/**
* Perform a stabbing query on the node
*
* @param point the time to query at
* @return all intervals containing time
*/
public Markers stab(Integer point) {
Markers result = new Markers();
for (Entry<Marker, List<Marker>> entry : intervals.entrySet()) {
if (entry.getKey().intersects(point)) { //
for (Marker interval : entry.getValue()) result.add(interval);
} else if (entry.getKey().getStart() > point) break;
}
if (point < center && leftNode != null) result.add(leftNode.stab(point));
else if (point > center && rightNode != null) result.add(rightNode.stab(point));
return result;
}
/**
* Perform an interval intersection query on the node
*
* @param target: the interval to intersect
* @return all intervals containing 'target'
*/
public Markers query(Interval target) {
Markers result = new Markers();
for (Entry<Marker, List<Marker>> entry : intervals.entrySet()) {
if (entry.getKey().intersects(target)) {
for (Marker interval : entry.getValue()) result.add(interval);
} else if (entry.getKey().getStart() > target.getEnd()) break;
}
if (target.getStart() < center && leftNode != null) result.add(leftNode.query(target));
if (target.getEnd() > center && rightNode != null) result.add(rightNode.query(target));
return result;
}
/**
* Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF
* entries in 'results'
*/
protected void query(Interval queryMarker, int idx, Markers results) {
// Negative index? Nothing to do
if (idx < 0) return;
if (debug)
Gpr.debug("Node: " + toString(idx) + (results.isEmpty() ? "" : "\n\tResults: " + results));
// Check all intervals intersecting
queryIntersects(queryMarker, idx, results);
// Recurse left or right
int midPos = mid[idx];
if ((queryMarker.getEnd() < midPos) && (left[idx] >= 0)) {
query(queryMarker, left[idx], results);
}
if ((midPos < queryMarker.getStart()) && (right[idx] >= 0)) {
query(queryMarker, right[idx], results);
}
}
/** Query VCF entries intersecting 'marker' at node 'idx' */
protected void queryIntersects(Interval queryMarker, int idx, Markers results) {
if (intersectFilePosStart[idx] == null) return;
if (debug) Gpr.debug("queryIntersects\tidx: " + idx);
// Read entries from disk
List<VcfEntry> vcfEntries = readEntries(idx);
// Find matching entries
for (VcfEntry ve : vcfEntries) {
// If any variant within the vcfEntry intersects the query
// marker, we store this VCF entry as a result
for (Variant var : ve.variants()) {
if (var.intersects(queryMarker)) {
if (debug) Gpr.debug("\tAdding matching result: " + ve);
results.add(ve);
break; // Store this entry only once
}
}
// Past query's end coordinate? We don't need to look any further
if (queryMarker.getEnd() < ve.getStart()) return;
}
}
public IntervalNodeOri(Markers markers) {
intervals = new TreeMap<Marker, List<Marker>>();
SortedSet<Integer> endpoints = new TreeSet<Integer>();
for (Interval interval : markers) {
endpoints.add(interval.getStart());
endpoints.add(interval.getEnd());
}
if (endpoints.isEmpty()) {
center = 0;
return;
}
int median = getMedian(endpoints);
center = median;
Markers left = new Markers();
Markers right = new Markers();
for (Marker interval : markers) {
if (interval.getEnd() < median) left.add(interval);
else if (interval.getStart() > median) right.add(interval);
else {
List<Marker> posting = intervals.get(interval);
if (posting == null) {
posting = new ArrayList<Marker>();
intervals.put(interval, posting);
}
posting.add(interval);
}
}
if (left.size() > 0) leftNode = new IntervalNodeOri(left);
if (right.size() > 0) rightNode = new IntervalNodeOri(right);
}