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?
- Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
+ MODE_ITERATOR, null);
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
- protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
- String key)
+ protected void setFeatureAttribute(SequenceFeature sf,
+ Map<String, Object> obj, String key)