JAL-3076 fetch Ensembl sequence as JSON instead of Fasta

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

diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index 102dffb..c6b794a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -117,21 +117,9 @@ public class EnsemblLookup extends EnsemblRestClient
     return true;
   }
 
-  @Override
-  protected String getRequestMimeType(boolean multipleIds)
-  {
-    return "application/json";
-  }
-
-  @Override
-  protected String getResponseMimeType()
-  {
-    return "application/json";
-  }
-
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @return
@@ -143,7 +131,7 @@ public class EnsemblLookup extends EnsemblRestClient
 
   /**
    * Returns the gene id related to the given identifier (which may be for a
-   * gene, transcript or protein)
+   * gene, transcript or protein), or null if none is found
    * 
    * @param identifier
    * @param objectType
@@ -151,34 +139,7 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getGeneId(String identifier, String objectType)
   {
-    List<String> ids = Arrays.asList(new String[] { identifier });
-
-    BufferedReader br = null;
-    try
-    {
-      URL url = getUrl(identifier, objectType);
-      if (url != null)
-      {
-        br = getHttpResponse(url, ids);
-      }
-      return br == null ? null : parseResponse(br);
-    } catch (IOException e)
-    {
-      // ignore
-      return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
+    return parseGeneId(getResult(identifier, objectType));
   }
 
   /**
@@ -189,36 +150,32 @@ public class EnsemblLookup extends EnsemblRestClient
    * 
    * @param br
    * @return
-   * @throws IOException
    */
-  protected String parseResponse(BufferedReader br) throws IOException
+  protected String parseGeneId(JSONObject val)
   {
+    if (val == null)
+    {
+      return null;
+    }
     String geneId = null;
-    JSONParser jp = new JSONParser();
-    try
+    String type = val.get(OBJECT_TYPE).toString();
+    if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
     {
-      JSONObject val = (JSONObject) jp.parse(br);
-      String type = val.get(OBJECT_TYPE).toString();
-      if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
-      {
-        // got the gene - just returns its id
-        geneId = val.get(JSON_ID).toString();
-      }
-      else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
-      {
-        // got the transcript - return its (Gene) Parent
-        geneId = val.get(PARENT).toString();
-      }
-      else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
-      {
-        // got the protein - get its Parent, restricted to type Transcript
-        String transcriptId = val.get(PARENT).toString();
-        geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
-      }
-    } catch (ParseException e)
+      // got the gene - just returns its id
+      geneId = val.get(JSON_ID).toString();
+    }
+    else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
     {
-      // ignore
+      // got the transcript - return its (Gene) Parent
+      geneId = val.get(PARENT).toString();
     }
+    else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+    {
+      // got the protein - get its Parent, restricted to type Transcript
+      String transcriptId = val.get(PARENT).toString();
+      geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+    }
+
     return geneId;
   }