JAL-2050 make SequenceFeature.score final, adjust constructor calls

[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 dda77d7..79d6c0a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -48,6 +48,8 @@ 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
@@ -468,11 +470,31 @@ 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)
+    {
+      for (Entry<String, String> entry : params.entrySet())
+      {
+        urlstring.append("&").append(entry.getKey()).append("=")
+                .append(entry.getValue());
+      }
+    }
+
     URL url = new URL(urlstring.toString());
     return url;
   }
 
   /**
+   * Override this method to add any additional x=y URL parameters needed
+   * 
+   * @return
+   */
+  protected Map<String, String> getAdditionalParameters()
+  {
+    return null;
+  }
+
+  /**
    * A sequence/id POST request currently allows up to 50 queries
    * 
    * @see http://rest.ensembl.org/documentation/info/sequence_id_post
@@ -669,7 +691,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       int newBegin = Math.min(mappedRange[0], mappedRange[1]);
       int newEnd = Math.max(mappedRange[0], mappedRange[1]);
       SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
-              group);
+              group, sf.getScore());
       targetSequence.addSequenceFeature(copy);
 
       /*