pappso::PrecisionFactory Class Reference

#include <precision.h>

Static Public Member Functions
static PrecisionPtr	fromString (const QString &str)
	get a precision pointer from a string
static PrecisionPtr	getDaltonInstance (pappso_double value)
	get a Dalton precision pointer
static PrecisionPtr	getPpmInstance (pappso_double value)
	get a ppm precision pointer
static PrecisionPtr	getResInstance (pappso_double value)
	get a resolution precision pointer
static PrecisionPtr	getPrecisionPtrFractionInstance (PrecisionPtr origin, double fraction)
	get the fraction of an existing precision pointer
static PrecisionPtr	getPrecisionPtrInstance (Enums::PrecisionUnit unit, double value)
	get a precision pointer instance

Private Types
using	MapDaltonPrecision = std::map<pappso_double, DaltonPrecision *>
using	MapPpmPrecision = std::map<pappso_double, PpmPrecision *>
using	MapResPrecision = std::map<pappso_double, ResPrecision *>

Static Private Attributes
static MapDaltonPrecision	m_mapDalton
static MapPpmPrecision	m_mapPpm
static MapResPrecision	m_mapRes

Detailed Description

Definition at line 126 of file precision.h.

Member Typedef Documentation

MapDaltonPrecision

using pappso::PrecisionFactory::MapDaltonPrecision = std::map<pappso_double, DaltonPrecision *>

private

Definition at line 128 of file precision.h.

MapPpmPrecision

using pappso::PrecisionFactory::MapPpmPrecision = std::map<pappso_double, PpmPrecision *>

private

Definition at line 129 of file precision.h.

MapResPrecision

using pappso::PrecisionFactory::MapResPrecision = std::map<pappso_double, ResPrecision *>

private

Definition at line 130 of file precision.h.

Member Function Documentation

fromString()

PrecisionPtr pappso::PrecisionFactory::fromString ( const QString & str )

static

get a precision pointer from a string

Parameters

str	is of the form : "nominal_value unit", example : "0.02 dalton"

Definition at line 80 of file precision.cpp.

{
 
  // The format of the string is <number><space *><string> with string either
  // "ppm" or "dalton" or "res".
  //
  // If there only once component, that is, <string> is omitted and charge is
  // not provided, then "dalton" is considered.
 
  QStringList list = str.split(QRegularExpression("\\s+"), Qt::SkipEmptyParts);
 
  if(list.size() > 0)
    {
      bool ok;
      pappso_double value = list[0].toDouble(&ok);
      if(!ok)
        {
          throw ExceptionNotPossible(QObject::tr("ERROR getting precision from string :\nunable to "
                                                 "convert %1 to number in %2")
                                       .arg(value)
                                       .arg(str));
        }
      if(list.size() == 1)
        {
          return PrecisionFactory::getDaltonInstance(value);
        }
      else if(list.size() == 2)
        {
          if(list[1].toLower() == "dalton")
            {
              return PrecisionFactory::getDaltonInstance(value);
            }
 
          if(list[1].toLower() == "ppm")
            {
              return PrecisionFactory::getPpmInstance(value);
            }
 
          if(list[1].toLower() == "res")
            {
              return PrecisionFactory::getResInstance(value);
            }
 
          throw ExceptionNotPossible(QObject::tr("ERROR getting precision from string :\nprecision "
                                                 "unit %1 to not known in  %2")
                                       .arg(list[1])
                                       .arg(str));
        }
    }
 
  throw ExceptionNotPossible(QObject::tr("ERROR getting precision from string "
                                         ":\nunable to convert %1 to precision")
                               .arg(str));
}

References getDaltonInstance(), getPpmInstance(), and getResInstance().

Referenced by pappso::FilterChargeDeconvolution::buildFilterFromString(), pappso::FilterComplementIonEnhancer::buildFilterFromString(), pappso::FilterMzExclusion::buildFilterFromString(), and pappso::MzIntegrationParams::initialize().

getDaltonInstance()

PrecisionPtr pappso::PrecisionFactory::getDaltonInstance ( pappso_double value )

static

get a Dalton precision pointer

Parameters

value

the precision value in dalton

Definition at line 136 of file precision.cpp.

{
  MapDaltonPrecision::iterator it = m_mapDalton.find(value);
  if(it == m_mapDalton.end())
    {
      // not found
      std::pair<MapDaltonPrecision::iterator, bool> insert_res = m_mapDalton.insert(
        std::pair<pappso_double, DaltonPrecision *>(value, new DaltonPrecision(value)));
      it = insert_res.first;
    }
  else
    {
      // found
    }
  return it->second;
}

References m_mapDalton.

Referenced by pappso::PrecisionWidget::PrecisionWidget(), pappso::cbor::psm::PsmFeatures::PsmFeatures(), pappso::cbor::psm::PsmSpecGlob::PsmSpecGlob(), fromString(), pappso::AaModification::getInstanceXtandemMod(), getPrecisionPtrInstance(), pappso::masschroq::QuantificationMethod::getXicExtractionMeanPrecisionPtr(), pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(), pappso::XtandemSpectrumProcess::process(), pappso::PrecisionWidget::setDaltonValueChanged(), and pappso::masschroq::QuantificationMethod::setJsonObject().

getPpmInstance()

PrecisionPtr pappso::PrecisionFactory::getPpmInstance ( pappso_double value )

static

get a ppm precision pointer

Parameters

value

the precision value in ppm

Definition at line 155 of file precision.cpp.

{
  if(!value)
    throw ExceptionNotPossible(
      QObject::tr("Fatal error at precision.cpp "
                  "-- ERROR trying to set a Resolution precision value of 0. "
                  "Program aborted."));
 
  MapPpmPrecision::iterator it = m_mapPpm.find(value);
 
  if(it == m_mapPpm.end())
    {
      // Not found.
      std::pair<MapPpmPrecision::iterator, bool> insert_res =
        m_mapPpm.insert(std::pair<pappso_double, PpmPrecision *>(value, new PpmPrecision(value)));
      it = insert_res.first;
    }
  else
    {
      // found
    }
  return it->second;
}

References m_mapPpm.

Referenced by pappso::MzIntegrationParams::MzIntegrationParams(), pappso::PrecisionWidget::PrecisionWidget(), pappso::cbor::psm::PsmSpecGlob::PsmSpecGlob(), pappso::masschroq::QuantificationMethod::QuantificationMethod(), pappso::MassSpectrum::equals(), fromString(), getPrecisionPtrInstance(), pappso::masschroq::QuantificationMethod::getXicExtractionMeanPrecisionPtr(), pappso::masschroq::QuantificationMethod::setJsonObject(), pappso::PrecisionWidget::setPpmValueChanged(), and pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum().

getPrecisionPtrFractionInstance()

PrecisionPtr pappso::PrecisionFactory::getPrecisionPtrFractionInstance ( PrecisionPtr origin, double fraction )

static

get the fraction of an existing precision pointer

Parameters

origin	the original precision pointer
fraction	the fraction to apply on the original precision

Definition at line 209 of file precision.cpp.

{
  Enums::PrecisionUnit unit = origin->unit();
  double value              = origin->getNominal() * fraction;
 
 
  return getPrecisionPtrInstance(unit, value);
}

References pappso::PrecisionBase::getNominal(), getPrecisionPtrInstance(), and pappso::PrecisionBase::unit().

Referenced by pappso::FilterChargeDeconvolution::FilterChargeDeconvolution(), and pappso::FilterChargeDeconvolution::buildFilterFromString().

getPrecisionPtrInstance()

PrecisionPtr pappso::PrecisionFactory::getPrecisionPtrInstance ( Enums::PrecisionUnit unit, double value )

static

get a precision pointer instance

Parameters

unit	the precision unit
value	the precision value

Definition at line 219 of file precision.cpp.

{
 
  switch(unit)
    {
      case Enums::PrecisionUnit::dalton:
        return getDaltonInstance(value);
      case Enums::PrecisionUnit::ppm:
        return getPpmInstance(value);
      case Enums::PrecisionUnit::res:
        return getResInstance(value);
      case Enums::PrecisionUnit::mz:
        return getDaltonInstance(value);
      case Enums::PrecisionUnit::none:
        throw ExceptionNotPossible(QObject::tr("Unknown precision unit"));
 
      default:
        throw ExceptionNotPossible(QObject::tr("Unknown precision unit"));
        break;
    }
 
  return nullptr;
}

References pappso::Enums::dalton, getDaltonInstance(), getPpmInstance(), getResInstance(), pappso::Enums::mz, pappso::Enums::none, pappso::Enums::ppm, and pappso::Enums::res.

Referenced by pappso::XtandemPresetReader::getMs2FiltersOptions(), and getPrecisionPtrFractionInstance().

getResInstance()

PrecisionPtr pappso::PrecisionFactory::getResInstance ( pappso_double value )

static

get a resolution precision pointer

Parameters

value

the precision value in resolution

Definition at line 181 of file precision.cpp.

{
  // qDebug() << "Requested a Resolution precision instance for value:" <<
  // value;
 
  if(!value)
    throw ExceptionNotPossible(
      QObject::tr("Fatal error at precision.cpp "
                  "-- ERROR trying to set a Resolution precision value of 0. "
                  "Program aborted."));
 
  MapResPrecision::iterator it = m_mapRes.find(value);
 
  if(it == m_mapRes.end())
    {
      // not found
      std::pair<MapResPrecision::iterator, bool> insert_res =
        m_mapRes.insert(std::pair<pappso_double, ResPrecision *>(value, new ResPrecision(value)));
      it = insert_res.first;
    }
  else
    {
      // found
    }
  return it->second;
}

References m_mapRes.

Referenced by pappso::PrecisionWidget::PrecisionWidget(), fromString(), getPrecisionPtrInstance(), pappso::MzIntegrationParams::reset(), pappso::MzIntegrationParams::setBinSizeModel(), and pappso::PrecisionWidget::setResValueChanged().

Member Data Documentation

m_mapDalton

PrecisionFactory::MapDaltonPrecision pappso::PrecisionFactory::m_mapDalton

staticprivate

Initial value:

= [] {
  MapDaltonPrecision ret;
 
  return ret;
}()

Definition at line 133 of file precision.h.

Referenced by getDaltonInstance().

m_mapPpm

PrecisionFactory::MapPpmPrecision pappso::PrecisionFactory::m_mapPpm

staticprivate

Initial value:

= [] {
  MapPpmPrecision ret;
 
  return ret;
}()

Definition at line 134 of file precision.h.

Referenced by getPpmInstance().

m_mapRes

PrecisionFactory::MapResPrecision pappso::PrecisionFactory::m_mapRes

staticprivate

Initial value:

= [] {
  MapResPrecision ret;
 
  return ret;
}()

Definition at line 135 of file precision.h.

Referenced by getResInstance().

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

• pappsomspp/core/precision.h
• pappsomspp/core/precision.cpp