From 5950febf61a94e527963a1eb68b0c59dd3387163 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 24 May 2017 15:45:16 +0100
Subject: [PATCH] JAL-2529 add object_type=cdna to EnsemblCdna parameters

---
 src/jalview/ext/ensembl/EnsemblCdna.java          |   20 +++++++++++++++++++
 src/jalview/ext/ensembl/EnsemblSeqProxy.java      |   22 +++++++++++++++++++++
 test/jalview/ext/ensembl/EnsemblSeqProxyTest.java |    2 --
 3 files changed, 42 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index dc000c6..6d031b7 100644
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -24,6 +24,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
+import java.util.HashMap;
+import java.util.Map;
+
 import com.stevesoft.pat.Regex;
 
 /**
@@ -44,6 +47,13 @@ public class EnsemblCdna extends EnsemblSeqProxy
   private static final Regex ACCESSION_REGEX = new Regex(
           "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
 
+  private static Map<String, String> params = new HashMap<String, String>();
+
+  static
+  {
+    params.put("object_type", "transcript");
+  }
+
   /*
    * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
@@ -128,4 +138,14 @@ public class EnsemblCdna extends EnsemblSeqProxy
     return false;
   }
 
+  /**
+   * Parameter object_type=cdna added to ensure cdna and not peptide is returned
+   * (JAL-2529)
+   */
+  @Override
+  protected Map<String, String> getAdditionalParameters()
+  {
+    return params;
+  }
+
 }
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index dda77d7..dcf2eb4 100644
--- 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
diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
index c8fa3c2..aa2c315 100644
--- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
+++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java
@@ -168,8 +168,6 @@ public class EnsemblSeqProxyTest
     Alignment ral = new Alignment(sqs);
     for (SequenceI tr : trueSqs)
     {
-      // 12/05/2017 failing for EnsemblCdna which is returning protein
-      // Ensembl helpdesk ticket 187998
       SequenceI[] rseq;
       Assert.assertNotNull(
               rseq = ral.findSequenceMatch(tr.getName()),
-- 
1.7.10.2