// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Code for profiling.
// ==========================================================================

// TODO(holtgrew): This could use some cleanup.

#include <ctime>
#include <chrono>

//SEQAN_NO_GENERATED_FORWARDS: no forwards are generated for this file

#ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_
#define SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_

namespace seqan2
{

// todo: substitute defines with inlines
#ifndef SEQAN_PROFILE

    #define SEQAN_PROSET(i,v)           do {} while (false)
    #define SEQAN_PROADD(i,v)           do {} while (false)
    #define SEQAN_PROSUB(i,v)           do {} while (false)
    #define SEQAN_PROVAL(i)             0
    #define SEQAN_PROEXTRAS(i)          do {} while (false)
    #define SEQAN_PROMARK(m)            do {} while (false)
    #define SEQAN_PROENDMARK(m)         do {} while (false)
    #define SEQAN_PRORESET              do {} while (false)
    #define SEQAN_PROGETTIME            0
    #define SEQAN_PROTIMESTART(a)       do {} while (false)
    #define SEQAN_PROTIMEDIFF(a)        0
    #define SEQAN_PROTIMEUPDATE(a)      0
    // replace malloc and free in external tools
    // with SEQAN_PROMALLOC and SEQAN_PROFREE to profile
    // their memory usage
    #define SEQAN_PROMALLOC(s)          malloc(s)
    #define SEQAN_PROFREE(p)            free(p)

#else

    #define SEQAN_PROSET(i,v)           _profileSet(i,v)
    #define SEQAN_PROADD(i,v)           _profileAdd(i,v)
    #define SEQAN_PROSUB(i,v)           _profileSub(i,v)
    #define SEQAN_PROVAL(i)             (ProfileData_<>::_proValue[i])
    #define SEQAN_PROEXTRAS(i)          {ProfileData_<>::_proExtraCount = i;}
    #define SEQAN_PROMARK(m)            _profileMark(m)
    #define SEQAN_PROENDMARK(m)         _profileEndMark(m)
    #define SEQAN_PRORESET              _profileReset()
    #define SEQAN_PROGETTIME            sysTime()
    #define SEQAN_PROTIMESTART(a)       _proFloat a = sysTime()
    #define SEQAN_PROTIMEDIFF(a)        (sysTime() - a)
    #define SEQAN_PROTIMEUPDATE(a)      (_profileUpdate(a))
    #define SEQAN_PROMALLOC(s)          _profileMalloc(s)
    #define SEQAN_PROFREE(p)            _profileFree(p)

#endif

#ifdef STDLIB_VS
    typedef int64_t   ProfileInt_; //IOREV _notio_
#else
    typedef int64_t ProfileInt_; //IOREV _notio_
#endif

    typedef double    _proFloat;


    typedef _proFloat ProfileTimeValue_; //IOREV _notio_

    enum ProfileConstants_ {
        SEQAN_PROPAGESIZE         = 4096, // B in byte
        SEQAN_PROFLOAT            = 0,
        SEQAN_PROINT              = 1,
        SEQAN_PROTIME             = 2,
        SEQAN_PROTYPEMASK         = 3,
        SEQAN_PROSTATE            = 4
    };

    enum ProfileValueIndex_ {
        SEQAN_PROSYSTIME          = 0,
        SEQAN_PROCPUTIME          = 1,
        SEQAN_PROMEMORY           = 2,    // current memory usage (state value)
        SEQAN_PROIO               = 3,    // IOs done (measured in Blocks of size B)
        SEQAN_PROIORANDOM         = 4,    // IOs calls done (read/write calls done)
        SEQAN_PROIOVOLUME         = 5,    // current disk usage (state value)
        SEQAN_PRODEPTH            = 6,    // algorithmic rec. depth or loop count
        SEQAN_PROOPENFILES        = 7,    // currently opened files
        SEQAN_PROIWAIT            = 8,    // waiting time (initiating)
        SEQAN_PROCWAIT            = 9,    // waiting time (completing)
        SEQAN_PROEXTRA1           = 10,
        SEQAN_PROEXTRA2           = 11,
        SEQAN_PROEXTRA3           = 12,
        SEQAN_PROINDEXCOUNT       = 13,
        SEQAN_PROEXTRACOUNT       = 3
    };

    const char ProfileValueType_[] = {
        SEQAN_PROTIME,
        SEQAN_PROTIME,
        SEQAN_PROINT + SEQAN_PROSTATE,
        SEQAN_PROINT,
        SEQAN_PROINT,
        SEQAN_PROINT + SEQAN_PROSTATE,
        SEQAN_PROINT + SEQAN_PROSTATE,
        SEQAN_PROINT + SEQAN_PROSTATE,
        SEQAN_PROFLOAT,
        SEQAN_PROFLOAT,
        SEQAN_PROFLOAT + SEQAN_PROSTATE,
        SEQAN_PROFLOAT + SEQAN_PROSTATE,
        SEQAN_PROFLOAT + SEQAN_PROSTATE
    };

    typedef ProfileTimeValue_ ProfileTStates_[SEQAN_PROINDEXCOUNT]; //IOREV _notio_
    typedef _proFloat  ProfileTTimes[SEQAN_PROINDEXCOUNT]; //IOREV _notio_



    struct ProfileFile_;
//IOREV

    template <typename T = void>
    struct ProfileData_
    {
//IOREV _notio_
        static ProfileTStates_  _proValue;
        static ProfileTTimes    _proLastUpdate;
        static int          _proExtraCount;

        static clock_t      _proCpuTimeLast;            // clock_t wraps around every 72mins
        static ProfileInt_      _proCpuTimeOffset;          // we have to work around this

        static ProfileFile_*    _proPFile;
        static ProfileFile_*    _proPFileStream;
    };

    template <typename T> ProfileTStates_   ProfileData_<T>::_proValue = {};
    template <typename T> ProfileTStates_   ProfileData_<T>::_proLastUpdate = {};
    template <typename T> int           ProfileData_<T>::_proExtraCount = 0;
    template <typename T> clock_t       ProfileData_<T>::_proCpuTimeLast = 0;
    template <typename T> ProfileInt_       ProfileData_<T>::_proCpuTimeOffset = 0;
    template <typename T> ProfileFile_*     ProfileData_<T>::_proPFile = NULL;
    template <typename T> ProfileFile_*     ProfileData_<T>::_proPFileStream = NULL;


    inline ProfileFile_* & _proPFile()          { return ProfileData_<>::_proPFile; }
//IOREV
    inline ProfileFile_* & _proPFileStream()    { return ProfileData_<>::_proPFileStream; }
//IOREV

/*!
 * @fn cpuTime
 * @headerfile <seqan/basic.h>
 * @brief Returns the cpu time in seconds.
 *
 * @signature double cpuTime();
 *
 * @return double CPU time stamp in seconds.
 *
 * Calls <tt>clock</tt> to retrieve the processor time used by the running thread. This implies that the thread's
 * processor time does not tick if the thread is suspended. While this has its advantages, benchmarks should generally
 * focus on wall clock time, not processor time. Wall clock time is returned by sysTime.
 *
 * @see sysTime
 */


// HINT: The unit of all time functions is second.
    inline _proFloat cpuTime() {
        clock_t now = clock();
        if (ProfileData_<>::_proCpuTimeLast > now) {        // test for time wrap
            ProfileData_<>::_proCpuTimeOffset += (~0u);     // got one
            ProfileData_<>::_proCpuTimeOffset ++;
//          printf("\n!!WRAP!! old:%d, now:%d    ofs:%d\n",ProfileData_<>::_proCpuTimeLast,now,ProfileData_<>::_proCpuTimeOffset);
        }
        ProfileData_<>::_proCpuTimeLast = now;
        return (ProfileData_<>::_proCpuTimeOffset + now) / (_proFloat)CLOCKS_PER_SEC;
    }

/*!
 * @fn sysTime
 * @headerfile <seqan/basic.h>
 * @brief Returns the system time in seconds.
 *
 * @signature double sysTime();
 *
 * @return double A <tt>double</tt>, system time stamp in seconds. Types: nolink:double
 *
 * In contrast to @link cpuTime @endlink, the system time corresponds to the wall clock time under Linux and Mac OS X.
 * Under Windows sysTime returns the result of cpuTime.
 *
 * Use this for benchmarking uner Linux and Mac Os X.
 *
 * Calls <tt>clock_gettime</tt> under Linux and <tt>gettimeofday</tt> under Mac OS X.
 *
 * @section Examples
 *
 * We can use sysTime to instrument our code for profiling/timing information quite robustly. The following demonstrates
 * how the Function.sysTime is used in many SeqAn apps for collecting timing information.
 *
 * @code{.cpp}
 * bool printTiming = true;
 *
 * // ...
 *
 * double startTime = sysTime();
 * // Do some complex calculation.
 * if (printTiming)
 *     std::cerr << "Some complex calculation too " << sysTime() - startTime << " s." << std::endl;
 * @endcode
 *
 * @see cpuTime
 */
    inline _proFloat sysTime()
    {
        return static_cast<_proFloat>(std::chrono::system_clock::now().time_since_epoch() /
                                      std::chrono::duration<_proFloat>(1));
    }

    struct ProfileFile_ {
//IOREV not generic, uses FILE* instead of File() and custom IO

        FILE   *out;
        bool   running;

        _proFloat dumpStep;            // 0 .. manual dump mode, >0 .. live stream
        _proFloat dumpNext;

        ProfileTStates_ all, last;
        std::string mark;
        unsigned    lines;

        ProfileFile_() {
            running = false;
        }

        ProfileFile_(char const *fname, _proFloat _dumpStep = 300.0) { // five minutes default dump interval
            running = false;
            start(fname, _dumpStep);
        }

        ~ProfileFile_() {
            if (running) stop();
        }

        inline void start(char const *fname, _proFloat _dumpStep = 300.0, bool append = false) {
            if (append)
                out = fopen(fname, "a");
            else {
                out = fopen(fname, "w");
                dumpHeader();
            }

            if (!out) printf("WARNING: proFile could not be opened.\n");

            setTime(ProfileData_<>::_proValue);
            syncAll(all);
            syncAll(last);
            running      = true;
            lines        = 0;
            dumpStep     = _dumpStep;
            dumpNext     = sysTime();
            dump(last);
        }

        inline void stop() {
            dump(last);
            maximize(all, last);
            if (dumpStep == 0) {
                mark = "Zusammenfassung";
                dump(all);
            }
            fclose(out);
            running = false;
        }

        inline void syncTime(ProfileTStates_ &dst) {
            std::memcpy(dst, ProfileData_<>::_proValue, 2 * sizeof(ProfileTimeValue_));
        }

        inline void sync(ProfileTStates_ &dst) {
            std::memcpy(&(dst[2]), &(ProfileData_<>::_proValue[2]), sizeof(ProfileTStates_) - 2 * sizeof(ProfileTimeValue_));
        }

        inline void syncAll(ProfileTStates_ &dst) {
            std::memcpy(dst, ProfileData_<>::_proValue, sizeof(ProfileTStates_));
        }

        inline static void setTime(ProfileTStates_ &dst) {
            dst[0] = sysTime();
            dst[1] = cpuTime();
        }

        inline void maximize(ProfileTStates_ &dst, ProfileTStates_ const &src) {
            for(int i = 0; i < SEQAN_PROINDEXCOUNT; ++i)
                if (((ProfileValueType_[i] & SEQAN_PROSTATE) != 0))
                    if (dst[i] < src[i])
                        dst[i] = src[i];
        }

        inline void dumpTab() {
            if (!bol)
                fprintf(out, " \t");
            bol = false;
        }

        inline void dumpEndl() { fprintf(out, "\n"); }

        inline void dumpHeader() {
            fprintf(out, "\"Echtzeit\"\t\"CPU-Zeit\"\t\"Speicher\"\t\"I/O-Zugriffe\"\t\"wahlfreie I/Os\"\t\"I/O-Volumen\"\t\"Rekursionstiefe\"\t\"Offene Dateien\"\t\"Idle-Zeit vor I/O\"\t\"Idle-Zeit nach I/O\"\n");
        }

        inline void dumpTime(_proFloat seconds) {
            if (seconds < 0) {
                fputc('-', out);
                seconds = -seconds;
            }
            int secs    = (int)seconds;
            int mins    = secs/60;  secs -= 60*mins;
            int hours   = mins/60;  mins -= 60*hours;
            fprintf(out, "%d:%02d:%02d", hours, mins, secs);
        }

        inline void dumpTimeEx(_proFloat seconds) {
            int milli   = (int)(seconds * 1000.0);
            int secs    = (int)seconds;
            int mins    = secs/60;  secs -= 60*mins;
            int hours   = mins/60;  mins -= 60*hours;
            fprintf(out, "%d:%02d:%02d.%03d", hours, mins, secs, milli);
        }

        inline void dumpValue(ProfileTStates_ &stat, int valNum) {
            _proFloat f = stat[valNum];
            if ((ProfileValueType_[valNum] & SEQAN_PROSTATE) == 0)
                f = ProfileData_<>::_proValue[valNum] - f;

            switch (ProfileValueType_[valNum] & SEQAN_PROTYPEMASK) {
                case SEQAN_PROINT:                                      // state value -> print last seen maximum
                    fprintf(out, "%.0f", f);
                    break;

                case SEQAN_PROFLOAT:
                    fprintf(out, "%f", f);
                    break;

                case SEQAN_PROTIME:
                    dumpTimeEx(f);
            }
        }

        inline void dumpSysValues(ProfileTStates_ &stat) {
            for(int i = 0; i < SEQAN_PROINDEXCOUNT - SEQAN_PROEXTRACOUNT; ++i) {
                dumpTab();
                dumpValue(stat, i);
            }
        }

        inline void dumpExtraValues(ProfileTStates_ &stat) {
            for(int i = 0; i < ProfileData_<>::_proExtraCount; ++i) {
                dumpTab();
                dumpValue(stat, SEQAN_PROINDEXCOUNT - SEQAN_PROEXTRACOUNT + i);
            }
    }

        inline void dumpMark() {
            if (!mark.empty()) {
                dumpTab();
                fprintf(out, "\"%s\"", mark.c_str());
                mark.erase();
            }
        }

        inline void dump(ProfileTStates_ &stat) {
            setTime(ProfileData_<>::_proValue);
            dumpNext += dumpStep;
            bol = true;
            bool _flush = ((dumpStep == 0.0)) || ((lines & 16) == 0);

            dumpSysValues(stat);
            dumpExtraValues(stat);
            dumpMark();
            dumpEndl();
            if (_flush) fflush(out);
            ++lines;
        }

        inline void signalDumpTest(_proFloat now) {
            if (dumpStep > 0 && now > dumpNext && running) {
                dump(last);
                maximize(all, last);
                sync(last);
            }
        }

        inline void signalNewMax(int valNum) {
            if (running)
                if (last[valNum] < ProfileData_<>::_proValue[valNum])
                    last[valNum] = ProfileData_<>::_proValue[valNum];
        }

        inline void setMark(const char *text) {
            if (running) {
                mark = text;
                if (dumpStep == 0.0) {
                    dump(last);                 // manual dump;
                    maximize(all, last);
                    sync(last);
                }
            }
        }

        inline void reset() {
            syncTime(last);
        }

        inline void setEndMark(const char *text) {
            if (running) {
                setMark(text);
                reset();
            }
        }

    private:

        bool bol;   // begin of line
    };



/*
    inline void _profileSignalDumpTest(_proFloat now);
    inline void _profileSignalNewMax(int valNum);
    inline void _profileMark(const char *text);
    inline void _profileEndMark(const char *text);
    inline void _profileReset();

    inline void _profileSet(int valNum, _proFloat value);
    inline void _profileAdd(int valNum, _proFloat value);
    inline void _profileSub(int valNum, _proFloat value);

    // simple interface for external programs
    inline void *_profileMalloc(size_t size);
    inline void _profileFree(void *_ptr);
*/

    inline void _profileSignalDumpTest(_proFloat now) {
//IOREV _notio_
        if (ProfileData_<>::_proPFileStream) ProfileData_<>::_proPFileStream->signalDumpTest(now);
    }

    inline void _profileSignalNewMax(int valNum) {
//IOREV _notio_
        if (((ProfileValueType_[valNum] & SEQAN_PROSTATE) != 0)) {
            if (ProfileData_<>::_proPFileStream) ProfileData_<>::_proPFileStream->signalNewMax(valNum);
            if (ProfileData_<>::_proPFile)       ProfileData_<>::_proPFile->signalNewMax(valNum);
        }
    }

    inline void _profileMark(const char *text) {
//IOREV _notio_
        if (ProfileData_<>::_proPFileStream) ProfileData_<>::_proPFileStream->setMark(text);
        if (ProfileData_<>::_proPFile)       ProfileData_<>::_proPFile->setMark(text);
    }

    inline void _profileEndMark(const char *text) {
//IOREV _notio_
        if (ProfileData_<>::_proPFileStream) { ProfileData_<>::_proPFileStream->setEndMark(text); }
        if (ProfileData_<>::_proPFile)       { ProfileData_<>::_proPFile->setEndMark(text); }
    }

    inline void _profileReset() {
//IOREV _notio_
        if (ProfileData_<>::_proPFileStream) { ProfileData_<>::_proPFileStream->reset(); }
        if (ProfileData_<>::_proPFile)       { ProfileData_<>::_proPFile->reset(); }
    }




    template <typename TValue>
    inline void _profileSet(ProfileValueIndex_ valNum, TValue value) {
//IOREV _notio_
        _proFloat now = sysTime();
        ProfileData_<>::_proLastUpdate[valNum] = now;
        if (ProfileData_<>::_proValue[valNum] < value) {
            ProfileData_<>::_proValue[valNum] = value;
            _profileSignalNewMax(valNum);
        } else
            ProfileData_<>::_proValue[valNum] = value;
        _profileSignalDumpTest(now);
    }

    template <typename TValue>
    inline void _profileAdd(ProfileValueIndex_ valNum, TValue value) {
//IOREV _notio_
        _proFloat now = sysTime();
        ProfileData_<>::_proValue[valNum] += value;
        ProfileData_<>::_proLastUpdate[valNum] = now;
        if (valNum == SEQAN_PROIO) _profileAdd(SEQAN_PROIORANDOM, 1);
        _profileSignalNewMax(valNum);
        _profileSignalDumpTest(now);
    }

    template <typename TValue>
    inline void _profileSub(ProfileValueIndex_ valNum, TValue value) {
//IOREV _notio_
        _proFloat now = sysTime();
        ProfileData_<>::_proValue[valNum] -= value;
        ProfileData_<>::_proLastUpdate[valNum] = now;
        _profileSignalDumpTest(now);
    }

    // simple interface for external programs
    inline void *_profileMalloc(size_t size) {
//IOREV _notio_
        size_t *ptr = reinterpret_cast<size_t*>(malloc(size + sizeof(size_t)));
        if (ptr) {
            _profileAdd(SEQAN_PROMEMORY, (_proFloat)(*ptr = size));
//          printf("_profileMalloc %x size %d\n", ptr, size);
            ++ptr;
        }
        return ptr;
    }

    inline void _profileFree(void *_ptr) {
//IOREV _notio_
        size_t *ptr = reinterpret_cast<size_t*>(_ptr);
        if (ptr) {
            --ptr;
//          printf("_profileFree   %x size %d\n", _ptr, *ptr);
            _profileSub(SEQAN_PROMEMORY, (_proFloat)*ptr);
        }
        free(ptr);
    }

    inline _proFloat _profileUpdate(_proFloat& a) {
//IOREV _notio_
        _proFloat x = sysTime() - a;
        a += x;
        return x;
    }
}

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_PROFILING_H_
