X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxy.java;h=24d1b95304412e428b731ca6b78454cc7b97e04c;hb=17ff1f476e009b3a3c7e892e416edc2a4af8a2bc;hp=4da4f152401d1db11a292a3bf251cdf0a02d5fe0;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 4da4f15..24d1b95 100644
--- 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;
@@ -792,8 +782,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       return false;
     }
 
-    long start = System.currentTimeMillis();
-    // SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
+//    long start = System.currentTimeMillis();
     List<SequenceFeature> sfs = sourceSequence.getFeatures()
             .getPositionalFeatures();
     MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
@@ -805,10 +794,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);
-    System.out.println("transferFeatures (" + (sfs.size()) + " --> "
-            + targetSequence.getFeatures().getFeatureCount(true) + ") to "
-            + targetSequence.getName() + " took "
-            + (System.currentTimeMillis() - start) + "ms");
+//    System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+//            + targetSequence.getFeatures().getFeatureCount(true) + ") to "
+//            + targetSequence.getName() + " took "
+//            + (System.currentTimeMillis() - start) + "ms");
     return result;
   }
 
@@ -900,7 +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);