src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   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;
  17
  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;
  27 import java.util.Map;
  28
  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;
  34
  35 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  36 {
  37   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  38           SlivkaService service, boolean conservation)
  39   {
  40     super(client, service, !conservation ? "Annotations disorder"
  41             : "Alignment Conservation");
  42     if (conservation)
  43     {
  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")));
  51     }
  52   }
  53
  54   @Override
  55   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  56   {
  57     StringBuilder builder = new StringBuilder();
  58     for (SequenceI seq : seqs)
  59     {
  60       builder.append(">").append(seq.getName()).append("\n");
  61       builder.append(seq.getSequence()).append("\n");
  62     }
  63     InputStream stream = new ByteArrayInputStream(builder.toString().getBytes());
  64     RemoteFile file = client.uploadFile(stream, "input.fasta", "application/fasta");
  65     SlivkaForm form = service.getForm();
  66     HashMap<String, String> values = new HashMap<>(paramset != null ? paramset.size() : 0);
  67     if (paramset != null)
  68     {
  69       for (ArgumentI arg : paramset)
  70       {
  71         values.put(arg.getName(), arg.getValue());
  72       }
  73     }
  74     for (FormField field : form.getFields())
  75     {
  76       switch (field.getType())
  77       {
  78       case FILE:
  79         form.insert(field.getName(), file);
  80         break;
  81       case BOOLEAN:
  82         String value = values.get(field.getName());
  83         form.insert(field.getName(), value != null && !value.isBlank() ? true : false);
  84         break;
  85       default:
  86         form.insert(field.getName(), field.valueOf(values.get(field.getName())));
  87       }
  88     }
  89     return new JobId(service.getName(), service.getName(), form.submit());
  90   }
  91
  92   @Override
  93   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  94           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  95           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  96   {
  97     RemoteFile annotFile = null;
  98     RemoteFile featFile = null;
  99     try
 100     {
 101       List<RemoteFile> files = client.getJobResults(job.getJobId());
 102       for (RemoteFile f : files)
 103       {
 104         if (f.getMimeType().equals("application/jalview-annotations"))
 105         {
 106           annotFile = f;
 107         }
 108         else if (f.getMimeType().equals("application/jalview-features"))
 109         {
 110           featFile = f;
 111         }
 112       }
 113     } catch (IOException e)
 114     {
 115       throw new IOError(e);
 116     }
 117     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
 118     BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
 119     new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
 120     if (featFile != null)
 121     {
 122       new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
 123     }
 124     return Arrays.asList(aln.getAlignmentAnnotation());
 125   }
 126 }