import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.JSONUtils;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.IOException;
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
+
List<String> queries = new ArrayList<>();
queries.add(query);
SequenceI seq = parseFeaturesJson(queries);
if (seq == null)
return null;
return new Alignment(new SequenceI[] { seq });
+
}
/**
if (rvals == null)
return null;
while (rvals.hasNext())
- {
+ {
try
{
Map<String, Object> obj = (Map<String, Object>) rvals.next();
{
type = SequenceOntologyI.CDS;
}
-
+
String desc = getFirstNotNull(obj, "alleles", "external_name",
JSON_ID);
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
+
} catch (Throwable t)
{
// ignore - keep trying other features