24 #include "../msrunid.h"
25 #include "../msrunreader.h"
27 #include "../../processing/filters/filtermorpho.h"
77 Trace getCommonDeltaRt(
84 void addPeptideAsSeamark(
const T &peptide_str,
85 std::size_t ms2_spectrum_index);
90 void computePeptideRetentionTimes();
92 std::size_t getNumberOfCorrectedValues()
const;
96 const std::vector<MsRunRetentionTimeSeamarkPoint<T>> &getSeamarks()
const;
97 const std::vector<double> &getAlignedRetentionTimeVector()
const;
98 const std::vector<RtPoint> &getMs1RetentionTimeVector()
const;
100 bool isAligned()
const;
103 translateOriginal2AlignedRetentionTime(
double original_retention_time)
const;
106 double getFrontRetentionTimeReference()
const;
107 double getBackRetentionTimeReference()
const;
108 const std::vector<MsRunRetentionTimeSeamarkPoint<T>>
109 getSeamarksReferences()
const;
112 void getCommonDeltaRt(
115 void correctNewTimeValues(
Trace &ms1_aligned_points,
116 double correction_parameter);
118 void linearRegressionMs2toMs1(
Trace &ms1_aligned_points,
119 const Trace &common_points);
131 std::size_t m_valuesCorrected = 0;
136 ComputeRetentionTimeReference::maximum_intensity;
mean filter apply mean of y values inside the window : this results in a kind of smoothing
std::vector< RtPoint > m_ms1RetentionTimeVector
std::vector< double > m_alignedRetentionTimeVector
std::vector< PeptideMs2Point > m_allMs2Points
FilterMorphoMean m_ms1MeanFilter
FilterMorphoMean m_ms2MeanFilter
ComputeRetentionTimeReference
pappso::MsRunReaderSPtr msp_msrunReader
std::vector< MsRunRetentionTimeSeamarkPoint< T > > m_seamarks
FilterMorphoMedian m_ms2MedianFilter
pappso::MsRunIdCstSPtr mcsp_msrunId
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< MsRunReader > MsRunReaderSPtr
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
double precursorIntensity
std::size_t spectrumIndex