From 94b83b671d9714a407048da057db2a611e7efb6e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 4 Nov 2015 17:59:56 +0000
Subject: [PATCH] JAL-1950 hook up JSON result dump parser to hmmerClient

---
 src/jalview/ws/ebi/hmmerClient.java |   40 +++++++++++++++--------------------
 1 file changed, 17 insertions(+), 23 deletions(-)

diff --git a/src/jalview/ws/ebi/hmmerClient.java b/src/jalview/ws/ebi/hmmerClient.java
index 474f01b..37e6775 100644
--- a/src/jalview/ws/ebi/hmmerClient.java
+++ b/src/jalview/ws/ebi/hmmerClient.java
@@ -5,10 +5,8 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 
-import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
-import java.util.StringTokenizer;
 import java.util.regex.Matcher;
 
 import org.apache.axis.transport.http.HTTPConstants;
@@ -58,6 +56,7 @@ public class hmmerClient
     System.out.println("Result\n" + res);
     return;
   }
+
   /**
    * 
    * @param input
@@ -162,8 +161,8 @@ public class hmmerClient
           if ("PEND".equals(st) || "RUN".equals("st"))
           {
             JSONArray iters = jobstate.getJSONArray("result");
-            lastiter = iters.getJSONObject(iters.length() - 1)
-                    .getString("uuid");
+            lastiter = iters.getJSONObject(iters.length() - 1).getString(
+                    "uuid");
             if (lastiter.length() > 0)
             {
               java.util.regex.Pattern p = java.util.regex.Pattern
@@ -212,7 +211,7 @@ public class hmmerClient
     // $ua->get( $rootUrl."/results/".$lastIteration->{uuid} . "/score"
     return lastiter;
     /*
-     *  * #Job should have finished, but we may have converged, so get the last
+     * * #Job should have finished, but we may have converged, so get the last
      * job. my $results = $json->decode( $response->content ); my $lastIteration
      * = pop( @{ $results->{result} } ); #Now fetch the results of the last
      * iteration my $searchResult = $ua->get( $rootUrl."/results/" .
@@ -243,21 +242,21 @@ public class hmmerClient
     // get results
 
     searchResult = new AppletFormatAdapter().readFile(baseUrl
-            + "/download/" + jobid
-                    + "/score?format=afa&t=.gz", FormatAdapter.URL, "FASTA");
+            + "/download/" + jobid + "/score?format=afa&t=.gz",
+            FormatAdapter.URL, "FASTA");
 
-    // extract gapped columns as '.' - inserts to query profile
-    // match up to dataset.
+    // TODO extract gapped columns as '.' - inserts to query profile
 
-    // and do scores
+    // TODO match up jackhammer results to dataset.
 
-    FileParse csvsource = new FileParse(baseUrl + "/download/" + jobid
-            + "/score?format=csv", FormatAdapter.URL);
-    if (!csvsource.isValid())
+    // do scores
+    FileParse jsonsource = new FileParse(baseUrl + "/download/" + jobid
+            + "/score?format=json", FormatAdapter.URL);
+    if (!jsonsource.isValid())
     {
       throw new IOException("Couldn't access scores for Jackhammer results");
     }
-    readJackhmmerScores(searchResult, csvsource);
+    readJackhmmerScores(searchResult, jsonsource);
     return searchResult;
   }
 
@@ -273,18 +272,13 @@ public class hmmerClient
    * typ 4h1o_A
    */
   private static String[] _hmmsearchcols = new String[] { "acc", "name", "" };
+
   private void readJackhmmerScores(AlignmentI searchResult,
-          FileParse csvsource)
-          throws IOException
+          FileParse jsonsource) throws IOException, OutOfMemoryError
   {
-    String line;
-    BufferedReader rl = new BufferedReader(csvsource.getReader());
+    HmmerJSONProcessor hjp = new HmmerJSONProcessor(searchResult);
+    hjp.parseFrom(jsonsource);
 
-    while ((line = rl.readLine()) != null)
-    {
-      StringTokenizer st = new StringTokenizer(line, "\t");
-
-    }
     // http://www.ebi.ac.uk/Tools/hmmer/download/60048B38-7CEC-11E5-A230-CED6D26C98AD.5/score?format=csv
     // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
     // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
-- 
1.7.10.2