705 reworked Ensembl clients now fetching and mapping features &

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

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 4cc43ab..5238f98 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -1,6 +1,7 @@
 package jalview.ext.ensembl;
 
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 
 public class EnsemblProtein extends EnsemblSeqProxy
 {
@@ -22,6 +23,9 @@ public class EnsemblProtein extends EnsemblSeqProxy
     return EnsemblSeqType.PROTEIN;
   }
 
+  /**
+   * Returns false, as this fetcher does not retrieve DNA sequences.
+   */
   @Override
   public boolean isDnaCoding()
   {
@@ -37,4 +41,27 @@ public class EnsemblProtein extends EnsemblSeqProxy
     return "ENSP00000288602";
   }
 
+  /**
+   * Overrides base class method to do nothing - genomic features are not
+   * applicable to the protein product sequence
+   */
+  @Override
+  protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
+  {
+  }
+
+  @Override
+  protected EnsemblFeatureType[] getFeaturesToFetch()
+  {
+    // not applicable - can't fetch genomic features for a protein sequence
+    return null;
+  }
+
+  @Override
+  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  {
+    // not applicable - protein sequence is not a 'subset' of genomic sequence
+    return false;
+  }
+
 }