#include <alignment/datastructures/anchoring/ClusterList.hpp>

ClusterList::ClusterList()
{
    lowerSizeLimit = 20;
    lowerSizeLimitNumAnchors = 1;
    curp = cure = 0;
    onContigStart = true;
    curIndex = 0;
}

void ClusterList::Clear()
{
    onContigStart = true;
    numBases.clear();
    startPos.clear();
    numAnchors.clear();
}

bool ClusterList::Store(int n, DNALength p, DNALength e, int b)
{
    bool intervalIsEclipsed = true;
    bool intervalEclipses = false;
    if (onContigStart == true) {
        curp = p;
        cure = e;
        intervalIsEclipsed = false;
    } else {
        if (curp <= p and cure >= e) {
            intervalIsEclipsed = true;
        } else {
            if (p <= curp and e >= cure) {
                intervalEclipses = true;
            }
            intervalIsEclipsed = false;
        }
    }
    if (intervalIsEclipsed == false) {
        //
        // The current interval is unique: it does not eclipse any
        // other intervals and is not eclipsed by any.
        //
        if (n >= lowerSizeLimit) {
            if (intervalEclipses == false or onContigStart) {
                numBases.push_back(n);
                startPos.push_back(p);
                numAnchors.push_back(b);
                onContigStart = false;
                //
                // Record where the last interval is.  Since ther intervals
                // are sorted by position, only need to compare against the
                // current interval to make sure they are not overlapping
                // other intervals.
                //
                curp = p;
                cure = e;
            } else {
                //
                // The new interval eclipses the last one added.
                //
                if (n > numBases[numBases.size() - 1]) {
                    numBases[numBases.size() - 1] = n;
                    startPos[startPos.size() - 1] = p;
                    numAnchors[numAnchors.size() - 1] = b;
                    curp = p;
                    cure = e;
                }
            }
        }
    }
    return !intervalIsEclipsed;
}

void ClusterList::ResetCoordinates() { onContigStart = true; }