src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java

   1 package jalview.ws.slivkaws;
   2
   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;
  18
  19 import java.io.IOError;
  20 import java.io.IOException;
  21 import java.util.Arrays;
  22 import java.util.List;
  23 import java.util.Map;
  24
  25 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  26 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  27 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  28
  29 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  30 {
  31   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  32           SlivkaService service, boolean conservation)
  33   {
  34     super(client, service, !conservation ? "Protein sequence analysis"
  35         : "Alignment Conservation");
  36     if (conservation)
  37     {
  38       setAlignAnalysisUI(new AlignAnalysisUIText(getName(),
  39               SlivkaAnnotationServiceInstance.class,
  40               "Slivka.AACons", false, true, true, true, true, 2,
  41               MessageManager.getString("label.aacon_calculations"),
  42               MessageManager.getString("tooltip.aacon_calculations"),
  43               MessageManager.getString("label.aacon_settings"),
  44               MessageManager.getString("tooltip.aacon_settings")));
  45     }
  46     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  47   }
  48
  49   @Override
  50   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  51   {
  52     return super.submit(seqs, preset, paramset);
  53   }
  54
  55   @Override
  56   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  57           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  58           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  59   {
  60     RemoteFile annotFile = null;
  61     RemoteFile featFile = null;
  62     try
  63     {
  64       List<RemoteFile> files = client.getJobResults(job.getJobId());
  65       for (RemoteFile f : files)
  66       {
  67         if (f.getMimeType().equals("application/jalview-annotations"))
  68         {
  69           annotFile = f;
  70         }
  71         else if (f.getMimeType().equals("application/jalview-features"))
  72         {
  73           featFile = f;
  74         }
  75       }
  76     } catch (IOException e)
  77     {
  78       throw new IOError(e);
  79     }
  80     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
  81     if (annotFile == null
  82         || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
  83     {
  84       Cache.log.debug("No annotation from slivka job\n" + annotFile);
  85     }
  86     if (featFile == null
  87         || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
  88     {
  89       Cache.log.debug("No features from slivka job\n" + featFile);
  90     }
  91     return Arrays.asList(aln.getAlignmentAnnotation());
  92   }
  93 }