#ifndef _BLASR_MAPPING_METRICS_HPP_
#define _BLASR_MAPPING_METRICS_HPP_

#include <ctime>
#include <iostream>
#include <map>
#include <vector>

//In order to use clock_gettime in LINUX, add -lrt
#ifdef __APPLE__
#include <AvailabilityMacros.h>
#if MAC_OS_X_VERSION_MAX_ALLOWED < 101200
#include <mach/clock.h>
#include <mach/mach.h>
#include <mach/mach_time.h>
#include <cerrno>

typedef enum {
    CLOCK_REALTIME,
    CLOCK_MONOTONIC,
    CLOCK_PROCESS_CPUTIME_ID,
    CLOCK_THREAD_CPUTIME_ID
} clockid_t;
static mach_timebase_info_data_t __clock_gettime_inf;

int my_clock_gettime_(clockid_t clk_id, struct timespec *tp);
#endif  // MAC_OS_X_VERSION_MAX_ALLOWED < 101200
#endif  // __APPLE__

class Timer
{
public:
    bool keepHistogram, keepList;
    timespec cpuclock[2];
    int elapsedClockMsec;
    float elapsedTime;
    std::map<int, int> histogram;
    std::vector<int> msecList;
    long long totalElapsedClock;
    std::string header;

    Timer(std::string _header = "");

    int ListSize();

    void PrintHeader(std::ostream &out);

    void PrintListValue(std::ostream &out, int index);

    void Tick();

    void SetStoreElapsedTime(bool value);

    void SetStoreHistgram(bool value);

    void Tock();

    void Add(const Timer &rhs);

    void SetHeader(std::string _header);
};

class MappingClocks
{
public:
    Timer total;
    Timer findAnchors;
    Timer mapToGenome;
    Timer sortMatchPosList;
    Timer findMaxIncreasingInterval;
    Timer alignIntervals;
    std::vector<int> nCellsPerSample;
    std::vector<int> nBasesPerSample;

    void AddCells(int nCells);

    void AddBases(int nBases);

    int GetSize();

    MappingClocks();

    void PrintHeader(std::ostream &out);

    void PrintList(std::ostream &out, int index);

    void SetStoreList(bool value = true);

    void AddClockTime(const MappingClocks &rhs);
};

class MappingMetrics
{
public:
    MappingClocks clocks;
    int numReads;
    int numMappedReads;
    int numMappedBases;
    std::vector<int> mappedBases;
    std::vector<int> cellsPerAlignment;
    std::vector<int> anchorsPerAlignment;
    std::vector<int> sdpAnchors, sdpBases, sdpClock;
    long totalAnchors;
    int anchorsPerRead;
    long totalAnchorsForMappedReads;

    MappingMetrics();

    void StoreSDPPoint(int nBases, int nSDPAnchors, int nClock);

    void SetStoreList(bool value = true);

    void PrintSeconds(std::ostream &out, long sec);

    void PrintFraction(std::ostream &out, float frac);

    void RecordNumAlignedBases(int nBases);

    void RecordNumCells(int nCells);

    void Collect(MappingMetrics &rhs);

    void CollectSDPMetrics(MappingMetrics &rhs);

    void PrintSDPMetrics(std::ostream &out);

    void PrintFullList(std::ostream &out);

    void PrintSummary(std::ostream &out);

    void AddClock(MappingClocks &clocks);
};

#endif  // _BLASR_MAPPING_METRICS_HPP_