X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FIntermine.java;h=0d9ce02a3a2c274aea3407d6d23d062c397ed050;hb=refs%2Fheads%2FJAL-1550_intermine-sequence-annotation-client;hp=e738adff24b2e1a2a66ea74ec0d16740186be9d3;hpb=f4ce96548d478b01489f7a9157badb6efb1362bd;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Intermine.java b/src/jalview/ws/dbsources/Intermine.java
index e738adf..0d9ce02 100644
--- a/src/jalview/ws/dbsources/Intermine.java
+++ b/src/jalview/ws/dbsources/Intermine.java
@@ -3,6 +3,7 @@ package jalview.ws.dbsources;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.Sequence;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.ws.intermine.IntermineFetchClient;
@@ -62,32 +63,45 @@ public class Intermine extends DbSourceProxyImpl // implements DbSourceProxy
     return false;
   }
 
+  @SuppressWarnings("unchecked")
   @Override
   public AlignmentI getSequenceRecords(String query) throws Exception
   {
     startQuery();
     String jsonString = IntermineFetchClient.fetchData(query);
-
-    Object sequenceString = "";
+    Sequence[] retrievedSeq = null;
+    String sequence = "";
+    String name = "";
     System.out.println("Found json: " + jsonString);
     org.json.simple.parser.JSONParser jsonParser = new org.json.simple.parser.JSONParser();
     try
     {
       JSONObject jobj = (JSONObject) jsonParser.parse(jsonString);
       JSONArray responses = (JSONArray) jobj.get("features");
+      int count = 0;
       for (Iterator<JSONObject> rvals = responses.iterator(); rvals
               .hasNext();)
       {
+        retrievedSeq = new Sequence[responses.size()];
+
         JSONObject feature = rvals.next();
-        Object seq = feature.get("seq");
-        System.out.println("Sequence : " + seq.toString());
+        // name = feature.get("name").toString();
+        name = "name";
+        sequence = feature.get("seq").toString();
+        int start = Integer.valueOf(feature.get("start").toString());
+        int end = Integer.valueOf(feature.get("end").toString());
+
+        retrievedSeq[count++] = new Sequence(name, sequence, start, end);
+
+        System.out.println("Sequence : " + sequence);
+
       }
     } catch (Exception e)
     {
       e.printStackTrace();
     }
     stopQuery();
-    return parseResult(sequenceString.toString());
+    return parseResult(retrievedSeq);
   }
 
   @Override
@@ -104,7 +118,11 @@ public class Intermine extends DbSourceProxyImpl // implements DbSourceProxy
   }
 
 
-
+  private Alignment parseResult(Sequence[] seqs)
+  {
+    Alignment sequences = new Alignment(seqs);
+    return sequences;
+  }
 
 
   @Override