libpappsomspp
Library for mass spectrometry
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#include <msfileaccessor.h>
Public Member Functions | |
MsFileAccessor (const QString &file_name, const QString &xml_prefix) | |
MsFileAccessor (const MsFileAccessor &other) | |
virtual | ~MsFileAccessor () |
const QString & | getFileName () const |
MzFormat | getFileFormat () const |
get the raw format of mz data | |
FileReaderType | getFileReaderType () const |
get the file reader type | |
void | setPreferredFileReaderType (MzFormat format, FileReaderType reader_type) |
given an mz format, explicitly set the preferred reader | |
FileReaderType | getpreferredFileReaderType (MzFormat format) |
std::vector< MsRunIdCstSPtr > | getMsRunIds () |
void | setSelectedMsRunIdIndex (std::size_t index) |
std::size_t | getSelectedMsRunIdIndex () const |
MsRunIdCstSPtr | getSelectedMsRunId () |
MsRunReaderSPtr | msRunReaderSPtr (MsRunIdCstSPtr ms_run_id) |
MsRunReaderSPtr | msRunReaderSPtr (std::size_t ms_run_id_index) |
MsRunReaderSPtr | msRunReaderSPtrForSelectedMsRunIdIndex () |
MsRunReaderSPtr | getMsRunReaderSPtrByRunId (const QString &run_id, const QString &xml_id) |
get an msrun reader by finding the run_id in file | |
TimsMsRunReaderMs2SPtr | buildTimsMsRunReaderMs2SPtr () |
if possible, builds directly a dedicated Tims TOF tdf file reader | |
Static Public Member Functions | |
static MsRunReaderSPtr | buildMsRunReaderSPtr (MsRunIdCstSPtr ms_run_id) |
get an MsRunReader directly from a valid MsRun ID | |
static MsRunReaderSPtr | buildMsRunReaderSPtr (MsRunIdCstSPtr ms_run_id, pappso::FileReaderType preferred_file_reader_type) |
get an MsRunReader directly from a valid MsRun ID | |
Private Attributes | |
QString | m_fileName |
const QString | m_xmlPrefix |
MzFormat | m_fileFormat = MzFormat::unknown |
FileReaderType | m_fileReaderType |
std::map< MzFormat, FileReaderType > | m_preferredFileReaderTypeMap |
std::size_t | m_selectedMsRunIdIndex |
Definition at line 26 of file msfileaccessor.h.
pappso::MsFileAccessor::MsFileAccessor | ( | const QString & | file_name, |
const QString & | xml_prefix | ||
) |
Definition at line 31 of file msfileaccessor.cpp.
pappso::MsFileAccessor::MsFileAccessor | ( | const MsFileAccessor & | other | ) |
Definition at line 42 of file msfileaccessor.cpp.
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virtual |
Definition at line 50 of file msfileaccessor.cpp.
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static |
get an MsRunReader directly from a valid MsRun ID
no need to check the file format or filename : all is already part of the msrunid
ms_run_id | msrun identifier |
Definition at line 332 of file msfileaccessor.cpp.
References buildMsRunReaderSPtr(), and pappso::tims.
Referenced by buildMsRunReaderSPtr().
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static |
get an MsRunReader directly from a valid MsRun ID
no need to check the file format or filename : all is already part of the msrunid
ms_run_id | msrun identifier |
preferred_file_reader_type | the preferred file reader type to use (depending on the mz format) |
Definition at line 338 of file msfileaccessor.cpp.
References pappso::brukerTims, pappso::tims, pappso::tims_ms2, pappso::unknown, and pappso::xy.
TimsMsRunReaderMs2SPtr pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr | ( | ) |
if possible, builds directly a dedicated Tims TOF tdf file reader
Definition at line 216 of file msfileaccessor.cpp.
References pappso::TimsMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_xmlPrefix, and pappso::tims_ms2.
MzFormat pappso::MsFileAccessor::getFileFormat | ( | ) | const |
get the raw format of mz data
Definition at line 63 of file msfileaccessor.cpp.
References m_fileFormat.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
const QString & pappso::MsFileAccessor::getFileName | ( | ) | const |
Definition at line 56 of file msfileaccessor.cpp.
References m_fileName.
FileReaderType pappso::MsFileAccessor::getFileReaderType | ( | ) | const |
get the file reader type
Definition at line 186 of file msfileaccessor.cpp.
References m_fileReaderType.
std::vector< MsRunIdCstSPtr > pappso::MsFileAccessor::getMsRunIds | ( | ) |
Definition at line 70 of file msfileaccessor.cpp.
References pappso::PwizMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getFileFormat(), pappso::XyMsFileReader::getFileFormat(), pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), pappso::XyMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_preferredFileReaderTypeMap, m_xmlPrefix, pappso::pwiz, pappso::tims, and pappso::xy.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), getMsRunReaderSPtrByRunId(), getSelectedMsRunId(), msRunReaderSPtr(), and msRunReaderSPtrForSelectedMsRunIdIndex().
MsRunReaderSPtr pappso::MsFileAccessor::getMsRunReaderSPtrByRunId | ( | const QString & | run_id, |
const QString & | xml_id | ||
) |
get an msrun reader by finding the run_id in file
run_id | identifier within file of the MSrun |
xml_id | XML identifier given by the user to identify this MSrun in our experiment (not in the file) |
Definition at line 386 of file msfileaccessor.cpp.
References getMsRunIds(), m_fileName, msRunReaderSPtr(), and pappso::MsRunId::setXmlId().
FileReaderType pappso::MsFileAccessor::getpreferredFileReaderType | ( | MzFormat | format | ) |
Definition at line 172 of file msfileaccessor.cpp.
References m_fileReaderType, and m_preferredFileReaderTypeMap.
Referenced by msRunReaderSPtr().
MsRunIdCstSPtr pappso::MsFileAccessor::getSelectedMsRunId | ( | ) |
Definition at line 207 of file msfileaccessor.cpp.
References getMsRunIds(), and m_selectedMsRunIdIndex.
std::size_t pappso::MsFileAccessor::getSelectedMsRunIdIndex | ( | ) | const |
Definition at line 200 of file msfileaccessor.cpp.
References m_selectedMsRunIdIndex.
MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtr | ( | MsRunIdCstSPtr | ms_run_id | ) |
Definition at line 248 of file msfileaccessor.cpp.
References getpreferredFileReaderType(), m_fileFormat, m_fileName, pappso::pwiz, pappso::tims, pappso::tims_frames, pappso::tims_ms2, pappso::unknown, and pappso::xy.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), getMsRunReaderSPtrByRunId(), msRunReaderSPtr(), and msRunReaderSPtrForSelectedMsRunIdIndex().
MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtr | ( | std::size_t | ms_run_id_index | ) |
Definition at line 310 of file msfileaccessor.cpp.
References getMsRunIds(), and msRunReaderSPtr().
MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtrForSelectedMsRunIdIndex | ( | ) |
Definition at line 321 of file msfileaccessor.cpp.
References getMsRunIds(), m_selectedMsRunIdIndex, and msRunReaderSPtr().
void pappso::MsFileAccessor::setPreferredFileReaderType | ( | MzFormat | format, |
FileReaderType | reader_type | ||
) |
given an mz format, explicitly set the preferred reader
Definition at line 157 of file msfileaccessor.cpp.
References m_preferredFileReaderTypeMap.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void pappso::MsFileAccessor::setSelectedMsRunIdIndex | ( | std::size_t | index | ) |
Definition at line 193 of file msfileaccessor.cpp.
References m_selectedMsRunIdIndex.
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private |
Definition at line 102 of file msfileaccessor.h.
Referenced by buildTimsMsRunReaderMs2SPtr(), getFileFormat(), getMsRunIds(), and msRunReaderSPtr().
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private |
Definition at line 96 of file msfileaccessor.h.
Referenced by buildTimsMsRunReaderMs2SPtr(), getFileName(), getMsRunIds(), getMsRunReaderSPtrByRunId(), and msRunReaderSPtr().
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private |
Definition at line 105 of file msfileaccessor.h.
Referenced by buildTimsMsRunReaderMs2SPtr(), getFileReaderType(), getMsRunIds(), and getpreferredFileReaderType().
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private |
Definition at line 107 of file msfileaccessor.h.
Referenced by getMsRunIds(), getpreferredFileReaderType(), and setPreferredFileReaderType().
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private |
Definition at line 109 of file msfileaccessor.h.
Referenced by getSelectedMsRunId(), getSelectedMsRunIdIndex(), msRunReaderSPtrForSelectedMsRunIdIndex(), and setSelectedMsRunIdIndex().
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private |
Definition at line 100 of file msfileaccessor.h.
Referenced by buildTimsMsRunReaderMs2SPtr(), and getMsRunIds().