int end = Integer.parseInt(obj.get("end").toString());
String source = obj.get("source").toString();
String strand = obj.get("strand").toString();
+ Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToList((JSONArray) obj.get("alleles"));
String clinSig = JSONUtils
SequenceFeature sf = new SequenceFeature(type, desc, start, end,
source);
sf.setStrand("1".equals(strand) ? "+" : "-");
+ if (phase != null)
+ {
+ sf.setPhase(phase.toString());
+ }
setFeatureAttribute(sf, obj, "id");
setFeatureAttribute(sf, obj, "Parent");
setFeatureAttribute(sf, obj, "consequence_type");
}
/**
- * Returns the first non-null attribute found (if any) as a string
+ * Returns the first non-null attribute found (if any) as a string, formatted
+ * suitably for display as feature description or tooltip. Answers null if
+ * none of the attribute keys is present.
*
* @param obj
* @param keys
Object val = obj.get(key);
if (val != null)
{
- String s = val.toString();
+ String s = val instanceof JSONArray
+ ? JSONUtils.arrayToList((JSONArray) val)
+ : val.toString();
if (!s.isEmpty())
{
return s;