pappso::specpeptidoms::Alignment Struct Reference

#include <semiglobalalignment.h>

Public Member Functions
void	reset ()
	reinitialize to default score_values
QString	getPeptideString (const QString &protein_sequence) const
	convenient function to get peptide sequence from location
double	getNonAlignedMass () const
	convenient function to get the remaining non explained mass shift
std::size_t	getPositionStart () const
	get position of start on the protein sequence

Public Attributes
std::vector< std::size_t >	peaks
PeptideModel	m_peptideModel
int	score = 0
double	begin_shift = 0.0
double	end_shift = 0.0
std::vector< double >	shifts
std::size_t	SPC = 0
std::size_t	beginning = 0
std::size_t	end = 0

Detailed Description

Definition at line 55 of file semiglobalalignment.h.

Member Function Documentation

getNonAlignedMass()

double pappso::specpeptidoms::Alignment::getNonAlignedMass

(

)

const

convenient function to get the remaining non explained mass shift

non explained mass delta between the peptide chemical formula and the observed experimental spectrum precursor

Definition at line 66 of file semiglobalalignment.cpp.

{
  double sum_of_elems = std::accumulate(shifts.begin(), shifts.end(), 0);
  return begin_shift + sum_of_elems + end_shift;
}

Referenced by pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

getPeptideString()

QString pappso::specpeptidoms::Alignment::getPeptideString

(

const QString &

protein_sequence

)

const

convenient function to get peptide sequence from location

Definition at line 60 of file semiglobalalignment.cpp.

{
  return protein_sequence.mid(beginning, end - beginning);
}

getPositionStart()

std::size_t pappso::specpeptidoms::Alignment::getPositionStart

(

)

const

get position of start on the protein sequence

Definition at line 74 of file semiglobalalignment.cpp.

{
  return beginning;
}

Referenced by pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

reset()

void pappso::specpeptidoms::Alignment::reset

(

)

reinitialize to default score_values

Definition at line 45 of file semiglobalalignment.cpp.

{
  peaks.clear();
  m_peptideModel.reset();
  score       = 0;
  begin_shift = 0.0;
  end_shift   = 0.0;
  shifts.clear();
  SPC       = 0;
  beginning = 0;
  end       = 0;
}

References begin_shift, beginning, end, end_shift, m_peptideModel, peaks, pappso::specpeptidoms::PeptideModel::reset(), score, shifts, and SPC.

Member Data Documentation

begin_shift

double pappso::specpeptidoms::Alignment::begin_shift = 0.0

Definition at line 80 of file semiglobalalignment.h.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::getPotentialMassErrors(), reset(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

beginning

std::size_t pappso::specpeptidoms::Alignment::beginning = 0

Definition at line 86 of file semiglobalalignment.h.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::getPotentialMassErrors(), and reset().

end

std::size_t pappso::specpeptidoms::Alignment::end = 0

Definition at line 87 of file semiglobalalignment.h.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::getPotentialMassErrors(), reset(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

end_shift

double pappso::specpeptidoms::Alignment::end_shift = 0.0

Definition at line 82 of file semiglobalalignment.h.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::getPotentialMassErrors(), reset(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

m_peptideModel

PeptideModel pappso::specpeptidoms::Alignment::m_peptideModel

Definition at line 77 of file semiglobalalignment.h.

Referenced by reset(), pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

peaks

std::vector<std::size_t> pappso::specpeptidoms::Alignment::peaks

Definition at line 76 of file semiglobalalignment.h.

Referenced by reset().

score

int pappso::specpeptidoms::Alignment::score = 0

Definition at line 79 of file semiglobalalignment.h.

Referenced by reset(), pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

shifts

std::vector<double> pappso::specpeptidoms::Alignment::shifts

Definition at line 84 of file semiglobalalignment.h.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::getPotentialMassErrors(), reset(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

SPC

std::size_t pappso::specpeptidoms::Alignment::SPC = 0

Definition at line 85 of file semiglobalalignment.h.

Referenced by reset(), pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::storeAlignment().

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

• pappsomspp/core/processing/specpeptidoms/semiglobalalignment.h
• pappsomspp/core/processing/specpeptidoms/semiglobalalignment.cpp