+
+ /**
+ * retrieve an alignment annotated with scores from JackHmmer
+ *
+ * @param jobid
+ * @param dataset
+ * @return
+ */
+ AlignmentI retrieveJackhmmerResult(String jobid, AlignmentI dataset)
+ throws OutOfMemoryError, IOException
+ {
+ AlignmentI searchResult = null;
+
+ // get results
+
+ searchResult = new AppletFormatAdapter().readFile(baseUrl
+ + "/download/" + jobid
+ + "/score?format=afa&t=.gz", FormatAdapter.URL, "FASTA");
+
+ // match up to dataset.
+
+ // and do scores
+
+ FileParse csvsource = new FileParse(baseUrl + "/download/" + jobid
+ + "/score?format=csv", FormatAdapter.URL);
+ if (!csvsource.isValid())
+ {
+ throw new IOException("Couldn't access scores for Jackhammer results");
+ }
+ readJackhmmerScores(searchResult, csvsource);
+ return searchResult;
+ }
+
+ 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");
+
+ }
+ // 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
+ // each line scores a fragment
+ // so for a combined score ?
+
+ /**
+ * for a sequence q sort any t against q according to overallScore(q,t)
+ * maxFragment(q,t) in sequence features parlance: for alignment
+ * s.getFeature("overallScore",q) -> range on q and range on s
+ *
+ *
+ */
+
+ // 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
+ //
+ // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 2 2 7.6e-31 3.7e-28
+ // 102.219146728516 0.03 66 161 127 236 124 238 0.94 Tyrosine-protein
+ // phosphatase non-receptor typ 4h1o_A
+
+ }
+