pappso::Protein Class Reference

#include <protein.h>

Public Member Functions
	Protein ()
	Protein (const QString &description, const QString &sequence)
	Protein (const Protein &protein)
ProteinSp	makeProteinSp () const
bool	operator== (const Protein &other) const
	~Protein ()
const QString &	getSequence () const
void	setSequence (const QString &sequence)
const QString &	getAccession () const
virtual void	setAccession (const QString &accession)
const QString &	getDescription () const
void	setDescription (const QString &description)
Protein &	removeTranslationStop ()
	remove * characters at the end of the sequence More...
Protein &	reverse ()
	reverse characters in the sequence More...
unsigned int	size () const
	protein amino acid sequence size More...
pappso_double	getMass () const
	get monoisotopic mass of ProteinSp Protein::makeProteinSp() const More...

Private Attributes
QString	m_description
	free text to describe the protein More...
QString	m_accession
	a single unique identifier of the protein (usually the first word of description) More...
QString	m_sequence
	the amino acid sequence More...
unsigned int	m_length = 0
	number of amino acid More...

Static Private Attributes
static QRegExp	m_removeTranslationStopRegExp

Detailed Description

Definition at line 49 of file protein.h.

Constructor & Destructor Documentation

Protein() [1/3]

pappso::Protein::Protein

(

)

Definition at line 62 of file protein.cpp.

{
}

Protein() [2/3]

pappso::Protein::Protein	(	const QString &	description,
		const QString &	sequence
	)

Definition at line 65 of file protein.cpp.

  : m_description(description.simplified()),
    m_accession(m_description.split(" ").at(0)),
    m_sequence(sequence)
{
  m_description = m_description.remove(0, m_accession.size()).simplified();
  // m_sequence.replace(m_removeTranslationStopRegExp, "");
  m_length = m_sequence.size();
}

References m_accession, m_description, m_length, and m_sequence.

Protein() [3/3]

pappso::Protein::Protein

(

const Protein &

protein

)

Definition at line 74 of file protein.cpp.

  : m_description(protein.m_description),
    m_accession(protein.m_accession),
    m_sequence(protein.m_sequence),
    m_length(protein.m_length)
{
}

~Protein()

pappso::Protein::~Protein

(

)

Definition at line 146 of file protein.cpp.

{
}

Member Function Documentation

getAccession()

const QString & pappso::Protein::getAccession

(

)

const

Definition at line 127 of file protein.cpp.

{
  return m_accession;
}

References m_accession.

Referenced by getMass(), and pappso::FastaOutputStream::writeProtein().

getDescription()

const QString & pappso::Protein::getDescription

(

)

const

Definition at line 137 of file protein.cpp.

{
  return m_description;
}

References m_description.

Referenced by pappso::FastaOutputStream::writeProtein().

getMass()

pappso_double pappso::Protein::getMass

(

)

const

get monoisotopic mass of ProteinSp Protein::makeProteinSp() const

Definition at line 150 of file protein.cpp.

{
  try
    {
      // qDebug() << "ProteinXtp::getMass() begin " <<
      // getOnlyAminoAcidSequence().replace("[BZX]","E");
      // replace amino acid wildcard by E, just to give an random mass (assumed
      // it is not perfect)
      QString sequence(m_sequence);
      sequence.replace(QRegExp("[^WGASPVTLINDKQEMHFRCYUBZX]"), "");
      pappso::Peptide peptide(sequence.replace(QRegExp("[BZX]"), "E"));
      return peptide.getMass();
    }
  catch(pappso::PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Error computing mass for protein %1 :\n%2")
          .arg(getAccession())
          .arg(error.qwhat()));
    }
}

References getAccession(), pappso::Peptide::getMass(), m_sequence, and pappso::PappsoException::qwhat().

getSequence()

const QString & pappso::Protein::getSequence

(

)

const

Definition at line 122 of file protein.cpp.

{
  return m_sequence;
}

References m_sequence.

Referenced by pappso::FastaOutputStream::writeProtein().

makeProteinSp()

ProteinSp pappso::Protein::makeProteinSp

(

)

const

Definition at line 97 of file protein.cpp.

{
  return std::make_shared<Protein>(*this);
}

operator==()

bool pappso::Protein::operator==

(

const Protein &

other

)

const

Definition at line 104 of file protein.cpp.

{
  return (m_accession == other.m_accession);
}

References m_accession.

removeTranslationStop()

Protein & pappso::Protein::removeTranslationStop

(

)

remove * characters at the end of the sequence

Definition at line 83 of file protein.cpp.

{
  m_sequence.replace(m_removeTranslationStopRegExp, "");
  return (*this);
}

References m_removeTranslationStopRegExp, and m_sequence.

reverse()

Protein & pappso::Protein::reverse

(

)

reverse characters in the sequence

Definition at line 90 of file protein.cpp.

{
  std::reverse(m_sequence.begin(), m_sequence.end());
  return (*this);
}

References m_sequence.

setAccession()

void pappso::Protein::setAccession ( const QString &  accession )

virtual

Definition at line 132 of file protein.cpp.

{
  m_accession = accession.simplified();
}

References m_accession.

setDescription()

void pappso::Protein::setDescription

(

const QString &

description

)

Definition at line 142 of file protein.cpp.

{
  m_description = description.simplified();
}

References m_description.

setSequence()

void pappso::Protein::setSequence

(

const QString &

sequence

)

Definition at line 110 of file protein.cpp.

{
  m_sequence = sequence.simplified();
  m_length   = m_sequence.size();
}

References m_length, and m_sequence.

size()

unsigned int pappso::Protein::size

(

)

const

protein amino acid sequence size

Definition at line 116 of file protein.cpp.

{
  return m_length;
}

References m_length.

Member Data Documentation

m_accession

QString pappso::Protein::m_accession

private

a single unique identifier of the protein (usually the first word of description)

Definition at line 56 of file protein.h.

Referenced by Protein(), getAccession(), operator==(), and setAccession().

m_description

QString pappso::Protein::m_description

private

free text to describe the protein

Definition at line 53 of file protein.h.

Referenced by Protein(), getDescription(), and setDescription().

m_length

unsigned int pappso::Protein::m_length = 0

private

number of amino acid

Definition at line 60 of file protein.h.

Referenced by Protein(), setSequence(), and size().

m_removeTranslationStopRegExp

QRegExp pappso::Protein::m_removeTranslationStopRegExp

staticprivate

Definition at line 62 of file protein.h.

Referenced by removeTranslationStop().

m_sequence

QString pappso::Protein::m_sequence

private

the amino acid sequence

Definition at line 58 of file protein.h.

Referenced by Protein(), getMass(), getSequence(), removeTranslationStop(), reverse(), and setSequence().

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

• pappsomspp/protein/protein.h
• pappsomspp/protein/protein.cpp