import jalview.api.FeatureColourI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
}
if (format == null)
{
- Cache.log.warn(String.format(
+ Console.warn(String.format(
"Unknown input format %s, assuming fasta.",
fileParam.getMediaType()));
format = FileFormat.Fasta;
public void cancel(WebServiceJobHandle job)
throws IOException, UnsupportedOperationException
{
- Cache.log.warn(
+ Console.warn(
"slivka client does not support job cancellation");
}
}
return new FormatAdapter().readFile(f.getContentUrl().toString(),
DataSourceType.URL, format);
}
- Cache.log.warn("No alignment found on the server");
+ Console.warn("No alignment found on the server");
throw new IOException("no alignment found");
}
aln, service.getId(), f.getContentUrl().toString(),
DataSourceType.URL);
if (annotPresent)
- Cache.log.debug(format("loaded annotations for %s", service.getId()));
+ Console.debug(format("loaded annotations for %s", service.getId()));
}
else if (fmt.equalsIgnoreCase("jalview-features"))
{
DataSourceType.URL);
featPresent = ff.parse(aln, colours, true);
if (featPresent)
- Cache.log.debug(format("loaded features for %s", service.getId()));
+ Console.debug(format("loaded features for %s", service.getId()));
}
}
if (!annotPresent)
- Cache.log.debug(format("no annotations found for %s", service.getId()));
+ Console.debug(format("no annotations found for %s", service.getId()));
if (!featPresent)
- Cache.log.debug(format("no features found for %s", service.getId()));
+ Console.debug(format("no features found for %s", service.getId()));
return aln.getAlignmentAnnotation() != null ? Arrays.asList(aln.getAlignmentAnnotation())
: Collections.emptyList();
}