JAL-3076 fetch Ensembl sequence as JSON instead of Fasta

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

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 7570822..582eac6 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -22,9 +22,11 @@ package jalview.ext.ensembl;
 
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.io.FileParse;
 
+import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -82,14 +84,15 @@ class EnsemblFeatures extends EnsemblRestClient
   public AlignmentI getSequenceRecords(String query) throws IOException
   {
     // TODO: use a vararg String... for getSequenceRecords instead?
-    List<String> queries = new ArrayList<String>();
+    List<String> queries = new ArrayList<>();
     queries.add(query);
-    FileParse fp = getSequenceReader(queries);
-    if (fp == null || !fp.isValid())
+    BufferedReader fp = getSequenceReader(queries);
+    if (fp == null)
     {
       return null;
     }
-    FeaturesFile fr = new FeaturesFile(fp);
+    FeaturesFile fr = new FeaturesFile(
+            new FileParse(fp, null, DataSourceType.URL));
     return new Alignment(fr.getSeqsAsArray());
   }
 
@@ -109,9 +112,17 @@ class EnsemblFeatures extends EnsemblRestClient
     urlstring.append("?content-type=text/x-gff3");
 
     /*
+     * specify object_type=gene in case is shared by transcript and/or protein;
+     * currently only fetching features for gene sequences;
+     * refactor in future if needed to fetch for transcripts
+     */
+    urlstring.append("&").append(OBJECT_TYPE).append("=")
+            .append(OBJECT_TYPE_GENE);
+
+    /*
      * specify  features to retrieve
      * @see http://rest.ensembl.org/documentation/info/overlap_id
-     * could make the list a configurable entry in jalview.properties
+     * could make the list a configurable entry in .jalview_properties
      */
     for (EnsemblFeatureType feature : featuresWanted)
     {
@@ -132,13 +143,13 @@ class EnsemblFeatures extends EnsemblRestClient
    * describes the required encoding of the response.
    */
   @Override
-  protected String getRequestMimeType(boolean multipleIds)
+  protected String getRequestMimeType()
   {
     return "text/x-gff3";
   }
 
   /**
-   * Returns the MIME type for GFF3.
+   * Returns the MIME type for GFF3
    */
   @Override
   protected String getResponseMimeType()