+ 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]));
+ BufferedReader in = new BufferedReader(new InputStreamReader(annotFile.getContent()));
+ AnnotationFile f = new AnnotationFile();
+ f.parseAnnotationFrom(aln, null, in);
+ return Arrays.asList(aln.getAlignmentAnnotation());