#include <spomsprotein.h>

Inheritance diagram for pappso::specpeptidoms::SpOMSProtein:

Public Member Functions
	SpOMSProtein (const QString &description, const QString &sequence, const AaCode &aa_code)
virtual	~SpOMSProtein ()
const QString	getAccession () const
const QString &	getCompleteDescription () const
const QString &	getSequence () const
std::vector< SpOMSAa >	sliced (std::size_t position, std::size_t length) const

Private Attributes
QString	m_description
QString	m_sequence

Detailed Description

Definition at line 37 of file spomsprotein.h.

Constructor & Destructor Documentation

◆ SpOMSProtein()

pappso::specpeptidoms::SpOMSProtein::SpOMSProtein	(	const QString &	description,
		const QString &	sequence,
		const AaCode &	aa_code )

Definition at line 26 of file spomsprotein.cpp.

  : m_description(description), m_sequence(sequence)
{
  clear();
 
  SpOMSAa aa;
 
  for(const QChar &aa_str : m_sequence)
    {
      aa.aa   = (pappso::Enums::AminoAcidChar)aa_str.toLatin1();
      aa.code = aa_code.getAaCode(aa.aa);
      aa.mass = aa_code.getMass(aa.code);
      push_back(aa);
    }
 
  // by default the sequence is reversed
  std::reverse(begin(), end());
}

References pappso::AaCode::getAaCode(), pappso::AaCode::getMass(), m_description, and m_sequence.

◆ ~SpOMSProtein()

pappso::specpeptidoms::SpOMSProtein::~SpOMSProtein ( )

virtual

Definition at line 47 of file spomsprotein.cpp.

48{

49}

Member Function Documentation

◆ getAccession()

const QString pappso::specpeptidoms::SpOMSProtein::getAccession ( ) const

Definition at line 52 of file spomsprotein.cpp.

{
  return m_description.split(" ").at(0);
}

References m_description.

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

◆ getCompleteDescription()

const QString & pappso::specpeptidoms::SpOMSProtein::getCompleteDescription ( ) const

Definition at line 65 of file spomsprotein.cpp.

{
  return m_description;
}

References m_description.

◆ getSequence()

const QString & pappso::specpeptidoms::SpOMSProtein::getSequence ( ) const

Definition at line 58 of file spomsprotein.cpp.

{
  return m_sequence;
}

References m_sequence.

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::correctAlign(), pappso::specpeptidoms::SemiGlobalAlignment::preciseAlign(), and pappso::cbor::psm::PsmSpecPeptidOmsScan::sequenceAlignment().

◆ sliced()

std::vector< SpOMSAa > pappso::specpeptidoms::SpOMSProtein::sliced	(	std::size_t	position,
		std::size_t	length ) const

Definition at line 71 of file spomsprotein.cpp.

{
 
  std::vector<SpOMSAa> aa_vec;
 
  for(std::size_t i = 0; i < length; i++)
    {
      aa_vec.push_back(at(i + position));
    }
 
  return aa_vec;
}

Referenced by pappso::specpeptidoms::SemiGlobalAlignment::saveBestAlignment().

Member Data Documentation

◆ m_description

QString pappso::specpeptidoms::SpOMSProtein::m_description

private

Definition at line 52 of file spomsprotein.h.

Referenced by SpOMSProtein(), getAccession(), and getCompleteDescription().

◆ m_sequence

QString pappso::specpeptidoms::SpOMSProtein::m_sequence