import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.JSONUtils;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.JSONUtils;
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
- JSONArray responses = (JSONArray) jp.parse(br);
- Iterator rvals = responses.iterator();
- while (rvals.hasNext())
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ if (rvals == null)
String type = obj.get("feature_type").toString();
int start = Integer.parseInt(obj.get("start").toString());
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
String alleles = JSONUtils
String type = obj.get("feature_type").toString();
int start = Integer.parseInt(obj.get("start").toString());
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
String alleles = JSONUtils
String desc = getFirstNotNull(obj, "alleles", "external_name",
JSON_ID);
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
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);
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
- protected String getFirstNotNull(JSONObject obj, String... keys)
+ @SuppressWarnings("unchecked")
+ protected String getFirstNotNull(Map<String, Object> obj, String... keys)
- protected void setFeatureAttribute(SequenceFeature sf, JSONObject obj,
+ protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,