24 #include "../msrunid.h"
25 #include "../msrunreader.h"
27 #include "../../processing/filters/filtermorpho.h"
65 const MsRunId &getMsRunId()
const;
75 Trace getCommonDeltaRt(
85 void addPeptideAsSeamark(
const T &peptide_id, std::size_t ms2_spectrum_index);
96 void addPeptideAsSeamark(
const T &peptide_id,
98 double precursorIntensity);
101 std::size_t getNumberOfCorrectedValues()
const;
115 Trace getCommonSeamarksDeltaRt(
118 const std::vector<MsRunRetentionTimeSeamarkPoint<T>> &getSeamarks()
const;
123 const std::vector<double> &getAlignedRetentionTimeVector()
const;
125 void setAlignedRetentionTimeVector(
const std::vector<double> &aligned_times);
130 const std::vector<double> &getMs1RetentionTimeVector()
const;
132 bool isAligned()
const;
135 translateOriginal2AlignedRetentionTime(
double original_retention_time)
const;
139 translateAligned2OriginalRetentionTime(
double aligned_retention_time)
const;
144 void computeSeamarks();
147 double getFrontRetentionTimeReference()
const;
148 double getBackRetentionTimeReference()
const;
149 const std::vector<MsRunRetentionTimeSeamarkPoint<T>>
150 getSeamarksReferences()
const;
159 void getCommonDeltaRt(
162 void correctNewTimeValues(
Trace &ms1_aligned_points,
163 double correction_parameter);
165 void linearRegressionMs2toMs1(
Trace &ms1_aligned_points,
166 const Trace &common_points);
178 std::size_t m_valuesCorrected = 0;
183 ComputeRetentionTimeReference::maximum_intensity;
mean filter apply mean of y values inside the window : this results in a kind of smoothing
MS run identity MsRunId identifies an MS run with a unique ID (XmlId) and contains eventually informa...
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
std::vector< double > m_ms1RetentionTimeVector
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