import java.util.List;
import java.util.Set;
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
+import jalview.io.FeaturesFile;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
return false;
}
- public AlignmentI getAlignment(WSJob job) throws IOException
+ public AlignmentI getAlignment(WSJob job, List<SequenceI> dataset,
+ AlignViewportI viewport) throws IOException
{
Collection<RemoteFile> files;
var slivkaJob = client.getJob(job.getJobId());
return null;
}
+ public FeaturesFile getFeaturesFile(WSJob job,
+ List<SequenceI> dataset, AlignViewportI viewport) throws IOException
+ {
+ var slivkaJob = client.getJob(job.getJobId());
+ Collection<RemoteFile> files = slivkaJob.getResults();
+ for (RemoteFile f : files)
+ {
+ if (f.getMediaType().equals("application/jalview-features"))
+ {
+ return new FeaturesFile(f.getContentUrl().toString(), DataSourceType.URL);
+ }
+ }
+ return null;
+ }
+
+ public List<AlignmentAnnotation> getAnnotationFile(WSJob job,
+ List<SequenceI> dataset, AlignViewportI viewport) throws IOException
+ {
+ var slivkaJob = client.getJob(job.getJobId());
+ Collection<RemoteFile> files = slivkaJob.getResults();
+ for (RemoteFile f : files)
+ {
+ if (f.getMediaType().equals("application/jalview-annotations"))
+ {
+ Alignment aln = new Alignment(dataset.toArray(new SequenceI[0]));
+ AnnotationFile af = new AnnotationFile();
+ boolean valid = af.readAnnotationFileWithCalcId(aln, service.getId(),
+ f.getContentUrl().toString(), DataSourceType.URL);
+ if (valid)
+ {
+ return Arrays.asList(aln.getAlignmentAnnotation());
+ }
+ else
+ {
+ throw new IOException("Unable to read annotations from file " +
+ f.getContentUrl().toString());
+ }
+ }
+ }
+ return null;
+ }
+
@Override
public String toString()
{