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 56 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 65 of file semiglobalalignment.cpp.

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

References begin_shift, end_shift, and shifts.

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 59 of file semiglobalalignment.cpp.

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

References beginning, and end.

getPositionStart()

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

(

)

const

get position of start on the protein sequence

Definition at line 73 of file semiglobalalignment.cpp.

{
  return beginning;
}

References beginning.

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

reset()

void pappso::specpeptidoms::Alignment::reset

(

)

reinitialize to default score_values

Definition at line 44 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, score, shifts, and SPC.

Member Data Documentation

begin_shift

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

Definition at line 81 of file semiglobalalignment.h.

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

beginning

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

Definition at line 87 of file semiglobalalignment.h.

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

end

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

Definition at line 88 of file semiglobalalignment.h.

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

end_shift

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

Definition at line 83 of file semiglobalalignment.h.

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

m_peptideModel

PeptideModel pappso::specpeptidoms::Alignment::m_peptideModel

Definition at line 78 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 77 of file semiglobalalignment.h.

Referenced by reset().

score

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

Definition at line 80 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 85 of file semiglobalalignment.h.

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

SPC

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

Definition at line 86 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