libpappsomspp
Library for mass spectrometry
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#include <msrunretentiontime.h>
Classes | |
struct | PeptideMs2Point |
Public Member Functions | |
MsRunRetentionTime (MsRunReaderSPtr msrun_reader_sp) | |
MsRunRetentionTime (const MsRunRetentionTime< T > &other) | |
~MsRunRetentionTime () | |
void | setMs2MedianFilter (const FilterMorphoMedian &ms2MedianFilter) |
void | setMs2MeanFilter (const FilterMorphoMean &ms2MeanFilter) |
void | setMs1MeanFilter (const FilterMorphoMean &ms1MeanFilter) |
Trace | getCommonDeltaRt (const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const |
void | addPeptideAsSeamark (const T &peptide_str, std::size_t ms2_spectrum_index) |
collects all peptide evidences of a given MSrun seamarks has to be converted to peptide retention time using computePeptideRetentionTimes More... | |
void | computePeptideRetentionTimes () |
convert Peptide seamarks into PeptideMs2Point this is required before computing alignment More... | |
std::size_t | getNumberOfCorrectedValues () const |
Trace | align (const MsRunRetentionTime< T > &msrun_retention_time_reference) |
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & | getSeamarks () const |
const std::vector< double > & | getAlignedRetentionTimeVector () const |
const std::vector< RtPoint > & | getMs1RetentionTimeVector () const |
bool | isAligned () const |
double | translateOriginal2AlignedRetentionTime (double original_retention_time) const |
Protected Member Functions | |
double | getFrontRetentionTimeReference () const |
double | getBackRetentionTimeReference () const |
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > | getSeamarksReferences () const |
Private Types | |
enum | ComputeRetentionTimeReference { ComputeRetentionTimeReference::maximum_intensity, ComputeRetentionTimeReference::weighted_intensity, ComputeRetentionTimeReference::last } |
Private Member Functions | |
void | getCommonDeltaRt (Trace &delta_rt, const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const |
void | correctNewTimeValues (Trace &ms1_aligned_points, double correction_parameter) |
void | linearRegressionMs2toMs1 (Trace &ms1_aligned_points, const Trace &common_points) |
Private Attributes | |
FilterMorphoMedian | m_ms2MedianFilter |
FilterMorphoMean | m_ms2MeanFilter |
FilterMorphoMean | m_ms1MeanFilter |
pappso::MsRunReaderSPtr | msp_msrunReader |
pappso::MsRunIdCstSPtr | mcsp_msrunId |
std::vector< RtPoint > | m_ms1RetentionTimeVector |
std::vector< double > | m_alignedRetentionTimeVector |
std::vector< MsRunRetentionTimeSeamarkPoint< T > > | m_seamarks |
std::size_t | m_valuesCorrected = 0 |
std::vector< PeptideMs2Point > | m_allMs2Points |
ComputeRetentionTimeReference | m_retentionTimeReferenceMethod |
Definition at line 67 of file msrunretentiontime.h.
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Enumerator | |
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maximum_intensity | |
weighted_intensity | |
last |
Definition at line 77 of file msrunretentiontime.h.
MsRunRetentionTime::MsRunRetentionTime | ( | MsRunReaderSPtr | msrun_reader_sp | ) |
Definition at line 82 of file msrunretentiontime.cpp.
References pappso::a, pappso::b, pappso::MsRunRetentionTime< T >::m_ms1RetentionTimeVector, pappso::MsRunRetentionTime< T >::mcsp_msrunId, and pappso::MsRunRetentionTime< T >::msp_msrunReader.
MsRunRetentionTime::MsRunRetentionTime | ( | const MsRunRetentionTime< T > & | other | ) |
Definition at line 99 of file msrunretentiontime.cpp.
References pappso::MsRunRetentionTime< T >::m_alignedRetentionTimeVector, pappso::MsRunRetentionTime< T >::m_allMs2Points, pappso::MsRunRetentionTime< T >::m_ms1RetentionTimeVector, pappso::MsRunRetentionTime< T >::m_retentionTimeReferenceMethod, pappso::MsRunRetentionTime< T >::m_seamarks, pappso::MsRunRetentionTime< T >::m_valuesCorrected, pappso::MsRunRetentionTime< T >::mcsp_msrunId, and pappso::MsRunRetentionTime< T >::msp_msrunReader.
MsRunRetentionTime::~MsRunRetentionTime |
Definition at line 118 of file msrunretentiontime.cpp.
void MsRunRetentionTime::addPeptideAsSeamark | ( | const T & | peptide_str, |
std::size_t | ms2_spectrum_index | ||
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collects all peptide evidences of a given MSrun seamarks has to be converted to peptide retention time using computePeptideRetentionTimes
Definition at line 184 of file msrunretentiontime.cpp.
References pappso::MsRunRetentionTime< T >::PeptideMs2Point::entityHash, pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MsRunRetentionTime< T >::PeptideMs2Point::precursorIntensity, and pappso::MsRunRetentionTime< T >::PeptideMs2Point::retentionTime.
Trace MsRunRetentionTime::align | ( | const MsRunRetentionTime< T > & | msrun_retention_time_reference | ) |
Definition at line 416 of file msrunretentiontime.cpp.
References pappso::Trace::filter(), pappso::MsRunRetentionTime< T >::getBackRetentionTimeReference(), pappso::MsRunRetentionTime< T >::getFrontRetentionTimeReference(), pappso::MsRunRetentionTime< T >::getSeamarks(), pappso::MsRunRetentionTime< T >::getSeamarksReferences(), pappso::MsRunRetentionTime< T >::isAligned(), pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.
void MsRunRetentionTime::computePeptideRetentionTimes |
convert Peptide seamarks into PeptideMs2Point this is required before computing alignment
Definition at line 211 of file msrunretentiontime.cpp.
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Definition at line 579 of file msrunretentiontime.cpp.
const std::vector< double > & MsRunRetentionTime::getAlignedRetentionTimeVector |
Definition at line 154 of file msrunretentiontime.cpp.
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Definition at line 332 of file msrunretentiontime.cpp.
Referenced by pappso::MsRunRetentionTime< T >::align().
Trace MsRunRetentionTime::getCommonDeltaRt | ( | const std::vector< MsRunRetentionTimeSeamarkPoint< T >> & | other_seamarks | ) | const |
Definition at line 174 of file msrunretentiontime.cpp.
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Definition at line 265 of file msrunretentiontime.cpp.
References pappso::Trace::sortX(), and pappso::Trace::unique().
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Definition at line 322 of file msrunretentiontime.cpp.
Referenced by pappso::MsRunRetentionTime< T >::align().
const std::vector< RtPoint > & MsRunRetentionTime::getMs1RetentionTimeVector |
Definition at line 167 of file msrunretentiontime.cpp.
std::size_t MsRunRetentionTime::getNumberOfCorrectedValues |
Definition at line 161 of file msrunretentiontime.cpp.
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & MsRunRetentionTime::getSeamarks |
Definition at line 146 of file msrunretentiontime.cpp.
Referenced by pappso::MsRunRetentionTime< T >::align().
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Definition at line 396 of file msrunretentiontime.cpp.
Referenced by pappso::MsRunRetentionTime< T >::align().
bool MsRunRetentionTime::isAligned |
Definition at line 409 of file msrunretentiontime.cpp.
Referenced by pappso::MsRunRetentionTime< T >::align().
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Definition at line 525 of file msrunretentiontime.cpp.
References pappso::DataPoint::x, and pappso::DataPoint::y.
void MsRunRetentionTime::setMs1MeanFilter | ( | const FilterMorphoMean & | ms1MeanFilter | ) |
Definition at line 139 of file msrunretentiontime.cpp.
void MsRunRetentionTime::setMs2MeanFilter | ( | const FilterMorphoMean & | ms2MeanFilter | ) |
Definition at line 132 of file msrunretentiontime.cpp.
void MsRunRetentionTime::setMs2MedianFilter | ( | const FilterMorphoMedian & | ms2MedianFilter | ) |
Definition at line 124 of file msrunretentiontime.cpp.
double MsRunRetentionTime::translateOriginal2AlignedRetentionTime | ( | double | original_retention_time | ) | const |
Definition at line 344 of file msrunretentiontime.cpp.
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Definition at line 144 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 149 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 140 of file msrunretentiontime.h.
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Definition at line 143 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 139 of file msrunretentiontime.h.
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Definition at line 138 of file msrunretentiontime.h.
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Definition at line 151 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 146 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 147 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 142 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().
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Definition at line 141 of file msrunretentiontime.h.
Referenced by pappso::MsRunRetentionTime< T >::MsRunRetentionTime().