pappso::TimsBinDec Class Reference

#include <timsbindec.h>

Public Member Functions
	TimsBinDec (const QFileInfo &timsBinFile, int timsCompressionType)
	TimsBinDec (const TimsBinDec &other)
virtual	~TimsBinDec ()
TimsFrameSPtr	getTimsFrameSPtrByOffset (std::size_t frameId, const std::vector< pappso::TimsFrameRecord > &frame_record_list)
void	closeLinearRead ()
	close file access and flush cache

Private Member Functions
QFile *	getQfileLinear (std::size_t frameId, const std::vector< pappso::TimsFrameRecord > &frame_record_list)
	open one QFile handler for linear read
QFile *	getQfileRandom ()
	open one QFile handler for random read
void	startLinearRead (std::size_t start_frame_id, std::size_t chunk_deque_size, const std::vector< pappso::TimsFrameRecord > &frame_record_list)
	populate a fifo buffer with TimsFrameRawDataChunck accelerates inputs from file
TimsFrameSPtr	getTimsFrameFromRawDataChunck (const TimsFrameRawDataChunck &raw_data_chunck)
void	moveLinearReadForward (const std::vector< pappso::TimsFrameRecord > &frame_record_list)

Private Attributes
int	m_timsCompressionType
QString	m_timsBinFile
QFile *	mp_fileLinear = nullptr
QFile *	mp_fileRandom = nullptr
char *	mpa_decompressMemoryBuffer = nullptr
std::size_t	m_decompressMemoryBufferSize = 0
TimsFrameRawDataChunck	m_randemAccessFrameRawDataChunck
std::vector< TimsFrameRawDataChunck >	m_linearAccessRawDataChunckList
std::size_t	m_firstFrameId = 0
std::size_t	m_lastFrameId = 0
std::size_t	m_linearAccessRawDataChunckDequeSize = 100
std::size_t	m_linearForwardThreshold = 30

Detailed Description

Todo

write docs

Definition at line 44 of file timsbindec.h.

Constructor & Destructor Documentation

TimsBinDec() [1/2]

TimsBinDec::TimsBinDec	(	const QFileInfo &	timsBinFile,
		int	timsCompressionType )

Default constructor

Definition at line 40 of file timsbindec.cpp.

  : m_timsBinFile(timsBinFile.absoluteFilePath())
{
  m_timsCompressionType = timsCompressionType;
  if((timsCompressionType != 1) && (timsCompressionType != 2))
    {
      throw pappso::ExceptionNotImplemented(
        QObject::tr("compression type %1 not handled by this library")
          .arg(timsCompressionType));
    }
  if(m_timsBinFile.isEmpty())
    {
      throw pappso::PappsoException(
        QObject::tr("No TIMS binary file name specified"));
    }
  QFile file(m_timsBinFile);
  if(!file.open(QIODevice::ReadOnly))
    {
      throw PappsoException(
        QObject::tr("ERROR opening TIMS binary file %1 for read")
          .arg(timsBinFile.absoluteFilePath()));
    }
}

References m_timsBinFile, and m_timsCompressionType.

Referenced by TimsBinDec().

TimsBinDec() [2/2]

TimsBinDec::TimsBinDec

(

const TimsBinDec &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 65 of file timsbindec.cpp.

  : m_timsBinFile(other.m_timsBinFile)
{
}

References TimsBinDec(), and m_timsBinFile.

~TimsBinDec()

TimsBinDec::~TimsBinDec ( )

virtual

Destructor

Definition at line 70 of file timsbindec.cpp.

{
 
 
  if(mpa_decompressMemoryBuffer != nullptr)
    {
      delete[] mpa_decompressMemoryBuffer;
    }
 
  if(mp_fileLinear != nullptr)
    {
      mp_fileLinear->close();
      delete mp_fileLinear;
    }
  if(mp_fileRandom != nullptr)
    {
      mp_fileRandom->close();
      delete mp_fileRandom;
    }
}

References mp_fileLinear, mp_fileRandom, and mpa_decompressMemoryBuffer.

Member Function Documentation

closeLinearRead()

void pappso::TimsBinDec::closeLinearRead

(

)

close file access and flush cache

Definition at line 92 of file timsbindec.cpp.

{
  // qDebug();
  if(mp_fileLinear != nullptr)
    {
      mp_fileLinear->close();
      delete mp_fileLinear;
    }
  mp_fileLinear  = nullptr;
  m_firstFrameId = 0;
  m_lastFrameId  = 0;
  m_linearAccessRawDataChunckList.resize(0);
  // qDebug();
}

References m_firstFrameId, m_lastFrameId, m_linearAccessRawDataChunckList, and mp_fileLinear.

getQfileLinear()

QFile * TimsBinDec::getQfileLinear ( std::size_t frameId, const std::vector< pappso::TimsFrameRecord > & frame_record_list )

private

open one QFile handler for linear read

Definition at line 109 of file timsbindec.cpp.

{
  if(mp_fileLinear == nullptr)
    {
      mp_fileLinear = new QFile(m_timsBinFile);
      if(!mp_fileLinear->open(QIODevice::ReadOnly))
        {
          throw PappsoException(
            QObject::tr("ERROR opening TIMS binary file %1 for read")
              .arg(m_timsBinFile));
        }
 
      startLinearRead(
        frameId, m_linearAccessRawDataChunckDequeSize, frame_record_list);
    }
 
  return mp_fileLinear;
}

References m_linearAccessRawDataChunckDequeSize, m_timsBinFile, mp_fileLinear, and startLinearRead().

Referenced by getTimsFrameSPtrByOffset().

getQfileRandom()

QFile * pappso::TimsBinDec::getQfileRandom ( )

private

open one QFile handler for random read

Definition at line 131 of file timsbindec.cpp.

{
  if(mp_fileRandom == nullptr)
    {
      mp_fileRandom = new QFile(m_timsBinFile);
      if(!mp_fileRandom->open(QIODevice::ReadOnly))
        {
          throw PappsoException(
            QObject::tr("ERROR opening TIMS binary file %1 for read")
              .arg(m_timsBinFile));
        }
    }
  return mp_fileRandom;
}

References m_timsBinFile, and mp_fileRandom.

Referenced by getTimsFrameSPtrByOffset().

getTimsFrameFromRawDataChunck()

TimsFrameSPtr TimsBinDec::getTimsFrameFromRawDataChunck ( const TimsFrameRawDataChunck & raw_data_chunck )

private

Definition at line 254 of file timsbindec.cpp.

{
  // qDebug();
  TimsFrameSPtr frame_sptr;
  if(raw_data_chunck.getCompressedSize() > 0)
    {
      // qDebug();
      if(m_timsCompressionType == 2)
        {
          auto decompressed_size2 =
            ZSTD_getFrameContentSize(raw_data_chunck.getMemoryBuffer(),
                                     raw_data_chunck.getCompressedSize());
          // qDebug();
          if(decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN)
            {
              throw PappsoException(
                QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck "
                            "reading TIMS frame %1 TIMS binary file %2: "
                            " decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN, "
                            "frame_length=%3")
                  .arg(raw_data_chunck.getFrameId())
                  .arg(m_timsBinFile)
                  .arg(raw_data_chunck.getFrameLength()));
            }
          // qDebug();
          if(decompressed_size2 == ZSTD_CONTENTSIZE_ERROR)
            {
              // qDebug();
              throw PappsoException(
                QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck "
                            "reading TIMS frame %1 TIMS binary file %2: "
                            " decompressed_size2 == ZSTD_CONTENTSIZE_ERROR, "
                            "frame_length=%3")
                  .arg(raw_data_chunck.getFrameId())
                  .arg(m_timsBinFile)
                  .arg(raw_data_chunck.getFrameLength()));
            }
          qDebug() << " decompressed_size2=" << decompressed_size2;
 
          if(m_decompressMemoryBufferSize < (decompressed_size2 + 10))
            {
              if(mpa_decompressMemoryBuffer != nullptr)
                {
                  delete[] mpa_decompressMemoryBuffer;
                }
              m_decompressMemoryBufferSize = decompressed_size2 + 10;
              mpa_decompressMemoryBuffer =
                new char[m_decompressMemoryBufferSize];
            }
          std::size_t decompressed_size =
            ZSTD_decompress(mpa_decompressMemoryBuffer,
                            m_decompressMemoryBufferSize,
                            raw_data_chunck.getMemoryBuffer(),
                            raw_data_chunck.getCompressedSize());
          // qDebug();
 
          if(decompressed_size != decompressed_size2)
            {
              throw PappsoException(
                QObject::tr("ERROR TimsBinDec::getTimsFrameFromRawDataChunck "
                            "reading TIMS frame %1 TIMS binary file %2: "
                            "decompressed_size != decompressed_size2")
                  .arg(raw_data_chunck.getFrameId())
                  .arg(m_timsBinFile)
                  .arg(decompressed_size)
                  .arg(decompressed_size2));
            }
 
          // qDebug();
 
          frame_sptr =
            std::make_shared<TimsFrame>(raw_data_chunck.getFrameId(),
                                        raw_data_chunck.getFrameNumberOfScans(),
                                        mpa_decompressMemoryBuffer,
                                        decompressed_size);
        }
      else
        {
 
          if(m_timsCompressionType == 1)
            {
              frame_sptr = std::make_shared<TimsFrameType1>(
                raw_data_chunck.getFrameId(),
                raw_data_chunck.getFrameNumberOfScans(),
                raw_data_chunck.getMemoryBuffer(),
                raw_data_chunck.getCompressedSize());
            }
        }
      // delete[] mpa_decompressMemoryBuffer;
    }
  else
    {
      frame_sptr =
        std::make_shared<TimsFrame>(raw_data_chunck.getFrameId(),
                                    raw_data_chunck.getFrameNumberOfScans(),
                                    nullptr,
                                    0);
    }
  return frame_sptr;
}

References pappso::TimsFrameRawDataChunck::getCompressedSize(), pappso::TimsFrameRawDataChunck::getFrameId(), pappso::TimsFrameRawDataChunck::getFrameLength(), pappso::TimsFrameRawDataChunck::getFrameNumberOfScans(), pappso::TimsFrameRawDataChunck::getMemoryBuffer(), m_decompressMemoryBufferSize, m_timsBinFile, m_timsCompressionType, and mpa_decompressMemoryBuffer.

Referenced by getTimsFrameSPtrByOffset().

getTimsFrameSPtrByOffset()

TimsFrameSPtr TimsBinDec::getTimsFrameSPtrByOffset	(	std::size_t	frameId,
		const std::vector< pappso::TimsFrameRecord > &	frame_record_list )

Definition at line 147 of file timsbindec.cpp.

{
 
  qDebug() << "frameId:" << frameId;
 
  // QMutexLocker locker(&m_mutex);
  QFile *p_file = getQfileLinear(frameId, frame_record_list);
 
  if(mp_fileLinear->pos() <
     (qint64)frame_record_list[m_firstFrameId].tims_offset)
    {
    }
  else
    {
      if(frameId > m_lastFrameId)
        {
          if(frameId - m_lastFrameId < m_linearForwardThreshold)
            {
              // move forward
              moveLinearReadForward(frame_record_list);
            }
        }
    }
 
  auto it = std::find_if(m_linearAccessRawDataChunckList.begin(),
                         m_linearAccessRawDataChunckList.end(),
                         [frameId](const TimsFrameRawDataChunck &chunck) {
                           if(chunck.getFrameId() == frameId)
                             return true;
                           return false;
                         });
  if(it != m_linearAccessRawDataChunckList.end())
    {
      try
        {
          return getTimsFrameFromRawDataChunck(*it);
        }
      catch(PappsoException &error)
        {
 
          throw PappsoException(
            QObject::tr("ERROR reading TIMS binary file %1 with linear QFile: "
                        "%2")
              .arg(m_timsBinFile)
              .arg(error.qwhat()));
        }
    }
 
  // random access file
  // qDebug();
  p_file          = getQfileRandom();
  bool seekpos_ok = p_file->seek(frame_record_list[frameId].tims_offset);
  if(!seekpos_ok)
    {
      throw PappsoException(
        QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
                    "m_timsBinFile.seek(%3) failed")
          .arg(frameId)
          .arg(m_timsBinFile)
          .arg(frame_record_list[frameId].tims_offset));
    }
 
 
  try
    {
      m_randemAccessFrameRawDataChunck.readTimsFrame(
        p_file, frameId, frame_record_list);
    }
  catch(PappsoException &error)
    {
 
      throw PappsoException(
        QObject::tr("ERROR reading TIMS binary file %1 with random QFile: "
                    "%2")
          .arg(m_timsBinFile)
          .arg(error.qwhat()));
    }
 
  return getTimsFrameFromRawDataChunck(m_randemAccessFrameRawDataChunck);
}

References getQfileLinear(), getQfileRandom(), getTimsFrameFromRawDataChunck(), m_firstFrameId, m_lastFrameId, m_linearAccessRawDataChunckList, m_linearForwardThreshold, m_randemAccessFrameRawDataChunck, m_timsBinFile, moveLinearReadForward(), mp_fileLinear, and pappso::PappsoException::qwhat().

moveLinearReadForward()

void pappso::TimsBinDec::moveLinearReadForward ( const std::vector< pappso::TimsFrameRecord > & frame_record_list )

private

Definition at line 231 of file timsbindec.cpp.

{
  // qDebug();
  for(std::size_t i = 0; i < m_linearForwardThreshold; i++)
    {
      auto it = std::min_element(
        m_linearAccessRawDataChunckList.begin(),
        m_linearAccessRawDataChunckList.end(),
        [](const TimsFrameRawDataChunck &a, const TimsFrameRawDataChunck &b) {
          return a.getFrameId() < b.getFrameId();
        });
      m_lastFrameId++;
      m_firstFrameId++;
      if(m_lastFrameId >= frame_record_list.size())
        break;
      it->readTimsFrame(mp_fileLinear, m_lastFrameId, frame_record_list);
    }
  // qDebug();
}

References pappso::a, pappso::b, m_firstFrameId, m_lastFrameId, m_linearAccessRawDataChunckList, m_linearForwardThreshold, and mp_fileLinear.

Referenced by getTimsFrameSPtrByOffset().

startLinearRead()

void pappso::TimsBinDec::startLinearRead ( std::size_t start_frame_id, std::size_t chunk_deque_size, const std::vector< pappso::TimsFrameRecord > & frame_record_list )

private

populate a fifo buffer with TimsFrameRawDataChunck accelerates inputs from file

Definition at line 364 of file timsbindec.cpp.

{
  // qDebug();
  m_linearAccessRawDataChunckList.resize(chunk_deque_size);
  m_firstFrameId = start_frame_id;
  m_lastFrameId  = start_frame_id;
 
  QFile *p_file = mp_fileLinear;
  if(p_file == nullptr)
    {
      throw PappsoException(QObject::tr("ERROR mp_fileLinear == nullptr"));
    }
 
  bool seekpos_ok = p_file->seek(frame_record_list[start_frame_id].tims_offset);
  if(!seekpos_ok)
    {
      throw PappsoException(
        QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
                    "m_timsBinFile.seek(%3) failed")
          .arg(start_frame_id)
          .arg(m_timsBinFile)
          .arg(frame_record_list[start_frame_id].tims_offset));
    }
 
  try
    {
      for(TimsFrameRawDataChunck &chunck : m_linearAccessRawDataChunckList)
        {
 
          chunck.readTimsFrame(p_file, start_frame_id, frame_record_list);
          m_lastFrameId = start_frame_id;
          start_frame_id++;
        }
    }
  catch(PappsoException &error)
    {
 
      throw PappsoException(
        QObject::tr(
          "ERROR in TimsBinDec::startLinearRead reading TIMS binary file %1:\n "
          " start_frame_id=%2 m_firstFrameId=%3 m_lastFrameId=%4 "
          "%5")
          .arg(m_timsBinFile)
          .arg(start_frame_id)
          .arg(m_firstFrameId)
          .arg(m_lastFrameId)
          .arg(error.qwhat()));
    }
 
  // qDebug();
}

References m_firstFrameId, m_lastFrameId, m_linearAccessRawDataChunckList, m_timsBinFile, mp_fileLinear, and pappso::PappsoException::qwhat().

Referenced by getQfileLinear().

Member Data Documentation

m_decompressMemoryBufferSize

std::size_t pappso::TimsBinDec::m_decompressMemoryBufferSize = 0

private

Definition at line 107 of file timsbindec.h.

Referenced by getTimsFrameFromRawDataChunck().

m_firstFrameId

std::size_t pappso::TimsBinDec::m_firstFrameId = 0

private

Definition at line 113 of file timsbindec.h.

Referenced by closeLinearRead(), getTimsFrameSPtrByOffset(), moveLinearReadForward(), and startLinearRead().

m_lastFrameId

std::size_t pappso::TimsBinDec::m_lastFrameId = 0

private

Definition at line 114 of file timsbindec.h.

Referenced by closeLinearRead(), getTimsFrameSPtrByOffset(), moveLinearReadForward(), and startLinearRead().

m_linearAccessRawDataChunckDequeSize

std::size_t pappso::TimsBinDec::m_linearAccessRawDataChunckDequeSize = 100

private

Definition at line 115 of file timsbindec.h.

Referenced by getQfileLinear().

m_linearAccessRawDataChunckList

std::vector<TimsFrameRawDataChunck> pappso::TimsBinDec::m_linearAccessRawDataChunckList

private

Definition at line 112 of file timsbindec.h.

Referenced by closeLinearRead(), getTimsFrameSPtrByOffset(), moveLinearReadForward(), and startLinearRead().

m_linearForwardThreshold

std::size_t pappso::TimsBinDec::m_linearForwardThreshold = 30

private

Definition at line 116 of file timsbindec.h.

Referenced by getTimsFrameSPtrByOffset(), and moveLinearReadForward().

m_randemAccessFrameRawDataChunck

TimsFrameRawDataChunck pappso::TimsBinDec::m_randemAccessFrameRawDataChunck

private

Definition at line 109 of file timsbindec.h.

Referenced by getTimsFrameSPtrByOffset().

m_timsBinFile

QString pappso::TimsBinDec::m_timsBinFile

private

Definition at line 101 of file timsbindec.h.

Referenced by TimsBinDec(), TimsBinDec(), getQfileLinear(), getQfileRandom(), getTimsFrameFromRawDataChunck(), getTimsFrameSPtrByOffset(), and startLinearRead().

m_timsCompressionType

int pappso::TimsBinDec::m_timsCompressionType

private

Definition at line 100 of file timsbindec.h.

Referenced by TimsBinDec(), and getTimsFrameFromRawDataChunck().

mp_fileLinear

QFile* pappso::TimsBinDec::mp_fileLinear = nullptr

private

Definition at line 102 of file timsbindec.h.

Referenced by ~TimsBinDec(), closeLinearRead(), getQfileLinear(), getTimsFrameSPtrByOffset(), moveLinearReadForward(), and startLinearRead().

mp_fileRandom

QFile* pappso::TimsBinDec::mp_fileRandom = nullptr

private

Definition at line 103 of file timsbindec.h.

Referenced by ~TimsBinDec(), and getQfileRandom().

mpa_decompressMemoryBuffer

char* pappso::TimsBinDec::mpa_decompressMemoryBuffer = nullptr

private

Definition at line 106 of file timsbindec.h.

Referenced by ~TimsBinDec(), and getTimsFrameFromRawDataChunck().

---

The documentation for this class was generated from the following files:

• pappsomspp/core/vendors/tims/timsbindec.h
• pappsomspp/core/vendors/tims/timsbindec.cpp