JAL-2679 use object_type=Transcript for lookup of Parent for Protein

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

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 577111e..24d1b95 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -48,8 +48,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
 
 /**
  * Base class for Ensembl sequence fetchers
@@ -61,10 +59,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 {
   private static final String ALLELES = "alleles";
 
-  protected static final String PARENT = "Parent";
-
-  protected static final String ID = "ID";
-
   protected static final String NAME = "Name";
 
   protected static final String DESCRIPTION = "description";
@@ -472,14 +466,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     urlstring.append("?type=").append(getSourceEnsemblType().getType());
     urlstring.append(("&Accept=text/x-fasta"));
 
-    Map<String, String> params = getAdditionalParameters();
-    if (params != null)
+    String objectType = getObjectType();
+    if (objectType != null)
     {
-      for (Entry<String, String> entry : params.entrySet())
-      {
-        urlstring.append("&").append(entry.getKey()).append("=")
-                .append(entry.getValue());
-      }
+      urlstring.append("&").append(OBJECT_TYPE).append("=")
+              .append(objectType);
     }
 
     URL url = new URL(urlstring.toString());
@@ -487,11 +478,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * Override this method to add any additional x=y URL parameters needed
+   * Override this method to specify object_type request parameter
    * 
    * @return
    */
-  protected Map<String, String> getAdditionalParameters()
+  protected String getObjectType()
   {
     return null;
   }
@@ -560,7 +551,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected MapList getGenomicRangesFromFeatures(SequenceI sourceSequence,
           String accId, int start)
   {
-    // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
     List<SequenceFeature> sfs = sourceSequence.getFeatures()
             .getPositionalFeatures();
     if (sfs.isEmpty())
@@ -572,7 +562,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * generously initial size for number of cds regions
      * (worst case titin Q8WZ42 has c. 313 exons)
      */
-    List<int[]> regions = new ArrayList<int[]>(100);
+    List<int[]> regions = new ArrayList<>(100);
     int mappedLength = 0;
     int direction = 1; // forward
     boolean directionSet = false;
@@ -899,7 +889,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected List<SequenceFeature> findFeatures(SequenceI sequence,
           String term, String parentId)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     List<SequenceFeature> sfs = sequence.getFeatures()
             .getFeaturesByOntology(term);