#include <CompositeSequence.hh>

Inheritance diagram for core::sequence::CompositeSequence:

Collaboration diagram for core::sequence::CompositeSequence:

Public Member Functions
	CompositeSequence ()
	ctors More...

	CompositeSequence (CompositeSequence const &src)
	copy ctor More...

core::Size	n_seqs () const

utility::vector1< SequenceOP >	seqs () const

void	add_sequence (SequenceOP seq)

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

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

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

SequenceOP	seq (core::Size idx) const

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

virtual	~CompositeSequence ()
	dtor More...

virtual SequenceOP	clone () const
	Returns an owning pointer to a new CompositeSequence object, with data that is a deep copy of the information in this object. More...

virtual std::string	to_string () const

virtual std::string	type () const

Public Member Functions inherited from core::sequence::Sequence
	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 void	read_from_file (utility::file::FileName const &)
	initializes this sequence object from a file. More...

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...