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 70 of file protein.h.

Constructor & Destructor Documentation

Protein() [1/3]

pappso::Protein::Protein

(

)

Definition at line 83 of file protein.cpp.

{
  m_sequence.replace(m_removeTranslationStopRegExp, "");

References m_removeTranslationStopRegExp, and m_sequence.

Protein() [2/3]

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

Definition at line 86 of file protein.cpp.

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

Protein() [3/3]

pappso::Protein::Protein

(

const Protein &

protein

)

Definition at line 95 of file protein.cpp.

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

~Protein()

pappso::Protein::~Protein

(

)

Definition at line 167 of file protein.cpp.

Member Function Documentation

getAccession()

const QString & pappso::Protein::getAccession

(

)

const

Definition at line 148 of file protein.cpp.

{

getDescription()

const QString & pappso::Protein::getDescription

(

)

const

Definition at line 158 of file protein.cpp.

getMass()

pappso_double pappso::Protein::getMass

(

)

const

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

Definition at line 171 of file protein.cpp.

getSequence()

const QString & pappso::Protein::getSequence

(

)

const

Definition at line 143 of file protein.cpp.

{
  m_description = description.simplified();
}
Protein::~Protein()

References m_description.

makeProteinSp()

ProteinSp pappso::Protein::makeProteinSp

(

)

const

Definition at line 118 of file protein.cpp.

operator==()

bool pappso::Protein::operator==

(

const Protein &

other

)

const

Definition at line 125 of file protein.cpp.

{

removeTranslationStop()

Protein & pappso::Protein::removeTranslationStop

(

)

remove * characters at the end of the sequence

Definition at line 104 of file protein.cpp.

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

References m_accession.

reverse()

Protein & pappso::Protein::reverse

(

)

reverse characters in the sequence

Definition at line 111 of file protein.cpp.

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

References m_length, and m_sequence.

setAccession()

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

virtual

Definition at line 153 of file protein.cpp.

    {
      // qDebug() << "ProteinXtp::getMass() begin " <<
      // getOnlyAminoAcidSequence().replace("[BZX]","E");
      // replace amino acid wildcard by E, just to give an random mass (assumed

setDescription()

void pappso::Protein::setDescription

(

const QString &

description

)

Definition at line 163 of file protein.cpp.

    {
      throw pappso::PappsoException(
        QObject::tr("Error computing mass for protein %1 :\n%2")

setSequence()

void pappso::Protein::setSequence

(

const QString &

sequence

)

Definition at line 131 of file protein.cpp.

{
  m_accession = accession.simplified();
}

References m_accession.

size()

unsigned int pappso::Protein::size

(

)

const

protein amino acid sequence size

Definition at line 137 of file protein.cpp.

{
  return m_description;
}

References m_description.

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 77 of file protein.h.

Referenced by removeTranslationStop(), and setSequence().

m_description

QString pappso::Protein::m_description

private

free text to describe the protein

Definition at line 74 of file protein.h.

Referenced by getSequence(), and size().

m_length

unsigned int pappso::Protein::m_length = 0

private

number of amino acid

Definition at line 81 of file protein.h.

Referenced by reverse().

m_removeTranslationStopRegExp

QRegExp pappso::Protein::m_removeTranslationStopRegExp

staticprivate

Definition at line 83 of file protein.h.

Referenced by Protein().

m_sequence

QString pappso::Protein::m_sequence

private

the amino acid sequence

Definition at line 79 of file protein.h.

Referenced by Protein(), and reverse().

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

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