#ifndef _BLASR_FIND_MAX_INTERVAL_HPP_
#define _BLASR_FIND_MAX_INTERVAL_HPP_

#include <cmath>
#include <fstream>
#include <iostream>

#include <semaphore.h>

#include <alignment/algorithms/anchoring/BasicEndpoint.hpp>
#include <alignment/algorithms/anchoring/GlobalChain.hpp>
#include <alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp>
#include <alignment/datastructures/anchoring/ClusterList.hpp>
#include <alignment/datastructures/anchoring/MatchPos.hpp>
#include <alignment/datastructures/anchoring/WeightedInterval.hpp>
#include <alignment/statistics/VarianceAccumulator.hpp>

unsigned int NumRemainingBases(DNALength curPos, DNALength intervalLength);

class IntervalSearchParameters
{
public:
    bool advanceHalf;
    int globalChainType;
    float maxPValue;
    float aboveCategoryPValue;
    bool warp;
    bool fastMaxInterval;
    bool aggressiveIntervalCut;
    int verbosity;
    float ddPValueThreshold;
    IntervalSearchParameters();
};

template <typename T_Sequence, typename T_AnchorList>
class DefaultWeightFunction
{
public:
    float operator()(T_Sequence &text, T_Sequence &read, T_AnchorList matchPosList);
};

template <typename T_Pos>
class MatchPosQueryOrderFunctor
{
public:
    int operator()(T_Pos &pos);
};

template <typename T_MatchList>
void PrintLIS(T_MatchList &matchList, DNALength curPos, DNALength curGenomePos,
              DNALength nextGenomePos, DNALength clp, DNALength cle);

template <typename T_MatchList, typename T_SequenceDB>
void FilterMatchesAsLIMSTemplateSquare(T_MatchList &matches, DNALength queryLength,
                                       DNALength limsTemplateLength, T_SequenceDB &seqDB);

template <typename T_MatchList, typename T_SequenceBoundaryDB>
void AdvanceIndexToPastInterval(T_MatchList &pos, DNALength nPos, DNALength intervalLength,
                                DNALength contigLength, T_SequenceBoundaryDB &SeqBoundary,
                                DNALength startIndex, DNALength startIntervalBoundary,
                                DNALength &index, DNALength &indexIntervalBoundary);

template <typename T_MatchList>
int RemoveZeroLengthAnchors(T_MatchList &matchList);

template <typename T_MatchList>
int RemoveOverlappingAnchors(T_MatchList &matchList);

template <typename T_MatchList>
int SumAnchors(T_MatchList &pos, int start, int end);

template <typename T_MatchList, typename T_SequenceBoundaryDB>
void StoreLargestIntervals(T_MatchList &pos,
                           // End search for intervals at boundary positions
                           // stored in seqBoundaries
                           T_SequenceBoundaryDB &ContigStartPos,
                           // parameters
                           // How many values to search through for a max set.
                           DNALength intervalLength,
                           // How many sets to keep track of
                           int minSize, std::vector<DNALength> &start, std::vector<DNALength> &end);

template <typename T_MatchList, typename T_PValueFunction, typename T_WeightFunction,
          typename T_SequenceBoundaryDB, typename T_ReferenceSequence, typename T_Sequence>
int FindMaxIncreasingInterval(
    // Input
    // readDir is used to indicate if the interval that is being stored is
    // in the forward or reverse strand.  This is important later when
    // refining alignments so that the correct sequence is aligned back
    // to the reference.
    int readDir, T_MatchList &pos,
    // How many values to search through for a max set.
    DNALength intervalLength,
    // How many sets to keep track of
    VectorIndex nBest,
    // End search for intervals at boundary positions
    // stored in seqBoundaries
    T_SequenceBoundaryDB &ContigStartPos,
    // First rand intervals by their p-value
    T_PValueFunction &MatchPValueFunction,
    // When ranking intervals, sum over weights determined by MatchWeightFunction
    T_WeightFunction &MatchWeightFunction,
    // Output.
    // The increasing interval coordinates,
    // in order by queue weight.
    WeightedIntervalSet &intervalQueue, T_ReferenceSequence &reference, T_Sequence &query,
    IntervalSearchParameters &params,
    std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer, ClusterList &clusterList,
    VarianceAccumulator<float> &accumPValue, VarianceAccumulator<float> &accumWeight,
    VarianceAccumulator<float> &accumNumAnchorBases);

template <typename T_MatchList, typename T_PValueFunction, typename T_WeightFunction,
          typename T_SequenceBoundaryDB, typename T_ReferenceSequence, typename T_Sequence>
int FastFindMaxIncreasingInterval(
    int readDir, T_MatchList &pos, DNALength intervalLength, VectorIndex nBest,
    T_SequenceBoundaryDB &ContigStartPos, T_PValueFunction &MatchPValueFunction,
    T_WeightFunction &MatchWeightFunction, WeightedIntervalSet &intervalQueue,
    T_ReferenceSequence &reference, T_Sequence &query, IntervalSearchParameters &params,
    std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer, ClusterList &clusterList,
    VarianceAccumulator<float> &accumPValue, VarianceAccumulator<float> &accumWeight);

template <typename T_MatchList, typename T_PValueFunction, typename T_WeightFunction,
          typename T_SequenceBoundaryDB, typename T_ReferenceSequence, typename T_Sequence>
int ExhaustiveFindMaxIncreasingInterval(
    int readDir, T_MatchList &pos, DNALength intervalLength, VectorIndex nBest,
    T_SequenceBoundaryDB &ContigStartPos, T_PValueFunction &MatchPValueFunction,
    T_WeightFunction &MatchWeightFunction, WeightedIntervalSet &intervalQueue,
    T_ReferenceSequence &reference, T_Sequence &query, IntervalSearchParameters &params,
    std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer, ClusterList &clusterList,
    VarianceAccumulator<float> &accumPValue, VarianceAccumulator<float> &accumWeight);

#include "FindMaxIntervalImpl.hpp"
#endif