libpappsomspp
Library for mass spectrometry
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#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 More... | |
Private Member Functions | |
QFile * | getQfileLinear (std::size_t frameId, const std::vector< pappso::TimsFrameRecord > &frame_record_list) |
open one QFile handler for linear read More... | |
QFile * | getQfileRandom () |
open one QFile handler for random read More... | |
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 More... | |
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 |
Definition at line 44 of file timsbindec.h.
TimsBinDec::TimsBinDec | ( | const QFileInfo & | timsBinFile, |
int | timsCompressionType | ||
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Default constructor
Definition at line 40 of file timsbindec.cpp.
References m_timsBinFile, and m_timsCompressionType.
TimsBinDec::TimsBinDec | ( | const TimsBinDec & | other | ) |
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virtual |
Destructor
Definition at line 70 of file timsbindec.cpp.
References mp_fileLinear, mp_fileRandom, and mpa_decompressMemoryBuffer.
void pappso::TimsBinDec::closeLinearRead | ( | ) |
close file access and flush cache
Definition at line 92 of file timsbindec.cpp.
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private |
open one QFile handler for linear read
Definition at line 109 of file timsbindec.cpp.
References m_linearAccessRawDataChunckDequeSize, m_timsBinFile, mp_fileLinear, and startLinearRead().
Referenced by getTimsFrameSPtrByOffset().
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open one QFile handler for random read
Definition at line 131 of file timsbindec.cpp.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 254 of file timsbindec.cpp.
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().
TimsFrameSPtr TimsBinDec::getTimsFrameSPtrByOffset | ( | std::size_t | frameId, |
const std::vector< pappso::TimsFrameRecord > & | frame_record_list | ||
) |
Definition at line 147 of file timsbindec.cpp.
References getQfileLinear(), getQfileRandom(), getTimsFrameFromRawDataChunck(), m_firstFrameId, m_lastFrameId, m_linearAccessRawDataChunckList, m_linearForwardThreshold, m_randemAccessFrameRawDataChunck, m_timsBinFile, moveLinearReadForward(), mp_fileLinear, pappso::PappsoException::qwhat(), and pappso::TimsFrameRawDataChunck::readTimsFrame().
Referenced by pappso::TimsData::getTimsFrameCstSPtr().
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Definition at line 231 of file timsbindec.cpp.
References pappso::a, and pappso::b.
Referenced by getTimsFrameSPtrByOffset().
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populate a fifo buffer with TimsFrameRawDataChunck accelerates inputs from file
Definition at line 364 of file timsbindec.cpp.
References pappso::PappsoException::qwhat().
Referenced by getQfileLinear().
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Definition at line 107 of file timsbindec.h.
Referenced by getTimsFrameFromRawDataChunck().
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Definition at line 113 of file timsbindec.h.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 114 of file timsbindec.h.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 115 of file timsbindec.h.
Referenced by getQfileLinear().
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Definition at line 112 of file timsbindec.h.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 116 of file timsbindec.h.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 109 of file timsbindec.h.
Referenced by getTimsFrameSPtrByOffset().
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Definition at line 101 of file timsbindec.h.
Referenced by TimsBinDec(), getQfileLinear(), getTimsFrameFromRawDataChunck(), and getTimsFrameSPtrByOffset().
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Definition at line 100 of file timsbindec.h.
Referenced by TimsBinDec(), and getTimsFrameFromRawDataChunck().
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Definition at line 102 of file timsbindec.h.
Referenced by ~TimsBinDec(), getQfileLinear(), and getTimsFrameSPtrByOffset().
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Definition at line 103 of file timsbindec.h.
Referenced by ~TimsBinDec().
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Definition at line 106 of file timsbindec.h.
Referenced by ~TimsBinDec(), and getTimsFrameFromRawDataChunck().