pappso::masschroq::QuantificationMethod Class Reference

#include <quantificationmethod.h>

Public Member Functions
	QuantificationMethod (const QString &id)
	QuantificationMethod (const QuantificationMethod &other)
virtual	~QuantificationMethod ()
const QString &	getId () const
void	setXicExtractMethod (Enums::XicExtractMethod method)
Enums::XicExtractMethod	getXicExtractMethod () const
void	setXicExtractionLowerPrecisionPtr (pappso::PrecisionPtr precision)
void	setXicExtractionUpperPrecisionPtr (pappso::PrecisionPtr precision)
pappso::PrecisionPtr	getXicExtractionMeanPrecisionPtr () const
void	addXicFilter (const pappso::FilterNameInterfaceSPtr &filter)
void	setXicFilter (const pappso::FilterNameInterfaceSPtr &filter)
void	setTraceDetectionInterfaceCstSPtr (const pappso::TraceDetectionInterfaceCstSPtr &detection)
const pappso::TraceDetectionInterfaceCstSPtr &	getTraceDetectionInterfaceCstSPtr () const
const pappso::FilterNameInterfaceSPtr	getXicFilter () const
const FilterSuiteStringSPtr &	getFilterSuiteStringSPtr () const
const pappso::MzRange	getXicExtractionMzRange (double mz) const
pappso::ProjectParameters	getProjectParameters () const
void	setJsonObject (const QJsonObject &json_object)
QJsonObject	getJsonObject () const
pappso::PrecisionPtr	getXicExtractionLowerPrecisionPtr () const
pappso::PrecisionPtr	getXicExtractionUppersPrecisionPtr () const
void	setMatchBetweenRun (bool is_match)
bool	getMatchBetweenRun () const
void	setIsotopeMinimumRatio (double ratio)
double	getIsotopeMinimumRatio () const
void	setXicExtractionRtRange (double rt_range)
double	getXicExtractionRtRange () const

Private Attributes
const QString	m_id
Enums::XicExtractMethod	m_xicExtractMethod = Enums::XicExtractMethod::max
pappso::PrecisionPtr	mp_xicExtractionLowerPrecisionPtr = nullptr
pappso::PrecisionPtr	mp_xicExtractionUppersPrecisionPtr = nullptr
double	m_xicExtractionRetentionTimeAroundTarget = 300
	set the retention time range in seconds around the target rt
pappso::FilterSuiteStringSPtr	m_xicFilterSuite
	the xic filters
pappso::TraceDetectionInterfaceCstSPtr	mcsp_traceDetectionInterfaceCstSPtr
	the peak detection method for this quantification
bool	m_matchBetweenRun = true
double	m_isotopeMinimumRatio = 0
	the minimum percentage of theoretical intensity of the isotope pattern to compute

Detailed Description

Todo

write docs

Definition at line 51 of file quantificationmethod.h.

Constructor & Destructor Documentation

QuantificationMethod() [1/2]

pappso::masschroq::QuantificationMethod::QuantificationMethod

(

const QString &

id

)

Default constructor

Definition at line 39 of file quantificationmethod.cpp.

                                                                     : m_id(id)
{
  // by default
  qDebug();
  mp_xicExtractionLowerPrecisionPtr  = PrecisionFactory::getPpmInstance(10);
  mp_xicExtractionUppersPrecisionPtr = PrecisionFactory::getPpmInstance(10);
  m_isotopeMinimumRatio              = 0.8;
 
  qDebug();
  setXicFilter(std::make_shared<FilterMorphoAntiSpike>(5));
 
  qDebug();
  mcsp_traceDetectionInterfaceCstSPtr =
    std::make_shared<TraceDetectionZivy>(1, 3, 2, 5000, 3000);
  qDebug();
}

References pappso::PrecisionFactory::getPpmInstance(), m_id, m_isotopeMinimumRatio, mcsp_traceDetectionInterfaceCstSPtr, mp_xicExtractionLowerPrecisionPtr, mp_xicExtractionUppersPrecisionPtr, and setXicFilter().

QuantificationMethod() [2/2]

pappso::masschroq::QuantificationMethod::QuantificationMethod

(

const QuantificationMethod &

other

)

Definition at line 56 of file quantificationmethod.cpp.

  : m_id(other.m_id)
{
  m_isotopeMinimumRatio                    = other.m_isotopeMinimumRatio;
  m_matchBetweenRun                        = other.m_matchBetweenRun;
  m_xicExtractMethod                       = other.m_xicExtractMethod;
  m_xicFilterSuite                         = other.m_xicFilterSuite;
  mcsp_traceDetectionInterfaceCstSPtr      = other.mcsp_traceDetectionInterfaceCstSPtr;
  mp_xicExtractionLowerPrecisionPtr        = other.mp_xicExtractionLowerPrecisionPtr;
  mp_xicExtractionUppersPrecisionPtr       = other.mp_xicExtractionUppersPrecisionPtr;
  m_xicExtractionRetentionTimeAroundTarget = other.m_xicExtractionRetentionTimeAroundTarget;
}

References m_id, m_isotopeMinimumRatio, m_matchBetweenRun, m_xicExtractionRetentionTimeAroundTarget, m_xicExtractMethod, m_xicFilterSuite, mcsp_traceDetectionInterfaceCstSPtr, mp_xicExtractionLowerPrecisionPtr, and mp_xicExtractionUppersPrecisionPtr.

~QuantificationMethod()

pappso::masschroq::QuantificationMethod::~QuantificationMethod ( )

virtual

Destructor

Definition at line 71 of file quantificationmethod.cpp.

{
}

Member Function Documentation

addXicFilter()

void pappso::masschroq::QuantificationMethod::addXicFilter

(

const pappso::FilterNameInterfaceSPtr &

filter

)

Definition at line 122 of file quantificationmethod.cpp.

{
  if(m_xicFilterSuite.get() == nullptr)
    {
      m_xicFilterSuite = std::make_shared<FilterSuiteString>(filter.get()->toString());
    }
  else
    {
      m_xicFilterSuite.get()->addFilter(filter);
    }
}

References pappso::filter, and m_xicFilterSuite.

Referenced by setJsonObject().

getFilterSuiteStringSPtr()

const FilterSuiteStringSPtr & pappso::masschroq::QuantificationMethod::getFilterSuiteStringSPtr

(

)

const

Definition at line 135 of file quantificationmethod.cpp.

{
  return m_xicFilterSuite;
}

References m_xicFilterSuite.

getId()

const QString & pappso::masschroq::QuantificationMethod::getId

(

)

const

Definition at line 76 of file quantificationmethod.cpp.

{
  return m_id;
}

References m_id.

getIsotopeMinimumRatio()

double pappso::masschroq::QuantificationMethod::getIsotopeMinimumRatio

(

)

const

Definition at line 109 of file quantificationmethod.cpp.

{
  return m_isotopeMinimumRatio;
}

References m_isotopeMinimumRatio.

Referenced by getProjectParameters(), and pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide().

getJsonObject()

QJsonObject pappso::masschroq::QuantificationMethod::getJsonObject

(

)

const

Definition at line 286 of file quantificationmethod.cpp.

{
  QJsonObject method;
 
  qDebug();
 
  QString xic_type = Utils::enumToString(m_xicExtractMethod);
 
  if(mp_xicExtractionUppersPrecisionPtr == nullptr)
    {
      throw PappsoException(
        "mp_xicExtractionUppersPrecisionPtr == "
        "nullptr");
    }
  if(mp_xicExtractionLowerPrecisionPtr == nullptr)
    {
      throw PappsoException(
        "mp_xicExtractionLowerPrecisionPtr == "
        "nullptr");
    }
  qDebug();
  QJsonObject precision;
  precision.insert("unit", Utils::enumToString(mp_xicExtractionUppersPrecisionPtr->unit()));
  precision.insert("down", mp_xicExtractionLowerPrecisionPtr->getNominal());
  precision.insert("up", mp_xicExtractionUppersPrecisionPtr->getNominal());
 
 
  QJsonObject extraction;
  extraction.insert("integration", xic_type);
  extraction.insert("precision", precision);
 
  method.insert("extraction", extraction);
  method.insert("match_between_run", m_matchBetweenRun);
  method.insert("isotope_minimum_ratio", m_isotopeMinimumRatio);
  method.insert("rt_range", m_xicExtractionRetentionTimeAroundTarget);
 
  // xic_filters
 
  if(m_xicFilterSuite.get() == nullptr)
    {
      throw PappsoException(
        "m_xicFilterSuite.get() == "
        "nullptr");
    }
  method.insert("pre_filter", m_xicFilterSuite.get()->toString());
 
 
  const TraceDetectionZivy *detection_zivy =
    dynamic_cast<const TraceDetectionZivy *>(getTraceDetectionInterfaceCstSPtr().get());
 
  if(detection_zivy == nullptr)
    {
      throw PappsoException(
        "m_quantificationMethod.getTraceDetectionInterfaceCstSPtr().get() == "
        "nullptr");
    }
 
  QJsonObject detection;
  detection.insert("type", "zivy");
  detection.insert("meanfilter", (int)detection_zivy->getSmoothingHalfEdgeWindows());
  detection.insert("minmax", (int)detection_zivy->getMinMaxHalfEdgeWindows());
  detection.insert("maxmin", (int)detection_zivy->getMaxMinHalfEdgeWindows());
  detection.insert("threshold_on_max", detection_zivy->getDetectionThresholdOnMinmax());
  detection.insert("threshold_on_min", detection_zivy->getDetectionThresholdOnMaxmin());
  method.insert("detection", detection);
 
 
  return method;
}

References pappso::masschroq::Utils::enumToString(), pappso::TraceDetectionZivy::getDetectionThresholdOnMaxmin(), pappso::TraceDetectionZivy::getDetectionThresholdOnMinmax(), pappso::TraceDetectionZivy::getMaxMinHalfEdgeWindows(), pappso::TraceDetectionZivy::getMinMaxHalfEdgeWindows(), pappso::TraceDetectionZivy::getSmoothingHalfEdgeWindows(), getTraceDetectionInterfaceCstSPtr(), m_isotopeMinimumRatio, m_matchBetweenRun, m_xicExtractionRetentionTimeAroundTarget, m_xicExtractMethod, m_xicFilterSuite, mp_xicExtractionLowerPrecisionPtr, and mp_xicExtractionUppersPrecisionPtr.

getMatchBetweenRun()

bool pappso::masschroq::QuantificationMethod::getMatchBetweenRun

(

)

const

Definition at line 94 of file quantificationmethod.cpp.

{
  return m_matchBetweenRun;
}

References m_matchBetweenRun.

Referenced by getProjectParameters(), and pappso::masschroq::MsRunGroup::quantify().

getProjectParameters()

ProjectParameters pappso::masschroq::QuantificationMethod::getProjectParameters

(

)

const

Definition at line 211 of file quantificationmethod.cpp.

{
  ProjectParameters parameters;
 
  ProjectParam project_param(
    {ProjectParamCategory::quantification, "", QVariant()});
  // xic_type="max"
  project_param.name = "mcq_xic_extraction_type";
  project_param.value.setValue(masschroq::Utils::enumToString(m_xicExtractMethod));
  parameters.setProjectParam(project_param);
 
  project_param.name = "mcq_mbr";
  project_param.value.setValue(getMatchBetweenRun());
  parameters.setProjectParam(project_param);
 
  project_param.name = "mcq_isotope_minimum_ratio";
  project_param.value.setValue(getIsotopeMinimumRatio());
  parameters.setProjectParam(project_param);
 
 
  if(mp_xicExtractionLowerPrecisionPtr->unit() == Enums::PrecisionUnit::ppm)
    {
 
      //<!--For XIC extraction on Da use: mz_range-->
      //<ppm_range min="10" max="10"/>
 
      project_param.name = "mcq_xic_ppm_range_min";
      project_param.value.setValue(mp_xicExtractionLowerPrecisionPtr->getNominal());
      parameters.setProjectParam(project_param);
 
      project_param.name = "mcq_xic_ppm_range_max";
      project_param.value.setValue(mp_xicExtractionUppersPrecisionPtr->getNominal());
      parameters.setProjectParam(project_param);
    }
  if(mp_xicExtractionLowerPrecisionPtr->unit() == Enums::PrecisionUnit::dalton)
    {
 
      //<!--For XIC extraction on Da use: mz_range-->
      //<ppm_range min="10" max="10"/>
 
      project_param.name = "mcq_xic_mz_range_min";
      project_param.value.setValue(mp_xicExtractionLowerPrecisionPtr->getNominal());
      parameters.setProjectParam(project_param);
 
      project_param.name = "mcq_xic_mz_range_max";
      project_param.value.setValue(mp_xicExtractionUppersPrecisionPtr->getNominal());
      parameters.setProjectParam(project_param);
    }
 
  project_param.name = "mcq_xic_pre_filter";
  if(m_xicFilterSuite.get() != nullptr)
    project_param.value.setValue(m_xicFilterSuite.get()->toString());
  else
    project_param.value.setValue("");
  parameters.setProjectParam(project_param);
 
 
  const TraceDetectionZivy *detection_zivy =
    dynamic_cast<const TraceDetectionZivy *>(mcsp_traceDetectionInterfaceCstSPtr.get());
 
  if(detection_zivy != nullptr)
    {
      project_param.name = "mcq_detection_zivy";
      project_param.value.setValue(QString("%1 %2 %3 %4 %5")
                                     .arg(detection_zivy->getSmoothingHalfEdgeWindows())
                                     .arg(detection_zivy->getMinMaxHalfEdgeWindows())
                                     .arg(detection_zivy->getMaxMinHalfEdgeWindows())
                                     .arg(detection_zivy->getDetectionThresholdOnMinmax())
                                     .arg(detection_zivy->getDetectionThresholdOnMaxmin()));
      parameters.setProjectParam(project_param);
    }
  return parameters;
}

References pappso::Enums::dalton, pappso::masschroq::Utils::enumToString(), pappso::TraceDetectionZivy::getDetectionThresholdOnMaxmin(), pappso::TraceDetectionZivy::getDetectionThresholdOnMinmax(), getIsotopeMinimumRatio(), getMatchBetweenRun(), pappso::TraceDetectionZivy::getMaxMinHalfEdgeWindows(), pappso::TraceDetectionZivy::getMinMaxHalfEdgeWindows(), pappso::TraceDetectionZivy::getSmoothingHalfEdgeWindows(), m_xicExtractMethod, m_xicFilterSuite, mcsp_traceDetectionInterfaceCstSPtr, mp_xicExtractionLowerPrecisionPtr, mp_xicExtractionUppersPrecisionPtr, pappso::ProjectParam::name, pappso::Enums::ppm, pappso::quantification, and pappso::ProjectParameters::setProjectParam().

getTraceDetectionInterfaceCstSPtr()

const TraceDetectionInterfaceCstSPtr & pappso::masschroq::QuantificationMethod::getTraceDetectionInterfaceCstSPtr

(

)

const

Definition at line 205 of file quantificationmethod.cpp.

{
  return mcsp_traceDetectionInterfaceCstSPtr;
}

References mcsp_traceDetectionInterfaceCstSPtr.

Referenced by pappso::masschroq::MbrPeptideMeasurements::detectQuantifyPeaks(), pappso::masschroq::PeptideMeasurements::detectQuantifyPeaks(), and getJsonObject().

getXicExtractionLowerPrecisionPtr()

PrecisionPtr pappso::masschroq::QuantificationMethod::getXicExtractionLowerPrecisionPtr

(

)

const

Definition at line 445 of file quantificationmethod.cpp.

{
  return mp_xicExtractionLowerPrecisionPtr;
}

References mp_xicExtractionLowerPrecisionPtr.

getXicExtractionMeanPrecisionPtr()

PrecisionPtr pappso::masschroq::QuantificationMethod::getXicExtractionMeanPrecisionPtr

(

)

const

Definition at line 142 of file quantificationmethod.cpp.

{
 
  if(mp_xicExtractionLowerPrecisionPtr->unit() == Enums::PrecisionUnit::ppm)
    {
      return PrecisionFactory::getPpmInstance(
        (mp_xicExtractionLowerPrecisionPtr->getNominal() +
         mp_xicExtractionUppersPrecisionPtr->getNominal()) /
        2);
    }
  return PrecisionFactory::getDaltonInstance(
    (mp_xicExtractionLowerPrecisionPtr->getNominal() +
     mp_xicExtractionUppersPrecisionPtr->getNominal()) /
    2);
}

References pappso::PrecisionFactory::getDaltonInstance(), pappso::PrecisionFactory::getPpmInstance(), mp_xicExtractionLowerPrecisionPtr, mp_xicExtractionUppersPrecisionPtr, and pappso::Enums::ppm.

Referenced by pappso::masschroq::PeptideMeasurementsBase::generateMeasurementsForIsotopeList().

getXicExtractionMzRange()

const MzRange pappso::masschroq::QuantificationMethod::getXicExtractionMzRange

(

double

mz

)

const

Definition at line 198 of file quantificationmethod.cpp.

{
 
  return MzRange(mz, mp_xicExtractionLowerPrecisionPtr, mp_xicExtractionUppersPrecisionPtr);
}

References mp_xicExtractionLowerPrecisionPtr, and mp_xicExtractionUppersPrecisionPtr.

Referenced by pappso::masschroq::PeptideMeasurementsBase::generateMeasurementsForIsotopeList(), and pappso::masschroq::PeptideMeasurementsBase::prepareMeasurementsForPeptide().

getXicExtractionRtRange()

double pappso::masschroq::QuantificationMethod::getXicExtractionRtRange

(

)

const

Definition at line 82 of file quantificationmethod.cpp.

{
  return m_xicExtractionRetentionTimeAroundTarget;
}

References m_xicExtractionRetentionTimeAroundTarget.

Referenced by pappso::masschroq::MsRunPeptideList::quantify(), and pappso::masschroq::MsRunPeptideList::quantifyMatchBetweenRun().

getXicExtractionUppersPrecisionPtr()

PrecisionPtr pappso::masschroq::QuantificationMethod::getXicExtractionUppersPrecisionPtr

(

)

const

Definition at line 451 of file quantificationmethod.cpp.

{
  return mp_xicExtractionUppersPrecisionPtr;
}

References mp_xicExtractionUppersPrecisionPtr.

getXicExtractMethod()

Enums::XicExtractMethod pappso::masschroq::QuantificationMethod::getXicExtractMethod

(

)

const

Definition at line 159 of file quantificationmethod.cpp.

{
  return m_xicExtractMethod;
}

References m_xicExtractMethod.

Referenced by pappso::masschroq::MsRunPeptideList::quantify(), and pappso::masschroq::MsRunPeptideList::quantifyMatchBetweenRun().

getXicFilter()

const FilterNameInterfaceSPtr pappso::masschroq::QuantificationMethod::getXicFilter

(

)

const

Definition at line 192 of file quantificationmethod.cpp.

{
  return m_xicFilterSuite;
}

References m_xicFilterSuite.

Referenced by pappso::masschroq::MsRunPeptideList::quantify(), and pappso::masschroq::MsRunPeptideList::quantifyMatchBetweenRun().

setIsotopeMinimumRatio()

void pappso::masschroq::QuantificationMethod::setIsotopeMinimumRatio

(

double

ratio

)

Definition at line 100 of file quantificationmethod.cpp.

{
  if((ratio < 1) && (ratio >= 0))
    {
      m_isotopeMinimumRatio = ratio;
    }
}

References m_isotopeMinimumRatio.

setJsonObject()

void pappso::masschroq::QuantificationMethod::setJsonObject

(

const QJsonObject &

json_object

)

Definition at line 357 of file quantificationmethod.cpp.

{
  m_matchBetweenRun     = quantification_method.value("match_between_run").toBool();
  m_isotopeMinimumRatio = quantification_method.value("isotope_minimum_ratio").toDouble();
  QString filter_str    = quantification_method.value("pre_filter").toString();
 
  qDebug() << filter_str;
  if(!filter_str.isEmpty())
    {
      FilterNameInterfaceSPtr filter_sp =
        std::make_shared<FilterSuiteString>(filter_str);
      addXicFilter(filter_sp);
      qDebug() << filter_str;
    }
  QJsonObject extraction = quantification_method.value("extraction").toObject();
 
  QJsonValue rt_range = extraction.value("rt_range");
  if(!rt_range.isUndefined())
    {
      setXicExtractionRtRange(rt_range.toDouble());
    }
 
  QString integration = extraction.value("integration").toString();
  if(integration == "sum")
    {
      setXicExtractMethod(Enums::XicExtractMethod::sum);
    }
  else if(integration == "max")
    {
      setXicExtractMethod(Enums::XicExtractMethod::max);
    }
  else
    {
      throw ExceptionNotFound(
        QObject::tr("missing "
                    "masschroq_methods>quantification_method>extraction>"
                    "integration %1 value")
          .arg(integration));
    }
 
  QJsonObject precision = extraction.value("precision").toObject();
  qDebug() << precision.value("down").toDouble();
  qDebug() << precision.value("up").toDouble();
 
  if(precision.value("unit").toString() == "dalton")
    {
      setXicExtractionLowerPrecisionPtr(
        PrecisionFactory::getDaltonInstance(precision.value("down").toDouble()));
      setXicExtractionUpperPrecisionPtr(
        PrecisionFactory::getDaltonInstance(precision.value("up").toDouble()));
    }
  else if(precision.value("unit").toString() == "ppm")
    {
      setXicExtractionLowerPrecisionPtr(
        PrecisionFactory::getPpmInstance(precision.value("down").toDouble()));
      setXicExtractionUpperPrecisionPtr(
        PrecisionFactory::getPpmInstance(precision.value("up").toDouble()));
    }
  else
    {
      throw ExceptionNotFound(
        QObject::tr("missing "
                    "masschroq_methods>quantification_method>extraction>precision>"
                    "unit"));
    }
 
 
  QJsonObject detection = quantification_method.value("detection").toObject();
  if(detection.value("type").toString() == "zivy")
    {
      std::shared_ptr<TraceDetectionZivy> sp_detection_zivy =
        std::make_shared<TraceDetectionZivy>(detection.value("meanfilter").toInt(),
                                                     detection.value("minmax").toInt(),
                                                     detection.value("maxmin").toInt(),
                                                     detection.value("threshold_on_max").toInt(),
                                                     detection.value("threshold_on_min").toInt());
      setTraceDetectionInterfaceCstSPtr(sp_detection_zivy);
    }
  else
    {
 
      throw ExceptionNotFound(
        QObject::tr("only masschroq_methods>quantification_method>detection>type == zivy "
                    "allowed"));
    }
}

References addXicFilter(), pappso::PrecisionFactory::getDaltonInstance(), pappso::PrecisionFactory::getPpmInstance(), m_isotopeMinimumRatio, m_matchBetweenRun, pappso::Enums::max, setTraceDetectionInterfaceCstSPtr(), setXicExtractionLowerPrecisionPtr(), setXicExtractionRtRange(), setXicExtractionUpperPrecisionPtr(), setXicExtractMethod(), and pappso::Enums::sum.

setMatchBetweenRun()

void pappso::masschroq::QuantificationMethod::setMatchBetweenRun

(

bool

is_match

)

Definition at line 457 of file quantificationmethod.cpp.

{
  m_matchBetweenRun = is_match;
}

References m_matchBetweenRun.

setTraceDetectionInterfaceCstSPtr()

void pappso::masschroq::QuantificationMethod::setTraceDetectionInterfaceCstSPtr

(

const pappso::TraceDetectionInterfaceCstSPtr &

detection

)

Definition at line 165 of file quantificationmethod.cpp.

{
  mcsp_traceDetectionInterfaceCstSPtr = detection;
}

References mcsp_traceDetectionInterfaceCstSPtr.

Referenced by setJsonObject().

setXicExtractionLowerPrecisionPtr()

void pappso::masschroq::QuantificationMethod::setXicExtractionLowerPrecisionPtr

(

pappso::PrecisionPtr

precision

)

Definition at line 172 of file quantificationmethod.cpp.

{
  mp_xicExtractionLowerPrecisionPtr = precision;
}

References mp_xicExtractionLowerPrecisionPtr.

Referenced by setJsonObject().

setXicExtractionRtRange()

void pappso::masschroq::QuantificationMethod::setXicExtractionRtRange

(

double

rt_range

)

Definition at line 88 of file quantificationmethod.cpp.

{
  m_xicExtractionRetentionTimeAroundTarget = rt_range;
}

References m_xicExtractionRetentionTimeAroundTarget.

Referenced by setJsonObject().

setXicExtractionUpperPrecisionPtr()

void pappso::masschroq::QuantificationMethod::setXicExtractionUpperPrecisionPtr

(

pappso::PrecisionPtr

precision

)

Definition at line 179 of file quantificationmethod.cpp.

{
  mp_xicExtractionUppersPrecisionPtr = precision;
}

References mp_xicExtractionUppersPrecisionPtr.

Referenced by setJsonObject().

setXicExtractMethod()

void pappso::masschroq::QuantificationMethod::setXicExtractMethod

(

Enums::XicExtractMethod

method

)

Definition at line 186 of file quantificationmethod.cpp.

{
  m_xicExtractMethod = method;
}

References m_xicExtractMethod.

Referenced by setJsonObject().

setXicFilter()

void pappso::masschroq::QuantificationMethod::setXicFilter

(

const pappso::FilterNameInterfaceSPtr &

filter

)

Definition at line 115 of file quantificationmethod.cpp.

{
  m_xicFilterSuite = std::make_shared<FilterSuiteString>(filter.get()->toString());
}

References pappso::filter, and m_xicFilterSuite.

Referenced by QuantificationMethod().

Member Data Documentation

m_id

const QString pappso::masschroq::QuantificationMethod::m_id

private

Definition at line 114 of file quantificationmethod.h.

Referenced by QuantificationMethod(), QuantificationMethod(), and getId().

m_isotopeMinimumRatio

double pappso::masschroq::QuantificationMethod::m_isotopeMinimumRatio = 0

private

the minimum percentage of theoretical intensity of the isotope pattern to compute

Definition at line 144 of file quantificationmethod.h.

Referenced by QuantificationMethod(), QuantificationMethod(), getIsotopeMinimumRatio(), getJsonObject(), setIsotopeMinimumRatio(), and setJsonObject().

m_matchBetweenRun

bool pappso::masschroq::QuantificationMethod::m_matchBetweenRun = true

private

Definition at line 139 of file quantificationmethod.h.

Referenced by QuantificationMethod(), getJsonObject(), getMatchBetweenRun(), setJsonObject(), and setMatchBetweenRun().

m_xicExtractionRetentionTimeAroundTarget

double pappso::masschroq::QuantificationMethod::m_xicExtractionRetentionTimeAroundTarget = 300

private

set the retention time range in seconds around the target rt

only the interesting part of the xic will be extracted, form the rt target

• range_in_seconds to rt target + range in seconds by default, all the LC run time is extracted

Parameters

range_in_seconds

range in seconds

Definition at line 129 of file quantificationmethod.h.

Referenced by QuantificationMethod(), getJsonObject(), getXicExtractionRtRange(), and setXicExtractionRtRange().

m_xicExtractMethod

Enums::XicExtractMethod pappso::masschroq::QuantificationMethod::m_xicExtractMethod = Enums::XicExtractMethod::max

private

Definition at line 115 of file quantificationmethod.h.

Referenced by QuantificationMethod(), getJsonObject(), getProjectParameters(), getXicExtractMethod(), and setXicExtractMethod().

m_xicFilterSuite

pappso::FilterSuiteStringSPtr pappso::masschroq::QuantificationMethod::m_xicFilterSuite

private

the xic filters

Definition at line 133 of file quantificationmethod.h.

Referenced by QuantificationMethod(), addXicFilter(), getFilterSuiteStringSPtr(), getJsonObject(), getProjectParameters(), getXicFilter(), and setXicFilter().

mcsp_traceDetectionInterfaceCstSPtr

pappso::TraceDetectionInterfaceCstSPtr pappso::masschroq::QuantificationMethod::mcsp_traceDetectionInterfaceCstSPtr

private

the peak detection method for this quantification

Definition at line 137 of file quantificationmethod.h.

Referenced by QuantificationMethod(), QuantificationMethod(), getProjectParameters(), getTraceDetectionInterfaceCstSPtr(), and setTraceDetectionInterfaceCstSPtr().

mp_xicExtractionLowerPrecisionPtr

pappso::PrecisionPtr pappso::masschroq::QuantificationMethod::mp_xicExtractionLowerPrecisionPtr = nullptr

private

Definition at line 117 of file quantificationmethod.h.

Referenced by QuantificationMethod(), QuantificationMethod(), getJsonObject(), getProjectParameters(), getXicExtractionLowerPrecisionPtr(), getXicExtractionMeanPrecisionPtr(), getXicExtractionMzRange(), and setXicExtractionLowerPrecisionPtr().

mp_xicExtractionUppersPrecisionPtr

pappso::PrecisionPtr pappso::masschroq::QuantificationMethod::mp_xicExtractionUppersPrecisionPtr = nullptr

private

Definition at line 118 of file quantificationmethod.h.

Referenced by QuantificationMethod(), QuantificationMethod(), getJsonObject(), getProjectParameters(), getXicExtractionMeanPrecisionPtr(), getXicExtractionMzRange(), getXicExtractionUppersPrecisionPtr(), and setXicExtractionUpperPrecisionPtr().

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The documentation for this class was generated from the following files:

• pappsomspp/core/masschroq/quantificationmethod.h
• pappsomspp/core/masschroq/quantificationmethod.cpp