#include <Sequence.hh>

Inheritance diagram for core::sequence::Sequence:

Public Member Functions
	Sequence ()
	ctor More...

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

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

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

	~Sequence () override
	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	replace_char (core::Size pos, char new_char)

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...

void	spacer_positions (utility::vector1< Size > const &spacer_positions)
	sets spacer_positions 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...

utility::vector1< Size >	spacer_positions () const
	Returns the spacer positions (chain breaks, e.g., from spaces or commas in original sequence text) 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_

utility::vector1< Size >	spacer_positions_

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)

Constructor & Destructor Documentation

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

inline

ctor

Referenced by clone().

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

inline

References sequence().

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

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

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

inline

copy constructor.

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

overridedefault

dtor

Member Function Documentation

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

Append a character.

References seq_.

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

Append a gap.

References gap_char(), and seq_.

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

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

virtual

Returns an owning pointer to a copy of this sequence.

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

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.

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.

References gap_char_.

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

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

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

References gap_char_.

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

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

sets id to the given value.

References id_, and protocols::denovo_design::movers::new_id().

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

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

Returns the id of this object.

References id_.

Referenced by core::sequence::CompositeSequence::add_sequence(), core::sequence::ChemicalShiftSequence::ChemicalShiftSequence(), operator<(), core::sequence::CompositeSequence::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.

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.

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.

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.

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<<(), replace_char(), resnum(), core::sequence::SequenceProfile::SequenceProfile(), ungapped_sequence(), and protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::write_profile().

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().

References id().

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

inline

assignment operator.

References gap_char(), gap_char_, id(), id_, seq_, sequence(), spacer_positions(), spacer_positions_, 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.

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

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

Returns the character at the given sequence position.

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

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.

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

virtual

References length(), and sequence().

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.

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

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

sets sequence to the given value.

References seq_, and sequence().

Referenced by protocols::splice::concatenate_profiles(), core::sequence::SequenceProfile::generate_from_sequence(), protocols::splice::SpliceManager::generate_profile_from_seq(), core::sequence::CompositeSequence::operator=(), operator=(), operator==(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile(), and protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::write_profile().

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

Returns the full sequence, which may include gaps.

References seq_.

Referenced by core::sequence::CompositeSequence::add_sequence(), core::sequence::ChemicalShiftSequence::ChemicalShiftSequence(), delete_position(), core::sequence::SequenceProfile::generate_from_sequence(), insert_char(), core::sequence::CompositeSequence::operator=(), operator==(), read_data(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::ChemicalShiftSequence::read_from_file(), core::sequence::SequenceProfile::read_from_file(), replace_char(), Sequence(), sequence(), and to_string().