pappso::masschroq::AlignmentMethod Class Reference

#include <alignmentmethod.h>

Public Member Functions
	AlignmentMethod (const QString &id)
	AlignmentMethod (const AlignmentMethod &other)
	~AlignmentMethod ()
const QString &	getId () const
void	setMs2TendencyWindow (std::uint8_t ms2_tendency_window)
void	setMs2SmoothingWindow (std::uint8_t ms2_smoothing_window)
void	setMs1SmoothingWindow (std::uint8_t ms1_smoothing_window)
void	setJsonObject (const QJsonObject &json_object)
QJsonObject	getJsonObject () const
std::uint8_t	getMs2TendencyWindow () const
std::uint8_t	getMs2SmoothingWindow () const
std::uint8_t	getMs1SmoothingWindow () const
pappso::ProjectParameters	getProjectParameters () const

Private Attributes
const QString	m_id
quint8	m_ms2TendencyWindow
quint8	m_ms2SmoothingWindow
quint8	m_ms1SmoothingWindow

Detailed Description

Todo

write docs

Definition at line 47 of file alignmentmethod.h.

Constructor & Destructor Documentation

AlignmentMethod() [1/2]

pappso::masschroq::AlignmentMethod::AlignmentMethod

(

const QString &

id

)

Default constructor

Definition at line 31 of file alignmentmethod.cpp.

                                                                 : m_id(id)
{
  m_ms1SmoothingWindow = 15;
  m_ms2SmoothingWindow = 5;
  m_ms2TendencyWindow  = 10;
}

References m_id, m_ms1SmoothingWindow, m_ms2SmoothingWindow, and m_ms2TendencyWindow.

AlignmentMethod() [2/2]

pappso::masschroq::AlignmentMethod::AlignmentMethod

(

const AlignmentMethod &

other

)

Definition at line 38 of file alignmentmethod.cpp.

  : m_id(other.m_id)
{
  m_ms1SmoothingWindow = other.m_ms1SmoothingWindow;
  m_ms2SmoothingWindow = other.m_ms2SmoothingWindow;
  m_ms2TendencyWindow  = other.m_ms2TendencyWindow;
}

References m_id, m_ms1SmoothingWindow, m_ms2SmoothingWindow, and m_ms2TendencyWindow.

~AlignmentMethod()

pappso::masschroq::AlignmentMethod::~AlignmentMethod

(

)

Destructor

Definition at line 47 of file alignmentmethod.cpp.

{
}

Member Function Documentation

getId()

const QString & pappso::masschroq::AlignmentMethod::getId

(

)

const

Definition at line 52 of file alignmentmethod.cpp.

{
  return m_id;
}

References m_id.

getJsonObject()

QJsonObject pappso::masschroq::AlignmentMethod::getJsonObject

(

)

const

Definition at line 135 of file alignmentmethod.cpp.

{
  QJsonObject method;
 
  method.insert("ms1_smoothing", m_ms1SmoothingWindow);
 
  method.insert("ms2_smoothing", m_ms2SmoothingWindow);
 
  method.insert("ms2_tendency", m_ms2TendencyWindow);
 
 
  return method;
}

References m_ms1SmoothingWindow, m_ms2SmoothingWindow, and m_ms2TendencyWindow.

getMs1SmoothingWindow()

std::uint8_t pappso::masschroq::AlignmentMethod::getMs1SmoothingWindow

(

)

const

Definition at line 77 of file alignmentmethod.cpp.

{
  return m_ms1SmoothingWindow;
}

References m_ms1SmoothingWindow.

Referenced by pappso::masschroq::MsRunPeptideList::buildMsRunRetentionTimeSpOnPeptideObservations().

getMs2SmoothingWindow()

std::uint8_t pappso::masschroq::AlignmentMethod::getMs2SmoothingWindow

(

)

const

Definition at line 83 of file alignmentmethod.cpp.

{
  return m_ms2SmoothingWindow;
}

References m_ms2SmoothingWindow.

Referenced by pappso::masschroq::MsRunPeptideList::buildMsRunRetentionTimeSpOnPeptideObservations().

getMs2TendencyWindow()

std::uint8_t pappso::masschroq::AlignmentMethod::getMs2TendencyWindow

(

)

const

Definition at line 89 of file alignmentmethod.cpp.

{
  return m_ms2TendencyWindow;
}

References m_ms2TendencyWindow.

Referenced by pappso::masschroq::MsRunPeptideList::buildMsRunRetentionTimeSpOnPeptideObservations().

getProjectParameters()

pappso::ProjectParameters pappso::masschroq::AlignmentMethod::getProjectParameters

(

)

const

Definition at line 95 of file alignmentmethod.cpp.

{
  pappso::ProjectParameters parameters;
  /*
          pappso::ProjectParam project_param(
            {pappso::ProjectParamCategory::quantification, "", QVariant()});
 
          project_param.name = "mcq_alignment_msrun_reference_for_rt_alignment";
          QString msrunid    = m_qxmlStreamReader.attributes()
                              .value("reference_data_id")
                              .toString();
          project_param.value.setValue(
            m_mcqrMetadataSet.getMcqrMetadaByDataId(msrunid).m_msrunFile);
          m_projectParameters.setProjectParam(project_param);
          */
 
  pappso::ProjectParam project_param(
    {pappso::ProjectParamCategory::quantification, "", QVariant()});
  project_param.name = "mcq_alignment_ms2_tendency_window";
  project_param.value.setValue((std::size_t)m_ms2TendencyWindow);
  parameters.setProjectParam(project_param);
  project_param.name = "mcq_alignment_ms1_smoothing_window";
  project_param.value.setValue((std::size_t)m_ms1SmoothingWindow);
  parameters.setProjectParam(project_param);
  project_param.name = "mcq_alignment_ms2_smoothing_window";
  project_param.value.setValue((std::size_t)m_ms2SmoothingWindow);
  parameters.setProjectParam(project_param);
 
  return parameters;
}

References m_ms1SmoothingWindow, m_ms2SmoothingWindow, m_ms2TendencyWindow, pappso::ProjectParam::name, pappso::quantification, and pappso::ProjectParameters::setProjectParam().

setJsonObject()

void pappso::masschroq::AlignmentMethod::setJsonObject

(

const QJsonObject &

json_object

)

Definition at line 127 of file alignmentmethod.cpp.

{
  setMs1SmoothingWindow(align_method.value("ms1_smoothing").toInt());
  setMs2SmoothingWindow(align_method.value("ms2_smoothing").toInt());
  setMs2TendencyWindow(align_method.value("ms2_tendency").toInt());
}

References setMs1SmoothingWindow(), setMs2SmoothingWindow(), and setMs2TendencyWindow().

setMs1SmoothingWindow()

void pappso::masschroq::AlignmentMethod::setMs1SmoothingWindow

(

std::uint8_t

ms1_smoothing_window

)

Definition at line 58 of file alignmentmethod.cpp.

{
  m_ms1SmoothingWindow = ms1_smoothing_window;
}

References m_ms1SmoothingWindow.

Referenced by setJsonObject().

setMs2SmoothingWindow()

void pappso::masschroq::AlignmentMethod::setMs2SmoothingWindow

(

std::uint8_t

ms2_smoothing_window

)

Definition at line 64 of file alignmentmethod.cpp.

{
  m_ms2SmoothingWindow = ms2_smoothing_window;
}

References m_ms2SmoothingWindow.

Referenced by setJsonObject().

setMs2TendencyWindow()

void pappso::masschroq::AlignmentMethod::setMs2TendencyWindow

(

std::uint8_t

ms2_tendency_window

)

Definition at line 70 of file alignmentmethod.cpp.

{
  m_ms2TendencyWindow = ms2_tendency_window;
}

References m_ms2TendencyWindow.

Referenced by setJsonObject().

Member Data Documentation

m_id

const QString pappso::masschroq::AlignmentMethod::m_id

private

Definition at line 85 of file alignmentmethod.h.

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

m_ms1SmoothingWindow

quint8 pappso::masschroq::AlignmentMethod::m_ms1SmoothingWindow

private

Definition at line 89 of file alignmentmethod.h.

Referenced by AlignmentMethod(), AlignmentMethod(), getJsonObject(), getMs1SmoothingWindow(), getProjectParameters(), and setMs1SmoothingWindow().

m_ms2SmoothingWindow

quint8 pappso::masschroq::AlignmentMethod::m_ms2SmoothingWindow

private

Definition at line 88 of file alignmentmethod.h.

Referenced by AlignmentMethod(), AlignmentMethod(), getJsonObject(), getMs2SmoothingWindow(), getProjectParameters(), and setMs2SmoothingWindow().

m_ms2TendencyWindow

quint8 pappso::masschroq::AlignmentMethod::m_ms2TendencyWindow

private

Definition at line 87 of file alignmentmethod.h.

Referenced by AlignmentMethod(), AlignmentMethod(), getJsonObject(), getMs2TendencyWindow(), getProjectParameters(), and setMs2TendencyWindow().

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

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