Represents the primary structure of a protein as a sequence of amino acids. More...

#include <cs19_protein.h>

Public Member Functions
	Protein ()
	Constructs a new "empty" Protein (i.e. More...

	Protein (const char *amino_acids)
	Constructs a new Protein object with an initial primary structure. More...

template<typename Sequence >
	Protein (const Sequence &amino_acids)
	Constructs a new Protein object with an initial primary structure. More...

template<class InputIterator >
	Protein (InputIterator first, InputIterator last)
	Constructs a new Protein object from a range of values `[first, last)`. More...

	Protein (std::initializer_list< char > list)
	Constructs a new Protein object with an initial primary structure. More...

char	operator[] (std::size_t index) const
	Returns the amino-acid character at a specified index in this protein. More...

template<typename Sequence >
Protein	operator+ (const Sequence &that) const
	Returns a concatenation of this protein with another. More...

Protein	operator+ (const char *that) const
	Returns a concatenation of this protein with another. More...

Protein	operator* (std::size_t repeat_count) const
	Returns a repeated concatenation of this protein. More...

template<typename Sequence >
bool	operator== (const Sequence &that) const
	Determines whether this protein's sequence of amino acids is equal to another sequence. More...

template<typename Sequence >
bool	operator!= (const Sequence &that) const
	Determines whether this protein's sequence of amino acids is not equal to another sequence. More...

bool	operator== (const char *that) const
	Determines whether this protein's sequence of amino acids is equal to another sequence. More...

bool	operator!= (const char *that) const
	Determines whether this protein's sequence of amino acids is not equal to another sequence. More...

auto	begin () const
	Returns an iterator pointing to the first amino acid in this protein. More...

auto	end () const
	Returns an iterator referring to the past-the-end element in this protein. More...

double	mass () const
	Computes and returns this protein's mass. More...

std::size_t	size () const
	Returns the length of this protein's primary structure. More...

std::string	to_string () const
	Returns a string representing the protein's amino-acid sequence. More...

template<typename Sequence >
Protein &	operator= (const Sequence &that)
	Replaces this protein's contents with another sequence. More...

Protein &	operator= (const char *that)
	Replaces this protein's contents with another sequence. More...

template<typename Sequence >
Protein *	operator+= (const Sequence &appendage)
	Appends a sequence of amino acids to this protein's primary structure. More...

Protein *	operator+= (const char *appendage)
	Appends a sequence of amino acids to this protein's primary structure. More...

Protein *	operator+= (char appendage)
	Appends a single amino acid to this protein's primary structure. More...

void	set (std::size_t index, char amino_acid)
	Replaces the amino acid at a given index in this protein. More...

Friends
std::ostream &	operator<< (std::ostream &out, const Protein &protein)
	Inserts a protein's sequence of amino-acid characters into an output stream. More...

std::istream &	operator>> (std::istream &in, Protein &protein)
	Replaces the contents of this protein with characters extracted from an input stream, using the same rules as string extraction. More...

Detailed Description

Represents the primary structure of a protein as a sequence of amino acids.

Constructor & Destructor Documentation

◆ Protein() [1/5]

cs19::Protein::Protein ( )

inline

Constructs a new "empty" Protein (i.e.

with no amino acids).

◆ Protein() [2/5]

cs19::Protein::Protein ( const char * amino_acids )

inline

Constructs a new Protein object with an initial primary structure.

Parameters

amino_acids a C-string denoting the primary structure

Exceptions

std::domain_error amino_acids contains any illegal characters

◆ Protein() [3/5]

template<typename Sequence >

cs19::Protein::Protein ( const Sequence & amino_acids )

inline

Constructs a new Protein object with an initial primary structure.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

amino_acids a sequence of characters denoting the primary structure

Exceptions

std::domain_error if amino_acids contains any illegal characters

◆ Protein() [4/5]

template<class InputIterator >

cs19::Protein::Protein	(	InputIterator	first,
		InputIterator	last
	)

inline

Constructs a new Protein object from a range of values [first, last).

Template Parameters

InputIterator an iterator type assumed to point to values convertible to char

Parameters

first	the initial position in the range
last	the final position in the range

Exceptions

std::domain_error if the range contains any illegal characters

◆ Protein() [5/5]

cs19::Protein::Protein ( std::initializer_list< char > list )

inline

Constructs a new Protein object with an initial primary structure.

Parameters

list	a list assumed to contain amino-acid characters

Exceptions

std::domain_error if list contains any illegal characters

Member Function Documentation

◆ begin()

auto cs19::Protein::begin ( ) const

inline

Returns an iterator pointing to the first amino acid in this protein.

Returns: a const iterator pointing to the first character in this protein's sequence

◆ end()

auto cs19::Protein::end ( ) const

inline

Returns an iterator referring to the past-the-end element in this protein.

Returns: a const iterator to the character past the end of this protein's sequence

◆ mass()

double cs19::Protein::mass ( ) const

inline

Computes and returns this protein's mass.

See: http://rosalind.info/problems/prtm/

Returns: a sum of the monoisotopic masses of this protein's amino acids

◆ operator!=() [1/2]

bool cs19::Protein::operator!= ( const char * that ) const

inline

Determines whether this protein's sequence of amino acids is not equal to another sequence.

Parameters

that	a C-string with which to compare

Returns: true if that does not contain the same sequence of amino-acid characters as this protein, otherwise false

◆ operator!=() [2/2]

template<typename Sequence >

bool cs19::Protein::operator!= ( const Sequence & that ) const

inline

Determines whether this protein's sequence of amino acids is not equal to another sequence.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

that	the sequence with which to compare

Returns: true if that does not contain the same sequence of amino-acid characters as this protein, otherwise false

◆ operator*()

Protein cs19::Protein::operator* ( std::size_t repeat_count ) const

inline

Returns a repeated concatenation of this protein.

Parameters

repeat_count the desired number of concatenations

Returns: a new Protein consisting of this protein's sequence repeated repeat_count times

◆ operator+() [1/2]

Protein cs19::Protein::operator+ ( const char * that ) const

inline

Returns a concatenation of this protein with another.

Parameters

that	a C-string containing the sequence to concatenate

Returns: a Protein consisting of this protein's amino acids concatenated with that

Exceptions

std::domain_error if that contains any illegal characters

◆ operator+() [2/2]

template<typename Sequence >

Protein cs19::Protein::operator+ ( const Sequence & that ) const

inline

Returns a concatenation of this protein with another.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

that	the sequence to concatenate

Returns: a Protein consisting of this protein's amino acids concatenated with that

Exceptions

std::domain_error if that contains any illegal characters

◆ operator+=() [1/3]

Protein* cs19::Protein::operator+= ( char appendage )

inline

Appends a single amino acid to this protein's primary structure.

Parameters

appendage a char denoting the amino acid to append

Exceptions

std::domain_error if appendage is an illegal character

◆ operator+=() [2/3]

Protein* cs19::Protein::operator+= ( const char * appendage )

inline

Appends a sequence of amino acids to this protein's primary structure.

Parameters

appendage a C-string denoting the amino acids to append

Exceptions

std::domain_error if appendage contains any illegal characters

◆ operator+=() [3/3]

template<typename Sequence >

Protein* cs19::Protein::operator+= ( const Sequence & appendage )

inline

Appends a sequence of amino acids to this protein's primary structure.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

appendage a sequence of characters denoting the amino acids to append

Exceptions

std::domain_error if appendage contains any illegal characters

◆ operator=() [1/2]

Protein& cs19::Protein::operator= ( const char * that )

inline

Replaces this protein's contents with another sequence.

Parameters

that	a C-string with which to replace this protein's contents

Exceptions

std::domain_error if that contains any illegal characters

◆ operator=() [2/2]

template<typename Sequence >

Protein& cs19::Protein::operator= ( const Sequence & that )

inline

Replaces this protein's contents with another sequence.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

that	the sequence with which to replace this protein's contents

Exceptions

std::domain_error if that contains any illegal characters

◆ operator==() [1/2]

bool cs19::Protein::operator== ( const char * that ) const

inline

Determines whether this protein's sequence of amino acids is equal to another sequence.

Parameters

that	a C-string with which to compare

Returns: true if that contains the same sequence of amino-acid characters as this protein, otherwise false

◆ operator==() [2/2]

template<typename Sequence >

bool cs19::Protein::operator== ( const Sequence & that ) const

inline

Determines whether this protein's sequence of amino acids is equal to another sequence.

Template Parameters

Sequence an iterable type assumed to contain amino-acid characters

Parameters

that	the sequence with which to compare

Returns: true if that contains the same sequence of amino-acid characters as this protein, otherwise false

◆ operator[]()

char cs19::Protein::operator[] ( std::size_t index ) const

inline

Returns the amino-acid character at a specified index in this protein.

Parameters

index the desired index in the sequence

Returns: the value a the requested index

Exceptions

std::out_of_range if index is an invalid index in this protein

◆ set()

void cs19::Protein::set	(	std::size_t	index,
		char	amino_acid
	)

inline

Replaces the amino acid at a given index in this protein.

Parameters

index	the index of the amino acid to replace
amino_acid	the replacement amino acid

Exceptions

std::domain_error	if `amino_acid` is an illegal character
std::out_of_range	if `index` is an invalid index in this protein

◆ size()

std::size_t cs19::Protein::size ( ) const

inline

Returns the length of this protein's primary structure.

Returns: the number of amino acids in this protein's primary structure

◆ to_string()

std::string cs19::Protein::to_string ( ) const

inline

Returns a string representing the protein's amino-acid sequence.

Returns: a string containing the amino-acid characters in this protein's primary structure.

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	out,
		const Protein &	protein
	)

friend

Inserts a protein's sequence of amino-acid characters into an output stream.

Parameters

out	the destination stream
protein	the Protein from which to insert

Returns: out

◆ operator>>

std::istream& operator>>	(	std::istream &	in,
		Protein &	protein
	)

friend

Replaces the contents of this protein with characters extracted from an input stream, using the same rules as string extraction.

Parameters

in	the source stream
protein	the Protein receiving the characters

Returns: in

Exceptions

std::domain_error if the token from the stream contains any illegal characters

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

cs19_protein.h

Public Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Protein() [1/5]

◆ Protein() [2/5]

◆ Protein() [3/5]

◆ Protein() [4/5]

◆ Protein() [5/5]

Member Function Documentation

◆ begin()

◆ end()

◆ mass()

◆ operator!=() [1/2]

◆ operator!=() [2/2]

◆ operator*()

◆ operator+() [1/2]

◆ operator+() [2/2]

◆ operator+=() [1/3]

◆ operator+=() [2/3]

◆ operator+=() [3/3]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==() [1/2]

◆ operator==() [2/2]

◆ operator[]()

◆ set()

◆ size()

◆ to_string()

Friends And Related Function Documentation

◆ operator<<

◆ operator>>