Loading...
Searching...
No Matches
cboroutputstream.cpp
Go to the documentation of this file.
/**
* \file pappsomspp/masschroq/output/cboroutputstream.cpp
* \date 02/01/2025
* \author Olivier Langella
* \brief quantification result cbor writer for MassChroqLight
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.fr>.
*
* This file is part of MassChroQ.
*
* MassChroQ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MassChroQ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MassChroQ. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#include "cboroutputstream.h"
#include <QDateTime>
#include <QCborMap>
#include <QThreadPool>
#include "pappsomspp/core/masschroq/peptide.h"
#include "pappsomspp/core/masschroq/peptideobservation.h"
#include "pappsomspp/core/utils.h"
#include "pappsomspp/core/masschroq/utils.h"
#include "pappsomspp/core/processing/filters/filterresample.h"
namespace pappso
{
masschroq::CborOutputStream::CborOutputStream(QIODevice *device)
{
mpa_writer = new cbor::CborStreamWriter(device);
mpa_writer->startMap();
}
masschroq::CborOutputStream::~CborOutputStream()
{
}
void
masschroq::CborOutputStream::setIsPeakShapeOutput(bool is_shape_output, double margin_in_seconds)
{
m_isPeakShapeOutput = is_shape_output;
m_peakShapeMarginInSeconds = margin_in_seconds;
}
void
masschroq::CborOutputStream::setIsTraceOutput(bool is_trace_output)
{
m_isTraceOutput = is_trace_output;
}
void
masschroq::CborOutputStream::writeActionBegin(const QString &operation)
{
mpa_writer->writeInformations(
"masschroq", masschroq::Utils::getVersion(), "quantification", operation);
}
void
masschroq::CborOutputStream::writeActionEnd()
{
mpa_writer->append(QLatin1String("end"));
mpa_writer->startMap();
mpa_writer->append(QLatin1String("timestamp"));
mpa_writer->append(QDateTime::currentDateTime().toString(Qt::ISODate));
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::close()
{
writeActionEnd();
mpa_writer->endMap();
delete mpa_writer;
}
void
masschroq::CborOutputStream::writeJsonObject(const QString &name, const QJsonObject &json_object)
{
mpa_writer->append(name);
QCborMap map;
map = map.fromJsonObject(json_object);
map.toCborValue().toCbor(*mpa_writer);
}
QCborStreamWriter &
masschroq::CborOutputStream::getCborStreamWriter()
{
return (*mpa_writer);
}
void
masschroq::CborOutputStream::writeMsRun(const masschroq::MsRun &msrun)
{
mpa_writer->append(QLatin1String("msrun"));
mpa_writer->startMap(3);
mpa_writer->append(QLatin1String("id"));
mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getXmlId());
mpa_writer->append(QLatin1String("filename"));
mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getFileName());
mpa_writer->append(QLatin1String("sample"));
mpa_writer->append(msrun.getMsRunReaderSPtr().get()->getMsRunId().get()->getSampleName());
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writePeptideMeasurements(
const masschroq::PeptideMeasurements &peptide_measurements,
const MsRunRetentionTime<QString> *msrun_retention_time_p)
{
masschroq::PeptideSp peptide_sp =
peptide_measurements.getPeptideObservationSp().get()->getPeptideSp();
mpa_writer->append(peptide_sp.get()->getId());
mpa_writer->startMap();
// mpa_writer->append(QLatin1String("peptide_id"));
// mpa_writer->append(peptide_sp.get()->getId());
mpa_writer->append(QLatin1String("proforma"));
mpa_writer->append(peptide_sp.get()->getPappsoPeptideSp().get()->toProForma());
mpa_writer->append(QLatin1String("mods"));
mpa_writer->append(peptide_sp.get()->getMods());
std::size_t size_measurement = peptide_measurements.getMeasurementList().size();
if(size_measurement > 0)
{
mpa_writer->append(QLatin1String("rt_target"));
mpa_writer->append(
peptide_measurements.getMeasurementList().at(0).msp_xicCoord.get()->rtTarget);
}
mpa_writer->append(QLatin1String("xics"));
mpa_writer->startArray(size_measurement);
for(const masschroq::PeptideMeasurements::Measurement &measure :
peptide_measurements.getMeasurementList())
{
// write(peptide_sp, measure, msrun_retention_time_p);
writeMeasurement(measure, msrun_retention_time_p);
}
mpa_writer->endArray();
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeMeasurement(
const masschroq::PeptideMeasurements::Measurement &measurement,
const MsRunRetentionTime<QString> *msrun_retention_time_p)
{
mpa_writer->startMap();
mpa_writer->append(QLatin1String("charge"));
mpa_writer->append(measurement.m_charge);
mpa_writer->append(QLatin1String("mz"));
mpa_writer->append(measurement.msp_xicCoord.get()->mzRange.getMz());
if(m_isXicCoordOutput)
{
measurement.msp_xicCoord.get()->writeCborStream(*mpa_writer);
}
if(measurement.m_peptideNaturalIsotopeAverageSp.get() != nullptr)
{
mpa_writer->append(QLatin1String("isotope"));
mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIsotopeNumber());
mpa_writer->append(QLatin1String("rank"));
mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIsotopeRank());
mpa_writer->append(QLatin1String("th_ratio"));
mpa_writer->append(measurement.m_peptideNaturalIsotopeAverageSp.get()->getIntensityRatio());
}
mpa_writer->append(QLatin1String("quality"));
mpa_writer->append(masschroq::Utils::enumToString(measurement.m_peakQualityCategory));
// label
if(measurement.mp_peptideLabel != nullptr)
{
mpa_writer->append(QLatin1String("label"));
mpa_writer->append(measurement.mp_peptideLabel->getLabel());
}
if(m_isTraceOutput && (measurement.msp_xicCoord.get()->xicSptr.get() != nullptr))
{
mpa_writer->append(QLatin1String("trace"));
writeTrace(*(measurement.msp_xicCoord.get()->xicSptr.get()));
}
if(measurement.m_tracePeakSp.get() != nullptr)
{
if(m_isPeakShapeOutput && (measurement.msp_xicCoord.get()->xicSptr.get() != nullptr))
{
mpa_writer->append(QLatin1String("peak_shape"));
mpa_writer->startMap();
mpa_writer->append(QLatin1String("trace"));
TraceSPtr trace_sp;
FilterResampleKeepXRange cut_xic(
measurement.m_tracePeakSp.get()->getLeftBoundary().x - m_peakShapeMarginInSeconds,
measurement.m_tracePeakSp.get()->getRightBoundary().x + m_peakShapeMarginInSeconds);
trace_sp = measurement.msp_xicCoord.get()->xicSptr;
trace_sp.get()->filter(cut_xic);
writeTrace(*(trace_sp.get()));
mpa_writer->endMap();
}
mpa_writer->append(QLatin1String("peak"));
writeTracePeak(*(measurement.m_tracePeakSp.get()), msrun_retention_time_p);
}
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeTrace(const Trace &trace)
{
mpa_writer->startMap(2);
mpa_writer->append(QLatin1String("x"));
mpa_writer->startArray(trace.size());
for(double x : trace.xValues())
{
mpa_writer->append(x);
}
mpa_writer->endArray();
mpa_writer->append(QLatin1String("y"));
mpa_writer->startArray(trace.size());
for(double y : trace.yValues())
{
mpa_writer->append(y);
}
mpa_writer->endArray();
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeTracePeak(
const TracePeak &peak, const MsRunRetentionTime<QString> *msrun_retention_time_p)
{
mpa_writer->startMap();
mpa_writer->append(QLatin1String("area"));
mpa_writer->append(peak.getArea());
mpa_writer->append(QLatin1String("max_intensity"));
mpa_writer->append(peak.getMaxXicElement().y);
mpa_writer->append(QLatin1String("rt"));
mpa_writer->startArray();
mpa_writer->append(peak.getLeftBoundary().x);
mpa_writer->append(peak.getMaxXicElement().x);
mpa_writer->append(peak.getRightBoundary().x);
mpa_writer->endArray();
if((msrun_retention_time_p != nullptr) && msrun_retention_time_p->isAligned())
{
mpa_writer->append(QLatin1String("aligned_rt"));
mpa_writer->startArray();
mpa_writer->append(
msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getLeftBoundary().x));
mpa_writer->append(
msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getMaxXicElement().x));
mpa_writer->append(
msrun_retention_time_p->translateOriginal2AlignedRetentionTime(peak.getRightBoundary().x));
mpa_writer->endArray();
}
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeMbrPeptideMeasurements(
const masschroq::MbrPeptideMeasurements &mbr_peptide_measurements,
const MsRunRetentionTime<QString> *msrun_retention_time_p)
{
masschroq::PeptideSp peptide_sp = mbr_peptide_measurements.getPeptideSp();
mpa_writer->append(peptide_sp.get()->getId());
mpa_writer->startMap();
mpa_writer->append(QLatin1String("proforma"));
mpa_writer->append(peptide_sp.get()->getPappsoPeptideSp().get()->toProForma());
mpa_writer->append(QLatin1String("mods"));
mpa_writer->append(peptide_sp.get()->getMods());
std::size_t size_measurement = mbr_peptide_measurements.getMeasurementList().size();
if(size_measurement > 0)
{
mpa_writer->append(QLatin1String("rt_target"));
mpa_writer->append(
mbr_peptide_measurements.getMeasurementList().at(0).msp_xicCoord.get()->rtTarget);
}
mpa_writer->append(QLatin1String("xics"));
mpa_writer->startArray(mbr_peptide_measurements.getMeasurementList().size());
for(const masschroq::PeptideMeasurements::Measurement &measure :
mbr_peptide_measurements.getMeasurementList())
{
// write(peptide_sp, measure, msrun_retention_time_p);
writeMeasurement(measure, msrun_retention_time_p);
}
mpa_writer->endArray();
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeQrDataBlock(UiMonitorInterface &monitor,
const masschroq::MsRunPeptideList &msrun_peptide_list,
bool is_mbr)
{
quint64 size;
if(is_mbr)
{
size = msrun_peptide_list.getMbrPeptideMeasurementsList().size();
monitor.setStatus(QString("Writing MBR quantification results for msrun %1")
.arg(msrun_peptide_list.getMsRunSp()
.get()
->getMsRunReaderSPtr()
.get()
->getMsRunId()
.get()
->getSampleName()));
}
else
{
size = msrun_peptide_list.getPeptideMeasurementsList().size();
monitor.setStatus(QString("Writing quantification results for msrun %1")
.arg(msrun_peptide_list.getMsRunSp()
.get()
->getMsRunReaderSPtr()
.get()
->getMsRunId()
.get()
->getSampleName()));
}
monitor.setTotalSteps(size);
mpa_writer->append(msrun_peptide_list.getMsRunSp()
.get()
->getMsRunReaderSPtr()
.get()
->getMsRunId()
.get()
->getXmlId());
mpa_writer->startMap();
writeMsRun(*(msrun_peptide_list.getMsRunSp().get()));
mpa_writer->append("peptide_measurements");
mpa_writer->startMap(size);
if(is_mbr)
{
for(const masschroq::MbrPeptideMeasurementsSp &measures :
msrun_peptide_list.getMbrPeptideMeasurementsList())
{
writeMbrPeptideMeasurements(*(measures.get()),
msrun_peptide_list.getMsRunRetentionTimeConstPtr());
monitor.count();
}
}
else
{
for(const masschroq::PeptideMeasurementsSp &measures :
msrun_peptide_list.getPeptideMeasurementsList())
{
writePeptideMeasurements(*(measures.get()),
msrun_peptide_list.getMsRunRetentionTimeConstPtr());
monitor.count();
}
}
monitor.setTotalSteps(0);
mpa_writer->endMap();
mpa_writer->endMap();
}
void
masschroq::CborOutputStream::writeVectorDouble(const std::vector<double> &vector)
{
mpa_writer->startArray(vector.size());
for(double x : vector)
{
mpa_writer->append(x);
}
mpa_writer->endArray();
}
void
masschroq::CborOutputStream::writeProjectParameters(const ProjectParameters &project_parameters)
{
project_parameters.writeParameters(*mpa_writer);
}
void
masschroq::CborOutputStream::writeMsRunRetentionTime(
const Trace &report_common_ms2, const MsRunRetentionTime<QString> &msrun_retention_time)
{
mpa_writer->startMap(5);
mpa_writer->append(QLatin1String("original"));
writeVectorDouble(msrun_retention_time.getMs1RetentionTimeVector());
mpa_writer->append(QLatin1String("aligned"));
writeVectorDouble(msrun_retention_time.getAlignedRetentionTimeVector());
mpa_writer->append(QLatin1String("ms2_delta_rt"));
writeTrace(report_common_ms2);
Trace median(report_common_ms2);
msrun_retention_time.getMs2MedianFilter().filter(median);
mpa_writer->append(QLatin1String("ms2_median"));
writeVectorDouble(median.yValues());
msrun_retention_time.getMs2MeanFilter().filter(median);
mpa_writer->append(QLatin1String("ms2_mean"));
writeVectorDouble(median.yValues());
mpa_writer->endMap();
}
} // namespace pappso
cboroutputstream.h
pappso::FilterMorphoWindowBase::filter
virtual Trace & filter(Trace &data_points) const override
Definition filtermorpho.cpp:78
pappso::FilterResampleKeepXRange
Definition filterresample.h:89
pappso::MsRunRetentionTime
Definition msrunretentiontime.h:43
pappso::MsRunRetentionTime::isAligned
bool isAligned() const
Definition msrunretentiontime.cpp:395
pappso::MsRunRetentionTime::getMs2MedianFilter
const FilterMorphoMedian & getMs2MedianFilter() const
Definition msrunretentiontime.cpp:72
pappso::MsRunRetentionTime::getAlignedRetentionTimeVector
const std::vector< double > & getAlignedRetentionTimeVector() const
get aligned retention time vector
Definition msrunretentiontime.cpp:123
pappso::MsRunRetentionTime::translateOriginal2AlignedRetentionTime
double translateOriginal2AlignedRetentionTime(double original_retention_time) const
Definition msrunretentiontime.cpp:288
pappso::MsRunRetentionTime::getMs1RetentionTimeVector
const std::vector< double > & getMs1RetentionTimeVector() const
get orginal retention time vector (not aligned)
Definition msrunretentiontime.cpp:136
pappso::MsRunRetentionTime::getMs2MeanFilter
const FilterMorphoMean & getMs2MeanFilter() const
Definition msrunretentiontime.cpp:86
pappso::ProjectParameters
Definition projectparameters.h:66
pappso::ProjectParameters::writeParameters
void writeParameters(CalcWriterInterface &writer) const
Definition projectparameters.cpp:208
pappso::TracePeak
Definition tracepeak.h:40
pappso::TracePeak::getLeftBoundary
DataPoint & getLeftBoundary()
Definition tracepeak.cpp:93
pappso::TracePeak::getArea
pappso_double getArea() const
Definition tracepeak.cpp:119
pappso::TracePeak::getMaxXicElement
DataPoint & getMaxXicElement()
Definition tracepeak.cpp:83
pappso::TracePeak::getRightBoundary
DataPoint & getRightBoundary()
Definition tracepeak.cpp:104
pappso::Trace
A simple container of DataPoint instances.
Definition trace.h:152
pappso::Trace::xValues
std::vector< pappso_double > xValues() const
Definition trace.cpp:697
pappso::Trace::yValues
std::vector< pappso_double > yValues() const
Definition trace.cpp:711
pappso::UiMonitorInterface
Definition uimonitorinterface.h:50
pappso::UiMonitorInterface::setStatus
virtual void setStatus(const QString &status)=0
current status of the process
pappso::UiMonitorInterface::setTotalSteps
virtual void setTotalSteps(std::size_t total_number_of_steps)
use it if the number of steps is known in an algorithm the total number of steps is usefull to report...
Definition uimonitorinterface.h:66
pappso::UiMonitorInterface::count
virtual void count()=0
count steps report when a step is computed in an algorithm
pappso::cbor::CborStreamWriter
overrides QCborStreamWriter base class to provide convenient functions
Definition cborstreamwriter.h:45
pappso::masschroq::CborOutputStream::m_peakShapeMarginInSeconds
double m_peakShapeMarginInSeconds
Definition cboroutputstream.h:118
pappso::masschroq::CborOutputStream::close
void close()
Definition cboroutputstream.cpp:83
pappso::masschroq::CborOutputStream::setIsTraceOutput
void setIsTraceOutput(bool is_trace_output)
set trace output flag
Definition cboroutputstream.cpp:60
pappso::masschroq::CborOutputStream::writeMbrPeptideMeasurements
void writeMbrPeptideMeasurements(const MbrPeptideMeasurements &peptide_measurements, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
Definition cboroutputstream.cpp:300
pappso::masschroq::CborOutputStream::setIsPeakShapeOutput
void setIsPeakShapeOutput(bool is_shape_output, double margin_in_seconds)
set peak shape output flag
Definition cboroutputstream.cpp:53
pappso::masschroq::CborOutputStream::m_isPeakShapeOutput
bool m_isPeakShapeOutput
Definition cboroutputstream.h:115
pappso::masschroq::CborOutputStream::mpa_writer
pappso::cbor::CborStreamWriter * mpa_writer
Definition cboroutputstream.h:113
pappso::masschroq::CborOutputStream::~CborOutputStream
virtual ~CborOutputStream()
Definition cboroutputstream.cpp:48
pappso::masschroq::CborOutputStream::writeJsonObject
void writeJsonObject(const QString &name, const QJsonObject &json_object)
Definition cboroutputstream.cpp:92
pappso::masschroq::CborOutputStream::writeTrace
void writeTrace(const pappso::Trace &trace)
Definition cboroutputstream.cpp:242
pappso::masschroq::CborOutputStream::m_isTraceOutput
bool m_isTraceOutput
Definition cboroutputstream.h:114
pappso::masschroq::CborOutputStream::writeMeasurement
void writeMeasurement(const PeptideMeasurements::Measurement &measurement, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
Definition cboroutputstream.cpp:163
pappso::masschroq::CborOutputStream::writeProjectParameters
void writeProjectParameters(const pappso::ProjectParameters &project_parameters)
Definition cboroutputstream.cpp:424
pappso::masschroq::CborOutputStream::writeActionEnd
void writeActionEnd()
Definition cboroutputstream.cpp:74
pappso::masschroq::CborOutputStream::getCborStreamWriter
QCborStreamWriter & getCborStreamWriter()
Definition cboroutputstream.cpp:101
pappso::masschroq::CborOutputStream::writeMsRunRetentionTime
void writeMsRunRetentionTime(const pappso::Trace &report_common_ms2, const pappso::MsRunRetentionTime< QString > &msrun_retention_time)
Definition cboroutputstream.cpp:430
pappso::masschroq::CborOutputStream::writeMsRun
void writeMsRun(const MsRun &msrun)
Definition cboroutputstream.cpp:108
pappso::masschroq::CborOutputStream::m_isXicCoordOutput
bool m_isXicCoordOutput
Definition cboroutputstream.h:116
pappso::masschroq::CborOutputStream::writeVectorDouble
void writeVectorDouble(const std::vector< double > &vector)
Definition cboroutputstream.cpp:413
pappso::masschroq::CborOutputStream::writeActionBegin
void writeActionBegin(const QString &operation)
Definition cboroutputstream.cpp:66
pappso::masschroq::CborOutputStream::CborOutputStream
CborOutputStream(QIODevice *device)
Definition cboroutputstream.cpp:42
pappso::masschroq::CborOutputStream::writeTracePeak
void writeTracePeak(const pappso::TracePeak &peak, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
Definition cboroutputstream.cpp:265
pappso::masschroq::CborOutputStream::writeQrDataBlock
void writeQrDataBlock(pappso::UiMonitorInterface &m_uiMonitor, const MsRunPeptideList &msrun_peptide_list, bool is_mbr)
Definition cboroutputstream.cpp:338
pappso::masschroq::CborOutputStream::writePeptideMeasurements
void writePeptideMeasurements(const PeptideMeasurements &peptide_measurements, const pappso::MsRunRetentionTime< QString > *msrun_retention_time_p)
Definition cboroutputstream.cpp:123
pappso::masschroq::MbrPeptideMeasurements
Definition mbrpeptidemeasurements.h:49
pappso::masschroq::MbrPeptideMeasurements::getPeptideSp
const PeptideSp & getPeptideSp() const
Definition mbrpeptidemeasurements.cpp:172
pappso::masschroq::MsRunPeptideList
Definition msrunpeptidelist.h:54
pappso::masschroq::MsRunPeptideList::getMbrPeptideMeasurementsList
const std::vector< MbrPeptideMeasurementsSp > & getMbrPeptideMeasurementsList() const
Definition msrunpeptidelist.cpp:507
pappso::masschroq::MsRunPeptideList::getMsRunSp
const MsRunSp & getMsRunSp() const
Definition msrunpeptidelist.cpp:222
pappso::masschroq::MsRunPeptideList::getPeptideMeasurementsList
const std::vector< PeptideMeasurementsSp > & getPeptideMeasurementsList() const
Definition msrunpeptidelist.cpp:501
pappso::masschroq::MsRunPeptideList::getMsRunRetentionTimeConstPtr
const pappso::MsRunRetentionTime< QString > * getMsRunRetentionTimeConstPtr() const
Definition msrunpeptidelist.cpp:495
pappso::masschroq::MsRun
Definition msrun.h:50
pappso::masschroq::MsRun::getMsRunReaderSPtr
const pappso::MsRunReaderSPtr & getMsRunReaderSPtr() const
Definition msrun.cpp:63
pappso::masschroq::PeptideBase::getPappsoPeptideSp
virtual const pappso::PeptideSp & getPappsoPeptideSp() const
get the peptide sequence
Definition peptidebase.cpp:42
pappso::masschroq::PeptideLabel::getLabel
const QString & getLabel() const
Definition peptidelabel.cpp:48
pappso::masschroq::PeptideMeasurementsBase::getMeasurementList
virtual const std::vector< Measurement > & getMeasurementList() const
Definition peptidemeasurementsbase.cpp:50
pappso::masschroq::PeptideMeasurements
Definition peptidemeasurements.h:58
pappso::masschroq::PeptideMeasurements::getPeptideObservationSp
const PeptideObservationSp & getPeptideObservationSp() const
Definition peptidemeasurements.cpp:166
pappso::masschroq::PeptideObservation::getPeptideSp
const PeptideSp & getPeptideSp() const
Definition peptideobservation.cpp:71
pappso::masschroq::Peptide::getMods
const QString & getMods() const
get optional information as text
Definition peptide.cpp:94
pappso::masschroq::Peptide::getId
const QString & getId() const
get peptide unique identifier
Definition peptide.cpp:82
pappso::masschroq::Utils::getVersion
static QString getVersion()
Definition utils.cpp:37
pappso::masschroq::Utils::enumToString
static QString enumToString(PeakQualityCategory peak_category)
Convenience function to return a string describing the specglob alingment type.
Definition utils.cpp:44
filterresample.h
peptide.h
utils.h
pappso::masschroq::PeptideMeasurementsSp
std::shared_ptr< PeptideMeasurements > PeptideMeasurementsSp
Definition peptidemeasurements.h:50
pappso::masschroq::MbrPeptideMeasurementsSp
std::shared_ptr< MbrPeptideMeasurements > MbrPeptideMeasurementsSp
Definition mbrpeptidemeasurements.h:44
pappso::masschroq::PeptideSp
std::shared_ptr< Peptide > PeptideSp
Definition peptide.h:46
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
pappso::PeptideIonCter::y
@ y
Definition peptide.h:87
pappso::PeptideIonCter::x
@ x
Definition peptide.h:92
pappso::TraceSPtr
std::shared_ptr< Trace > TraceSPtr
Definition trace.h:139
peptideobservation.h
pappso::DataPoint::x
pappso_double x
Definition datapoint.h:24
pappso::DataPoint::y
pappso_double y
Definition datapoint.h:25
pappso::masschroq::PeptideMeasurementsBase::Measurement
Definition peptidemeasurementsbase.h:74
pappso::masschroq::PeptideMeasurementsBase::Measurement::m_charge
std::uint8_t m_charge
Definition peptidemeasurementsbase.h:75
pappso::masschroq::PeptideMeasurementsBase::Measurement::m_tracePeakSp
pappso::TracePeakCstSPtr m_tracePeakSp
Definition peptidemeasurementsbase.h:79
pappso::masschroq::PeptideMeasurementsBase::Measurement::m_peptideNaturalIsotopeAverageSp
pappso::PeptideNaturalIsotopeAverageSp m_peptideNaturalIsotopeAverageSp
Definition peptidemeasurementsbase.h:80
pappso::masschroq::PeptideMeasurementsBase::Measurement::msp_xicCoord
pappso::XicCoordSPtr msp_xicCoord
Definition peptidemeasurementsbase.h:76
pappso::masschroq::PeptideMeasurementsBase::Measurement::m_peakQualityCategory
PeakQualityCategory m_peakQualityCategory
Definition peptidemeasurementsbase.h:77
pappso::masschroq::PeptideMeasurementsBase::Measurement::mp_peptideLabel
const PeptideLabel * mp_peptideLabel
Definition peptidemeasurementsbase.h:78
utils.h