1 package jalview.ws.slivkaws;
3 import jalview.api.FeatureColourI;
4 import jalview.bin.Cache;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentAnnotation;
7 import jalview.datamodel.SequenceI;
8 import jalview.datamodel.features.FeatureMatcherSetI;
9 import jalview.io.AnnotationFile;
10 import jalview.io.DataSourceType;
11 import jalview.io.FeaturesFile;
12 import jalview.util.MessageManager;
13 import jalview.ws.api.JobId;
14 import jalview.ws.api.SequenceAnnotationServiceI;
15 import jalview.ws.params.ArgumentI;
16 import jalview.ws.params.WsParamSetI;
17 import jalview.ws.uimodel.AlignAnalysisUIText;
19 import java.io.BufferedReader;
20 import java.io.ByteArrayInputStream;
21 import java.io.IOError;
22 import java.io.IOException;
23 import java.io.InputStream;
24 import java.io.InputStreamReader;
25 import java.util.Arrays;
26 import java.util.HashMap;
27 import java.util.List;
30 import uk.ac.dundee.compbio.slivkaclient.FormField;
31 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
32 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
33 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
34 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
36 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
38 public SlivkaAnnotationServiceInstance(SlivkaClient client,
39 SlivkaService service, boolean conservation)
41 super(client, service, !conservation ? "Annotations disorder"
42 : "Alignment Conservation");
45 setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
46 SlivkaAnnotationServiceInstance.class,
47 "Slivka.AACons", false, true, true, true, true, 2,
48 MessageManager.getString("label.aacon_calculations"),
49 MessageManager.getString("tooltip.aacon_calculations"),
50 MessageManager.getString("label.aacon_settings"),
51 MessageManager.getString("tooltip.aacon_settings")));
53 style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
57 public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
59 StringBuilder builder = new StringBuilder();
60 for (SequenceI seq : seqs)
62 builder.append(">").append(seq.getName()).append("\n");
63 builder.append(seq.getSequence()).append("\n");
65 InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
66 RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
67 SlivkaForm form = service.getForm();
68 HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
71 for (ArgumentI arg : paramset)
73 values.put(arg.getName(), arg.getValue());
76 for (FormField field : form.getFields())
78 switch (field.getType())
81 form.insert(field.getName(), file);
84 String value = values.get(field.getName());
85 form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
88 form.insert(field.getName(), field.valueOf(values.get(field.getName())));
91 return new JobId(service.getName(), service.getName(), form.submit());
95 public List<AlignmentAnnotation> getAnnotationResult(JobId job,
96 List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
97 Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
99 RemoteFile annotFile = null;
100 RemoteFile featFile = null;
103 List<RemoteFile> files = client.getJobResults(job.getJobId());
104 for (RemoteFile f : files)
106 if (f.getMimeType().equals("application/jalview-annotations"))
110 else if (f.getMimeType().equals("application/jalview-features"))
115 } catch (IOException e)
117 throw new IOError(e);
119 Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
120 BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
121 if (!new AnnotationFile().parseAnnotationFrom(aln, null, readerIn))
123 Cache.log.debug("No annotation from slivka job\n" + annotFile);
125 if (featFile != null)
127 if (!new FeaturesFile(featFile.getURL().toString(),
128 DataSourceType.URL).parse(aln, featureColours, true))
130 Cache.log.debug("No features from slivka job\n" + featFile);
133 return Arrays.asList(aln.getAlignmentAnnotation());