@SuppressWarnings("unchecked")
@Override
public IntervalAndSubIntervals<T> cloneShallow() {
IntervalAndSubIntervals<T> clone = (IntervalAndSubIntervals<T>) super.cloneShallow();
clone.reset();
return clone;
}
@SuppressWarnings("unchecked")
@Override
public IntervalAndSubIntervals<T> clone() {
IntervalAndSubIntervals<T> copy = (IntervalAndSubIntervals<T>) super.clone();
copy.reset();
for (T m : this) {
T mcopy = (T) m.clone();
mcopy.setParent(copy);
copy.add(mcopy);
}
return copy;
}
/** Apply a variant. */
@Override
@SuppressWarnings("unchecked")
public IntervalAndSubIntervals<T> apply(Variant variant) {
if (!shouldApply(variant)) return this;
IntervalAndSubIntervals<T> newMarker = (IntervalAndSubIntervals<T>) super.apply(variant);
if (newMarker == null) return null;
newMarker.reset();
for (T m : this) {
T mcopy = (T) m.apply(variant);
// Do not add if interval is completely removed
if (mcopy != null) {
mcopy.setParent(newMarker);
newMarker.add(mcopy);
}
}
return newMarker;
}
public IntervalAndSubIntervals(
Marker parent, int start, int end, boolean strandMinus, String id) {
super(parent, start, end, strandMinus, id);
reset();
}
public IntervalAndSubIntervals() {
super();
reset();
}