#include <Sequence.hh>

Inheritance diagram for core::sequence::Sequence:

Collaboration diagram for core::sequence::Sequence:

Public Member Functions
	Sequence ()
	ctor More...

	Sequence (std::string seq, std::string id, core::Size start=1)

	Sequence (core::pose::Pose const &pose)

	Sequence (Sequence const &src)
	copy constructor. More...

virtual	~Sequence ()
	dtor More...

virtual SequenceOP	clone () const
	Returns an owning pointer to a copy of this sequence. More...

virtual void	read_from_file (utility::file::FileName const &)
	initializes this sequence object from a file. More...

virtual core::Size	length () const
	Returns the number of characters in this object. More...

virtual void	insert_char (core::Size pos, char new_char)
	Inserts a character at the given position. More...

virtual void	delete_position (core::Size pos)
	Deletes the given position from the Sequence and shifts everything else back by one. More...

virtual std::string	to_string () const

virtual std::string	type () const

void	sequence (std::string sequence)
	sets sequence to the given value. More...

void	id (std::string new_id)
	sets id to the given value. More...

void	start (core::Size new_start)
	sets starting index to the given value. More...

void	gap_char (char gap_char)
	sets gap_char to the given value. More...

core::Size	ungapped_length () const
	Returns the number of characters in this object, ignoring gaps. More...

core::Size	start () const
	Returns the start of this object. More...

std::string	id () const
	Returns the id of this object. More...

char	gap_char () const
	Returns the character used to represent a gap for this object. More...

std::string	ungapped_sequence () const
	Returns the string representing this sequence without gaps. More...

std::string	sequence () const
	Returns the full sequence, which may include gaps. More...

Sequence &	operator= (Sequence const &rhs)
	assignment operator. More...

bool	operator< (const Sequence &s) const
	Returns true if this Sequence object's id is lexicographically less than the given Sequence object's id, returns false otherwise. Uses C++ string < operator to compare this Sequence object's id() to the given Sequence object's id(). More...

bool	operator== (const Sequence &s) const
	Returns true if the given Sequence object is equal to this Sequence object. Tests for string equality of id(), start(), and sequence(), and returns false if any of these are not equal. More...

char	operator[] (core::Size pos) const
	Returns the character at the given sequence position. More...

char	at (core::Size pos) const

void	insert_gap (core::Size pos)
	Inserts a gap at the given position, where insert_gap( 0 ) inserts the character at the beginning of the sequence, and insert_gap( length() ) inserts the character at the end of the sequence. More...

void	append_char (char new_char)
	Append a character. More...

void	append_gap ()
	Append a gap. More...

bool	is_gap (core::Size pos) const
	Returns true if this position in the sequence represents a gap, returns false otherwise. More...

void	read_data (std::istream &in)
	Initializes the information in this sequence from the given std::istream. The istream should yield three pieces of information in the following order: More...

core::Size	resnum (core::Size idx) const
	Returns the index of the given sequence position, which is the position in the sequence minus any gaps that occur earlier in the sequence. For example, if the sequence is —AT, resnum(5) will return 2. Returns 0 for unaligned positions. More...

Private Attributes
std::string	id_

core::Size	start_

char	gap_char_

std::string	seq_

Friends
std::ostream &	operator<< (std::ostream &out, const Sequence &seq)
	Prints the information a given Sequence object to the given std::ostream. More...

std::ostream &	operator<< (std::istream &out, Sequence &seq)
	Prints the information a given Sequence object to the given std::ostream. More...

std::istream &	operator>> (std::istream &in, Sequence &seq)

Detailed Description

Definition at line 39 of file Sequence.hh.

Constructor & Destructor Documentation

core::sequence::Sequence::Sequence ( )

inline

ctor

Definition at line 44 of file Sequence.hh.

Referenced by clone().

core::sequence::Sequence::Sequence	(	std::string	seq,
		std::string	id,
		core::Size	start = `1`
	)

inline

Definition at line 45 of file Sequence.hh.

References sequence().

core::sequence::Sequence::Sequence ( core::pose::Pose const & pose)

Definition at line 41 of file Sequence.cc.

References id_, core::pose::Pose::pdb_info(), sequence(), and core::pose::Pose::sequence().

core::sequence::Sequence::Sequence ( Sequence const & src)

inline

copy constructor.

Definition at line 56 of file Sequence.hh.

core::sequence::Sequence::~Sequence ( )

virtual

dtor

Definition at line 53 of file Sequence.cc.

Member Function Documentation

void core::sequence::Sequence::append_char ( char new_char)

Append a character.

Definition at line 156 of file Sequence.cc.

References seq_.

void core::sequence::Sequence::append_gap ( )

Append a gap.

Definition at line 160 of file Sequence.cc.

References gap_char(), and seq_.

char core::sequence::Sequence::at ( core::Size pos) const

Definition at line 123 of file Sequence.cc.

SequenceOP core::sequence::Sequence::clone ( ) const

virtual

Returns an owning pointer to a copy of this sequence.

Reimplemented in core::sequence::SequenceProfile, core::sequence::ChemicalShiftSequence, and core::sequence::CompositeSequence.

Definition at line 55 of file Sequence.cc.

References Sequence().

void core::sequence::Sequence::delete_position ( core::Size pos)

virtual

Deletes the given position from the Sequence and shifts everything else back by one.

Reimplemented in core::sequence::SequenceProfile, core::sequence::SequenceCoupling, and core::sequence::CompositeSequence.

Definition at line 142 of file Sequence.cc.

References length(), and sequence().

Referenced by core::sequence::CompositeSequence::delete_position(), and core::sequence::SequenceProfile::delete_position().

void core::sequence::Sequence::gap_char ( char gap_char)

sets gap_char to the given value.

Definition at line 80 of file Sequence.cc.

References gap_char_.

Referenced by core::sequence::SequenceCoupling::operator=(), core::sequence::CompositeSequence::operator=(), core::sequence::ChemicalShiftSequence::operator=(), core::sequence::SequenceProfile::operator=(), and operator=().

char core::sequence::Sequence::gap_char ( ) const

Returns the character used to represent a gap for this object.

Definition at line 92 of file Sequence.cc.

References gap_char_.

Referenced by core::sequence::CompositeSequence::add_sequence(), append_gap(), insert_gap(), core::sequence::SequenceCoupling::operator=(), core::sequence::CompositeSequence::operator=(), core::sequence::ChemicalShiftSequence::operator=(), and core::sequence::SequenceProfile::operator=().

void core::sequence::Sequence::id ( std::string new_id)

sets id to the given value.

Definition at line 72 of file Sequence.cc.

References id_.

Referenced by operator<(), core::sequence::SequenceCoupling::operator=(), core::sequence::CompositeSequence::operator=(), core::sequence::ChemicalShiftSequence::operator=(), core::sequence::SequenceProfile::operator=(), operator=(), and operator==().

std::string core::sequence::Sequence::id ( ) const

Returns the id of this object.

Definition at line 88 of file Sequence.cc.

References id_.

Referenced by core::sequence::CompositeSequence::add_sequence(), core::sequence::ChemicalShiftSequence::ChemicalShiftSequence(), operator<(), core::sequence::SequenceCoupling::operator=(), core::sequence::CompositeSequence::operator=(), core::sequence::ChemicalShiftSequence::operator=(), core::sequence::SequenceProfile::operator=(), read_data(), core::sequence::ChemicalShiftSequence::read_from_file(), and core::sequence::SequenceProfile::read_from_file().

void core::sequence::Sequence::insert_char	(	core::Size	pos,
		char	new_char
	)

virtual

Inserts a character at the given position.

Reimplemented in core::sequence::SequenceProfile, core::sequence::SequenceCoupling, and core::sequence::CompositeSequence.

Definition at line 130 of file Sequence.cc.

References length(), and sequence().

Referenced by core::sequence::CompositeSequence::insert_char(), core::sequence::SequenceProfile::insert_char(), and insert_gap().

void core::sequence::Sequence::insert_gap ( core::Size pos)

Inserts a gap at the given position, where insert_gap( 0 ) inserts the character at the beginning of the sequence, and insert_gap( length() ) inserts the character at the end of the sequence.

Definition at line 152 of file Sequence.cc.

References gap_char(), and insert_char().

bool core::sequence::Sequence::is_gap ( core::Size pos) const

Returns true if this position in the sequence represents a gap, returns false otherwise.

Definition at line 164 of file Sequence.cc.

References gap_char_, and length().

Referenced by resnum(), and ungapped_sequence().

Size core::sequence::Sequence::length ( ) const

virtual

Returns the number of characters in this object.

Reimplemented in core::sequence::CompositeSequence.

Definition at line 96 of file Sequence.cc.

References seq_.

Referenced by core::sequence::ChemicalShiftSequence::check_internals_(), core::sequence::SequenceProfile::check_internals_(), core::sequence::ChemicalShiftSequence::ChemicalShiftSequence(), delete_position(), core::sequence::SequenceProfile::delete_position(), core::sequence::SequenceProfile::generate_from_sequence(), insert_char(), core::sequence::SequenceProfile::insert_char(), is_gap(), core::sequence::operator<<(), resnum(), core::sequence::SequenceProfile::SequenceProfile(), and ungapped_sequence().

bool core::sequence::Sequence::operator< ( const Sequence & s) const

inline

Returns true if this Sequence object's id is lexicographically less than the given Sequence object's id, returns false otherwise. Uses C++ string < operator to compare this Sequence object's id() to the given Sequence object's id().

Definition at line 134 of file Sequence.hh.

References id().

Sequence& core::sequence::Sequence::operator= ( Sequence const & rhs)

inline

assignment operator.

Definition at line 119 of file Sequence.hh.

References gap_char(), gap_char_, id(), id_, seq_, sequence(), start(), and start_.

bool core::sequence::Sequence::operator== ( const Sequence & s) const

inline

Returns true if the given Sequence object is equal to this Sequence object. Tests for string equality of id(), start(), and sequence(), and returns false if any of these are not equal.

Definition at line 141 of file Sequence.hh.

References id(), sequence(), and start().

char core::sequence::Sequence::operator[] ( core::Size pos) const

Returns the character at the given sequence position.

Definition at line 117 of file Sequence.cc.

References seq_.

void core::sequence::Sequence::read_data ( std::istream & in)

Initializes the information in this sequence from the given std::istream. The istream should yield three pieces of information in the following order:

id
start
sequence

Definition at line 185 of file Sequence.cc.

References id(), sequence(), and start().

Referenced by core::sequence::operator>>().

void core::sequence::Sequence::read_from_file ( utility::file::FileName const & )

virtual

initializes this sequence object from a file.

Reimplemented in core::sequence::SequenceProfile, core::sequence::ChemicalShiftSequence, and core::sequence::SequenceCoupling.

Definition at line 61 of file Sequence.cc.

core::Size core::sequence::Sequence::resnum ( core::Size idx) const

Returns the index of the given sequence position, which is the position in the sequence minus any gaps that occur earlier in the sequence. For example, if the sequence is —AT, resnum(5) will return 2. Returns 0 for unaligned positions.

Definition at line 171 of file Sequence.cc.

References is_gap(), length(), and start().

void core::sequence::Sequence::sequence ( std::string sequence)

sets sequence to the given value.

Definition at line 68 of file Sequence.cc.

References seq_, and sequence().

Referenced by core::sequence::SequenceProfile::generate_from_sequence(), core::sequence::SequenceCoupling::operator=(), core::sequence::CompositeSequence::operator=(), core::sequence::ChemicalShiftSequence::operator=(), core::sequence::SequenceProfile::operator=(), operator=(), and operator==().

string core::sequence::Sequence::sequence ( ) const