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 compbio.data.msa.Category;
  26 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  27 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  28 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  29
  30 public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
  31 {
  32   public SlivkaAnnotationServiceInstance(SlivkaClient client,
  33           SlivkaService service, String category)
  34   {
  35     super(client, service, category);
  36     if (category == Category.CATEGORY_CONSERVATION)
  37     {
  38       /* FIXME: the category name is hardcoded for AACon, names other than
  39        * "AAConWS" doesn't work. */
  40       setAlignAnalysisUI(new AlignAnalysisUIText(getName(),
  41               SlivkaAnnotationServiceInstance.class,
  42               "Slivka.AACons", false, true, true, true, true, 2,
  43               MessageManager.getString("label.aacon_calculations"),
  44               MessageManager.getString("tooltip.aacon_calculations"),
  45               MessageManager.getString("label.aacon_settings"),
  46               MessageManager.getString("tooltip.aacon_settings")));
  47     }
  48     style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
  49   }
  50
  51   @Override
  52   public JobId submitToService(List<SequenceI> seqs, WsParamSetI preset, List<ArgumentI> paramset) throws Throwable
  53   {
  54     return super.submit(seqs, preset, paramset);
  55   }
  56
  57   @Override
  58   public List<AlignmentAnnotation> getAnnotationResult(JobId job,
  59           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
  60           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
  61   {
  62     RemoteFile annotFile = null;
  63     RemoteFile featFile = null;
  64     try
  65     {
  66       List<RemoteFile> files = client.getJobResults(job.getJobId());
  67       for (RemoteFile f : files)
  68       {
  69         if (f.getMimeType().equals("application/jalview-annotations"))
  70         {
  71           annotFile = f;
  72         }
  73         else if (f.getMimeType().equals("application/jalview-features"))
  74         {
  75           featFile = f;
  76         }
  77       }
  78     } catch (IOException e)
  79     {
  80       throw new IOError(e);
  81     }
  82     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
  83     if (annotFile == null
  84         || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
  85     {
  86       Cache.log.debug("No annotation from slivka job\n" + annotFile);
  87     }
  88     if (featFile == null
  89         || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
  90     {
  91       Cache.log.debug("No features from slivka job\n" + featFile);
  92     }
  93     return Arrays.asList(aln.getAlignmentAnnotation());
  94   }
  95 }