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.util.MessageManager;
12 import jalview.ws.api.JobId;
13 import jalview.ws.api.SequenceAnnotationServiceI;
14 import jalview.ws.params.ArgumentI;
15 import jalview.ws.params.WsParamSetI;
16 import jalview.ws.uimodel.AlignAnalysisUIText;
18 import java.io.BufferedReader;
19 import java.io.ByteArrayInputStream;
20 import java.io.IOError;
21 import java.io.IOException;
22 import java.io.InputStream;
23 import java.io.InputStreamReader;
24 import java.util.Arrays;
25 import java.util.HashMap;
26 import java.util.List;
29 import uk.ac.dundee.compbio.slivkaclient.FormField;
30 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
31 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
32 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
33 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
35 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
37 public SlivkaAnnotationServiceInstance(SlivkaClient client,
38 SlivkaService service, boolean conservation)
40 super(client, service, !conservation ? "Annotations disorder"
41 : "Alignment Conservation");
44 setAlignAnalysisUI(new AlignAnalysisUIText(getServiceType(),
45 SlivkaAnnotationServiceInstance.class,
46 "Slivka.AACons", false, true, true, true, true, 2,
47 MessageManager.getString("label.aacon_calculations"),
48 MessageManager.getString("tooltip.aacon_calculations"),
49 MessageManager.getString("label.aacon_settings"),
50 MessageManager.getString("tooltip.aacon_settings")));
52 style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
56 public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
58 StringBuilder builder = new StringBuilder();
59 for (SequenceI seq : seqs)
61 builder.append(">").append(seq.getName()).append("\n");
62 builder.append(seq.getSequence()).append("\n");
64 InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
65 RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
66 SlivkaForm form = service.getForm();
67 HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
70 for (ArgumentI arg : paramset)
72 values.put(arg.getName(), arg.getValue());
75 for (FormField field : form.getFields())
77 switch (field.getType())
80 form.insert(field.getName(), file);
83 String value = values.get(field.getName());
84 form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
87 form.insert(field.getName(), field.valueOf(values.get(field.getName())));
90 return new JobId(service.getName(), service.getName(), form.submit());
94 public List<AlignmentAnnotation> getAnnotationResult(JobId job,
95 List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
96 Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
98 RemoteFile annotFile = null;
99 RemoteFile featFile = null;
102 List<RemoteFile> files = client.getJobResults(job.getJobId());
103 for (RemoteFile f : files)
105 if (f.getMimeType().equals("application/jalview-annotations"))
109 else if (f.getMimeType().equals("application/jalview-features"))
114 } catch (IOException e)
116 throw new IOError(e);
118 Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
119 BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
120 new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
121 if (featFile != null)
123 new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
125 return Arrays.asList(aln.getAlignmentAnnotation());