package jalview.ws.slivkaws;
import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
: "Alignment Conservation");
if (conservation)
{
- setAlignAnalysisUI(new AlignAnalysisUIText(getServiceType(),
+ setAlignAnalysisUI(new AlignAnalysisUIText(service.getName(),
SlivkaAnnotationServiceInstance.class,
"Slivka.AACons", false, true, true, true, true, 2,
MessageManager.getString("label.aacon_calculations"),
}
Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
- new AnnotationFile().parseAnnotationFrom(aln, null, readerIn);
+ if (!new AnnotationFile().parseAnnotationFrom(aln, null, readerIn))
+ {
+ Cache.log.debug("No annotation from slivka job\n" + annotFile);
+ }
if (featFile != null)
{
- new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true);
+ if (!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());
}