public void add(GATKFeature record, boolean allowNameMismatch) {
if (record != null) {
if (!allowNameMismatch && !name.equals(record.getName()))
throw new ReviewedStingException(
"Attempt to add GATKFeature with non-matching name "
+ record.getName()
+ " to the track "
+ name);
}
records.add(record);
}
/**
* Fully qualified constructor: instantiates a new GATKFeatureRecordList object with specified
* GATKFeature track name, location on the reference, and list of associated GATKFeatures. This is
* a knee-deep COPY constructor: passed name, loc, and data element objects will be referenced
* from the created GATKFeatureRecordList (so that changing them from outside will affect data in
* this object), however, the data elements will be copied into a newly allocated list, so that
* the 'data' collection argument can be modified afterwards without affecting the state of this
* record list. WARNING: this constructor is (semi-)validating: passed name and location are
* allowed to be nulls (although it maybe unsafe, use caution), but if they are not nulls, then
* passed non-null GATKFeature data elements must have same track name, and their locations must
* overlap with the passed 'location' argument. Null data elements or null 'data' collection
* argument are allowed as well.
*
* @param name the name of the track
* @param data the collection of features at this location
* @param loc the location
*/
public RODRecordListImpl(String name, Collection<GATKFeature> data, GenomeLoc loc) {
this.records = new ArrayList<GATKFeature>(data == null ? 0 : data.size());
this.name = name;
this.location = loc;
if (data == null || data.size() == 0) return; // empty dataset, nothing to do
for (GATKFeature r : data) {
records.add(r);
if (r == null) continue;
if (!this.name.equals(r.getName())) {
throw new ReviewedStingException(
"Attempt to add GATKFeature with non-matching name "
+ r.getName()
+ " to the track "
+ name);
}
if (location != null && !location.overlapsP(r.getLocation())) {
throw new ReviewedStingException(
"Attempt to add GATKFeature that lies outside of specified interval "
+ location
+ "; offending GATKFeature:\n"
+ r.toString());
}
}
}