package jalview.ws.slivkaws;
import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.io.AnnotationFile;
+import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
+import jalview.util.MessageManager;
import jalview.ws.api.JobId;
import jalview.ws.api.SequenceAnnotationServiceI;
import jalview.ws.params.ArgumentI;
import jalview.ws.params.WsParamSetI;
+import jalview.ws.uimodel.AlignAnalysisUIText;
import java.io.ByteArrayInputStream;
+import java.io.IOError;
+import java.io.IOException;
import java.io.InputStream;
+import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements SequenceAnnotationServiceI
{
- public SlivkaAnnotationServiceInstance(SlivkaClient client, SlivkaService service)
+ public SlivkaAnnotationServiceInstance(SlivkaClient client,
+ SlivkaService service, boolean conservation)
{
- super(client, service, "Annotations");
+ super(client, service, !conservation ? "Annotations disorder"
+ : "Alignment Conservation");
+ if (conservation)
+ {
+ setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
+ SlivkaAnnotationServiceInstance.class,
+ "Slivka.AACons", false, true, true, true, true, 2,
+ MessageManager.getString("label.aacon_calculations"),
+ MessageManager.getString("tooltip.aacon_calculations"),
+ MessageManager.getString("label.aacon_settings"),
+ MessageManager.getString("tooltip.aacon_settings")));
+ }
+ style = ServiceClient.SEQUENCEANNOTATIONWSCLIENT;
}
@Override
List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
{
- // TODO Auto-generated method stub
- return null;
+ RemoteFile annotFile = null;
+ RemoteFile featFile = null;
+ try
+ {
+ List<RemoteFile> files = client.getJobResults(job.getJobId());
+ for (RemoteFile f : files)
+ {
+ if (f.getMimeType().equals("application/jalview-annotations"))
+ {
+ annotFile = f;
+ }
+ else if (f.getMimeType().equals("application/jalview-features"))
+ {
+ featFile = f;
+ }
+ }
+ } catch (IOException e)
+ {
+ throw new IOError(e);
+ }
+ Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
+ if (annotFile == null
+ || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
+ {
+ Cache.log.debug("No annotation from slivka job\n" + annotFile);
+ }
+ if (featFile == null
+ || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
+ {
+ Cache.log.debug("No features from slivka job\n" + featFile);
+ }
+ return Arrays.asList(aln.getAlignmentAnnotation());
}
}