From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 2 Nov 2015 15:12:26 +0000 (+0000)
Subject: JAL-1950 keys for hmm search score file parser. not quite decided if we’d be better... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bd14d85ec233ab83ba0a047e0d48055dda558cfc;p=jalview.git

JAL-1950 keys for hmm search score file parser. not quite decided if we’d be better off parsing the JSON dump to get these data.

---

diff --git a/src/jalview/ws/ebi/hmmerClient.java b/src/jalview/ws/ebi/hmmerClient.java
index c29d355..474f01b 100644
--- a/src/jalview/ws/ebi/hmmerClient.java
+++ b/src/jalview/ws/ebi/hmmerClient.java
@@ -246,6 +246,7 @@ public class hmmerClient
             + "/download/" + jobid
                     + "/score?format=afa&t=.gz", FormatAdapter.URL, "FASTA");
 
+    // extract gapped columns as '.' - inserts to query profile
     // match up to dataset.
 
     // and do scores
@@ -260,12 +261,25 @@ public class hmmerClient
     return searchResult;
   }
 
+  /**
+   * // 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 // 2 1cj1_J 1gri_B // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62
+   * 212.4 0.1 2 2 1.6e-17 7.9e-15 // 58.8796501159668 0.01 7 66 157 215 153 216
+   * 0.95 GROWTH FACTOR BOUND // PROTEIN 2 1cj1_J 1gri_B // 4h1o_A 4h1o_A 560
+   * jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25 // 92.4921493530273
+   * 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein // phosphatase non-receptor
+   * typ 4h1o_A
+   */
+  private static String[] _hmmsearchcols = new String[] { "acc", "name", "" };
   private void readJackhmmerScores(AlignmentI searchResult,
           FileParse csvsource)
           throws IOException
   {
     String line;
     BufferedReader rl = new BufferedReader(csvsource.getReader());
+
     while ((line = rl.readLine()) != null)
     {
       StringTokenizer st = new StringTokenizer(line, "\t");
@@ -273,6 +287,14 @@ public class hmmerClient
     }
     // 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
+    // 2 1cj1_J 1gri_B
+    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
+    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
+    // PROTEIN 2 1cj1_J 1gri_B
+    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
+    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
+    // phosphatase non-receptor typ 4h1o_A
     // each line scores a fragment
     // so for a combined score ?