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Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.ws.ebi

File hmmerClient.java

 

Coverage histogram

../../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

26
87
4
1
319
189
26
0.3
21.75
4
6.5

Classes

Class Line # Actions
hmmerClient 26 87 26
0.00%
 

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1    package jalview.ws.ebi;
2   
3    import jalview.datamodel.AlignmentI;
4    import jalview.io.AppletFormatAdapter;
5    import jalview.io.DataSourceType;
6    import jalview.io.FileFormat;
7    import jalview.io.FileParse;
8   
9    import java.io.File;
10    import java.io.IOException;
11    import java.util.regex.Matcher;
12   
13    import org.apache.axis.transport.http.HTTPConstants;
14    import org.apache.http.Header;
15    import org.apache.http.HttpResponse;
16    import org.apache.http.client.methods.HttpGet;
17    import org.apache.http.client.methods.HttpPost;
18    import org.apache.http.entity.StringEntity;
19    import org.apache.http.impl.client.DefaultHttpClient;
20    import org.apache.http.util.EntityUtils;
21    import org.json.JSONArray;
22    import org.json.JSONObject;
23   
24    import compbio.util.FileUtil;
25   
 
26    public class hmmerClient
27    {
28    /**
29    * URLs for ebi api
30    */
31    static String baseUrl = "http://www.ebi.ac.uk/Tools/hmmer",
32    jackH = "/search/jackhmmer", phmmer = "/search/phmmer",
33    hmmscan = "/search/hmmscan", hmmsearch = "/search/hmmsearch";
34   
35    static String edseq = ">2abl_A mol:protein length:163 ABL TYROSINE KINASE\nMGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHS\nWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAE\nLVHHHSTVADGLITTLHYPAP";
36   
 
37  0 toggle public static void main(String[] args)
38    {
39  0 String instr = edseq;
40  0 if (args.length > 0)
41    {
42  0 try
43    {
44  0 instr = FileUtil.readFileToString(new File(args[0]));
45    } catch (Exception f)
46    {
47  0 f.printStackTrace();
48  0 return;
49    }
50    }
51  0 String res = new hmmerClient().submitJackhmmerSearch(instr,
52    "jackhmmer", "pdb", 5);
53  0 if (res == null)
54    {
55  0 throw new Error("Failed.");
56    }
57  0 System.out.println("Result\n" + res);
58  0 return;
59    }
60   
61    /**
62    *
63    * @param input
64    * - fasta or other formatted sequence or alignment
65    * @param algo
66    * - jackhmmer
67    * @param db
68    * - pdb, uniprot, etc.
69    * @param niter
70    * number of iterations
71    * @return job id
72    */
 
73  0 toggle String submitJackhmmerSearch(String input, String algo, String db,
74    int niter)
75    {
76  0 JSONObject inparam = new JSONObject();
77  0 HttpPost jackhp = new HttpPost(baseUrl + jackH);
78  0 String lastiter = null;
79  0 try
80    {
81  0 inparam.put("algo", algo);
82  0 inparam.put("seq", input);
83  0 inparam.put("seqdb", db);
84  0 inparam.put("iterations", niter);
85    // #Now POST the request and generate the search job.
86    // dumb json post service
87  0 jackhp.setHeader("content-type", "application/json");
88  0 jackhp.setEntity(new StringEntity(inparam.toString()));
89    } catch (Exception f)
90    {
91  0 f.printStackTrace();
92  0 return null;
93    }
94  0 HttpResponse r = null;
95  0 try
96    {
97  0 DefaultHttpClient httpCl = new DefaultHttpClient();
98   
99  0 r = httpCl.execute(jackhp);
100   
101    } catch (Exception x)
102    {
103  0 System.err.println("Submit failed.");
104  0 x.printStackTrace();
105    }
106  0 if (r.getStatusLine().getStatusCode() != 201)
107    {
108  0 throw new Error(r.toString());
109    }
110    // get uid for job
111  0 String jobid = null, redir = null;
112  0 try
113    {
114  0 JSONObject res = new JSONObject(EntityUtils.toString(r.getEntity()));
115  0 jobid = res.getString("job_id");
116   
117  0 Header[] loc;
118  0 if ((loc = r.getHeaders(HTTPConstants.HEADER_LOCATION)) != null
119    && loc.length > 0)
120    {
121  0 if (loc.length > 1)
122    {
123  0 System.err
124    .println("Ignoring additional "
125    + (loc.length - 1)
126    + " location(s) provided in response header ( next one is '"
127    + loc[1].getValue() + "' )");
128    }
129  0 redir = loc[0].getValue();
130    }
131    } catch (Exception x)
132    {
133  0 System.err.println("job id extraction failed.");
134  0 x.printStackTrace();
135    }
136  0 int tries = 0;
137  0 boolean finished = false;
138  0 JSONObject jobstate = null;
139  0 do
140    {
141  0 try
142    {
143  0 DefaultHttpClient httpCl = new DefaultHttpClient();
144   
145  0 HttpGet jackcheck = new HttpGet(redir);
146  0 jackcheck.setHeader("content-type", "application/json");
147  0 r = httpCl.execute(jackcheck);
148  0 switch (r.getStatusLine().getStatusCode())
149    {
150  0 case 200:
151  0 jobstate = new JSONObject(EntityUtils.toString(r.getEntity()));
152  0 String st = jobstate.getString("status");
153  0 if ("DONE".equals(st))
154    {
155  0 finished = true;
156    }
157  0 if ("ERROR".equals(st))
158    {
159  0 System.err.println("Error");
160  0 finished = true;
161    }
162  0 if ("PEND".equals(st) || "RUN".equals("st"))
163    {
164  0 JSONArray iters = jobstate.getJSONArray("result");
165  0 lastiter = iters.getJSONObject(iters.length() - 1).getString(
166    "uuid");
167  0 if (lastiter.length() > 0)
168    {
169  0 java.util.regex.Pattern p = java.util.regex.Pattern
170    .compile(".+(\\d+)");
171  0 Matcher m = p.matcher(lastiter);
172  0 if (m.matches())
173    {
174  0 System.out.println("On iteration " + m.group(1));
175    }
176    }
177    }
178  0 break;
179   
180  0 default:
181  0 tries++;
182  0 Thread.sleep(2000);
183    }
184    } catch (Exception q)
185    {
186  0 q.printStackTrace();
187  0 return null;
188    }
189  0 } while (!finished && tries < 50);
190   
191  0 if (!finished)
192    {
193  0 System.err.println("Giving up with job " + jobid + " at " + redir);
194  0 return null;
195    }
196    // get results
197    // http://www.ebi.ac.uk/Tools/hmmer/download/60048B38-7CEC-11E5-A230-CED6D26C98AD.5/score?format=csv
198    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
199    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
200    // 2 1cj1_J 1gri_B
201    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
202    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
203    // PROTEIN 2 1cj1_J 1gri_B
204    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
205    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
206    // phosphatase non-receptor typ 4h1o_A
207    //
208    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 2 2 7.6e-31 3.7e-28
209    // 102.219146728516 0.03 66 161 127 236 124 238 0.94 Tyrosine-protein
210    // phosphatase non-receptor typ 4h1o_A
211    //
212    // $ua->get( $rootUrl."/results/".$lastIteration->{uuid} . "/score"
213  0 return lastiter;
214    /*
215    * * #Job should have finished, but we may have converged, so get the last
216    * job. my $results = $json->decode( $response->content ); my $lastIteration
217    * = pop( @{ $results->{result} } ); #Now fetch the results of the last
218    * iteration my $searchResult = $ua->get( $rootUrl."/results/" .
219    * $lastIteration->{uuid} . "/score", 'Accept' => 'application/json' );
220    * unless( $searchResult->status_line eq "200 OK"){ die
221    * "Failed to get search results\n"; }
222    *
223    * #Decode the content of the full set of results $results = $json->decode(
224    * $searchResult->content ); print
225    * "Matched ".$results->{'results'}->{'stats'}->{'nincluded'}." sequences
226    * ($lastIteration->{uuid})!\n"; #Now do something more interesting with the
227    * results......
228    */
229    }
230   
231    /**
232    * retrieve an alignment annotated with scores from JackHmmer
233    *
234    * @param jobid
235    * @param dataset
236    * @return
237    */
 
238  0 toggle AlignmentI retrieveJackhmmerResult(String jobid, AlignmentI dataset)
239    throws OutOfMemoryError, IOException
240    {
241  0 AlignmentI searchResult = null;
242   
243    // get results
244   
245  0 searchResult = new AppletFormatAdapter().readFile(baseUrl
246    + "/download/" + jobid + "/score?format=afa&t=.gz",
247    DataSourceType.URL, FileFormat.Fasta);
248   
249    // TODO extract gapped columns as '.' - inserts to query profile
250   
251    // TODO match up jackhammer results to dataset.
252   
253    // do scores
254  0 FileParse jsonsource = new FileParse(baseUrl + "/download/" + jobid
255    + "/score?format=json", DataSourceType.URL);
256  0 if (!jsonsource.isValid())
257    {
258  0 throw new IOException("Couldn't access scores for Jackhammer results");
259    }
260  0 readJackhmmerScores(searchResult, jsonsource);
261  0 return searchResult;
262    }
263   
264    /**
265    * // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
266    *
267    * // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND
268    * PROTEIN // 2 1cj1_J 1gri_B // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62
269    * 212.4 0.1 2 2 1.6e-17 7.9e-15 // 58.8796501159668 0.01 7 66 157 215 153 216
270    * 0.95 GROWTH FACTOR BOUND // PROTEIN 2 1cj1_J 1gri_B // 4h1o_A 4h1o_A 560
271    * jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25 // 92.4921493530273
272    * 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein // phosphatase non-receptor
273    * typ 4h1o_A
274    */
275    private static String[] _hmmsearchcols = new String[] { "acc", "name", "" };
276   
 
277  0 toggle private void readJackhmmerScores(AlignmentI searchResult,
278    FileParse jsonsource) throws IOException, OutOfMemoryError
279    {
280  0 HmmerJSONProcessor hjp = new HmmerJSONProcessor(searchResult);
281  0 hjp.parseFrom(jsonsource);
282   
283    // http://www.ebi.ac.uk/Tools/hmmer/download/60048B38-7CEC-11E5-A230-CED6D26C98AD.5/score?format=csv
284    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 1 2 4.4e-46 2.1e-43
285    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
286    // 2 1cj1_J 1gri_B
287    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
288    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
289    // PROTEIN 2 1cj1_J 1gri_B
290    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
291    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
292    // phosphatase non-receptor typ 4h1o_A
293    // each line scores a fragment
294    // so for a combined score ?
295   
296    /**
297    * for a sequence q sort any t against q according to overallScore(q,t)
298    * maxFragment(q,t) in sequence features parlance: for alignment
299    * s.getFeature("overallScore",q) -> range on q and range on s
300    *
301    *
302    */
303   
304    // 151.758316040039 0.04 11 151 3 139 1 150 0.94 GROWTH FACTOR BOUND PROTEIN
305    // 2 1cj1_J 1gri_B
306    // 1gri_A 1gri_A 217 jackhmmer - 163 4.7e-62 212.4 0.1 2 2 1.6e-17 7.9e-15
307    // 58.8796501159668 0.01 7 66 157 215 153 216 0.95 GROWTH FACTOR BOUND
308    // PROTEIN 2 1cj1_J 1gri_B
309    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 1 2 7.5e-28 3.6e-25
310    // 92.4921493530273 0.00 65 161 20 122 17 124 0.95 Tyrosine-protein
311    // phosphatase non-receptor typ 4h1o_A
312    //
313    // 4h1o_A 4h1o_A 560 jackhmmer - 163 2.1e-57 197.3 0.0 2 2 7.6e-31 3.7e-28
314    // 102.219146728516 0.03 66 161 127 236 124 238 0.94 Tyrosine-protein
315    // phosphatase non-receptor typ 4h1o_A
316   
317    }
318   
319    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
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