From 245c9609dc00df56054b35e76aff48a2dda0be50 Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 20 Oct 2014 12:13:06 +0100
Subject: [PATCH] Modifed the way Intermine.java parse alignment data

---
 .gitignore                              |    3 ++-
 src/jalview/ws/dbsources/Intermine.java |   30 ++++++++++++++++++++++++------
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/.gitignore b/.gitignore
index 46d39d0..78a6a7e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,4 +4,5 @@
 .externalToolBuilders/Jalview Release indices [Builder].launch
 /.DS_Store
 /.com.apple.timemachine.supported
-.settings/
\ No newline at end of file
+.settings/
+.gitattributes
\ No newline at end of file
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
-- 
1.7.10.2