import jalview.ws.params.WsParamSetI;
import jalview.ws.uimodel.AlignAnalysisUIText;
-import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.IOError;
import java.io.IOException;
import java.io.InputStream;
-import java.io.InputStreamReader;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
throw new IOError(e);
}
Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
- BufferedReader readerIn = new BufferedReader(new InputStreamReader(annotFile.getContent()));
- if (!new AnnotationFile().parseAnnotationFrom(aln, null, readerIn))
+ 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)
+ 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);
- }
+ Cache.log.debug("No features from slivka job\n" + featFile);
}
return Arrays.asList(aln.getAlignmentAnnotation());
}