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#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 ¶ms,
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 ¶ms,
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 ¶ms,
std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer, ClusterList &clusterList,
VarianceAccumulator<float> &accumPValue, VarianceAccumulator<float> &accumWeight);
#include "FindMaxIntervalImpl.hpp"
#endif
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