libpappsomspp
Library for mass spectrometry
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#include <mzxmloutput.h>
Classes | |
class | Translater |
Public Member Functions | |
MzxmlOutput (UiMonitorInterface &monitor, QIODevice *p_output_device) | |
~MzxmlOutput () | |
void | write (MsRunReader *p_msrunreader) |
void | close () |
void | maskMs1 (bool mask_ms1) |
void | setReadAhead (bool read_ahead) |
Private Member Functions | |
void | writeHeader (MsRunReader *p_msrunreader) |
void | writeQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum) |
std::size_t | getScanNumber (const QualifiedMassSpectrum &spectrum) const |
std::size_t | getPrecursorScanNumber (const QualifiedMassSpectrum &spectrum) const |
std::size_t | getScanNumberFromNativeId (const QString &native_id) const |
Private Attributes | |
UiMonitorInterface & | m_monitor |
QXmlStreamWriter * | mpa_outputStream |
bool | m_isReadAhead = false |
bool | m_ms1IsMasked = false |
Definition at line 43 of file mzxmloutput.h.
MzxmlOutput::MzxmlOutput | ( | UiMonitorInterface & | monitor, |
QIODevice * | p_output_device | ||
) |
Default constructor
Definition at line 75 of file mzxmloutput.cpp.
References mpa_outputStream.
MzxmlOutput::~MzxmlOutput | ( | ) |
void MzxmlOutput::close | ( | ) |
Definition at line 221 of file mzxmloutput.cpp.
References mpa_outputStream.
Referenced by ~MzxmlOutput(), and pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
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private |
Definition at line 254 of file mzxmloutput.cpp.
References pappso::QualifiedMassSpectrum::getPrecursorNativeId(), pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex(), and getScanNumberFromNativeId().
Referenced by writeQualifiedMassSpectrum().
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private |
Definition at line 242 of file mzxmloutput.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), getScanNumberFromNativeId(), and pappso::MassSpectrumId::getSpectrumIndex().
Referenced by writeQualifiedMassSpectrum().
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private |
Definition at line 228 of file mzxmloutput.cpp.
Referenced by getPrecursorScanNumber(), and getScanNumber().
void MzxmlOutput::maskMs1 | ( | bool | mask_ms1 | ) |
Definition at line 388 of file mzxmloutput.cpp.
References m_ms1IsMasked.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void MzxmlOutput::setReadAhead | ( | bool | read_ahead | ) |
Definition at line 93 of file mzxmloutput.cpp.
References m_isReadAhead.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void MzxmlOutput::write | ( | MsRunReader * | p_msrunreader | ) |
Definition at line 98 of file mzxmloutput.cpp.
References m_isReadAhead, m_monitor, m_ms1IsMasked, pappso::MsRunReader::readSpectrumCollection(), pappso::SpectrumCollectionHandlerInterface::setNeedMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::setReadAhead(), pappso::UiMonitorInterface::setTotalSteps(), pappso::MsRunReader::spectrumListSize(), and writeHeader().
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
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private |
Definition at line 118 of file mzxmloutput.cpp.
References pappso::MsRunReader::getMsRunId(), mpa_outputStream, PAPPSOMSPP_NAME, PAPPSOMSPP_VERSION, and pappso::MsRunReader::spectrumListSize().
Referenced by write().
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private |
Definition at line 267 of file mzxmloutput.cpp.
References change_endian(), pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::QualifiedMassSpectrum::getPrecursorCharge(), pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getPrecursorMz(), getPrecursorScanNumber(), pappso::QualifiedMassSpectrum::getRtInSeconds(), getScanNumber(), mpa_outputStream, and pappso::QualifiedMassSpectrum::size().
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private |
Definition at line 92 of file mzxmloutput.h.
Referenced by setReadAhead(), and write().
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private |
Definition at line 90 of file mzxmloutput.h.
Referenced by write().
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private |
Definition at line 93 of file mzxmloutput.h.
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private |
Definition at line 91 of file mzxmloutput.h.
Referenced by MzxmlOutput(), ~MzxmlOutput(), close(), writeHeader(), and writeQualifiedMassSpectrum().