1 package jalview.ws.slivkaws;
3 import jalview.api.FeatureColourI;
4 import jalview.datamodel.Alignment;
5 import jalview.datamodel.AlignmentAnnotation;
6 import jalview.datamodel.SequenceI;
7 import jalview.datamodel.features.FeatureMatcherSetI;
8 import jalview.io.AnnotationFile;
9 import jalview.io.DataSourceType;
10 import jalview.io.FeaturesFile;
11 import jalview.ws.api.JobId;
12 import jalview.ws.api.SequenceAnnotationServiceI;
13 import jalview.ws.params.ArgumentI;
14 import jalview.ws.params.WsParamSetI;
16 import java.io.BufferedReader;
17 import java.io.ByteArrayInputStream;
18 import java.io.IOError;
19 import java.io.IOException;
20 import java.io.InputStream;
21 import java.io.InputStreamReader;
22 import java.util.Arrays;
23 import java.util.HashMap;
24 import java.util.List;
27 import uk.ac.dundee.compbio.slivkaclient.FormField;
28 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
29 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
30 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
31 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
33 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
35 public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
37 super(client, service, "Annotations disorder");
41 public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
43 StringBuilder builder = new StringBuilder();
44 for (SequenceI seq : seqs)
46 builder.append(">").append(seq.getName()).append("\n");
47 builder.append(seq.getSequence()).append("\n");
49 InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
50 RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
51 SlivkaForm form = service.getForm();
52 HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
55 for (ArgumentI arg : paramset)
57 values.put(arg.getName(), arg.getValue());
60 for (FormField field : form.getFields())
62 switch (field.getType())
65 form.insert(field.getName(), file);
68 String value = values.get(field.getName());
69 form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
72 form.insert(field.getName(), field.valueOf(values.get(field.getName())));
75 return new JobId(service.getName(), service.getName(), form.submit());
79 public List<AlignmentAnnotation> getAnnotationResult(JobId job,
80 List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
81 Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
83 RemoteFile annotFile = null;
84 RemoteFile featFile = null;
87 List<RemoteFile> files = client.getJobResults(job.getJobId());
88 for (RemoteFile f : files)
90 if (f.getMimeType().equals("application/jalview-annotations"))
94 else if (f.getMimeType().equals("application/jalview-features"))
99 } catch (IOException e)
101 throw new IOError(e);
103 Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
104 BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
105 new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
106 if (featFile != null)
108 new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
110 return Arrays.asList(aln.getAlignmentAnnotation());