#include <SequenceAlignment.hh>

Inheritance diagram for core::sequence::SequenceAlignment:

Public Member Functions
	SequenceAlignment ()
	ctor More...

virtual	~SequenceAlignment ()
	dtor More...

SequenceAlignmentOP	clone () const

void	clear ()

void	add_sequence (SequenceOP myseq)

Size	size () const
	Returns the number of sequences. More...

Size	length () const
	Returns the length of all sequences in this SequenceAlignment. More...

SequenceOP	sequence (Size idx) const

std::string	to_string () const

void	read_data (std::istream &in)

void	score (Real const &sc)
	Accessors for the score of this SequenceAlignment. More...

Real	score () const

Real	score (std::string const &name) const

void	score (std::string const &name, Real const value)

std::map< std::string, core::Real >	scores () const

void	scores (std::map< std::string, core::Real > new_scores)

void	read_from_file (std::string const &filename)
	initialize this SequenceAlignment object from the given file. More...

core::id::SequenceMapping	sequence_mapping (core::Size const idx1, core::Size const idx2) const
	returns a SequenceMapping of the sequence at index idx1 mapped to the sequence at idx2. More...

void	remove_gapped_positions ()
	Removes positions that are gapped in all columns of the alignment. More...

Real	calculate_score_sum_of_pairs (ScoringSchemeOP ss) const
	calculates the score of this alignment under the given ScoringScheme by summing up all of pairwise alignment scores between all pairs of sequence. More...

utility::vector1< Real >	calculate_per_position_scores (ScoringSchemeOP ss) const
	calculates pairwise scores similar to calculate_score_sum_of_pairs. More...

bool	sequences_are_in_frame () const
	Returns true if all of the sequences are "in-frame," which means that residue x in the first sequence maps to residue x in all other sequences. This method intentionally ignores any sequence at the position where that sequence has a gap. More...

utility::vector1< core::Size >	sequence_indices (core::Size const column) const
	Returns a vector1 of the sequence indices in the given column of the SequenceAlignment that are calculated using the Sequence resnum() method. More...

void	comment (std::string const &comment)
	getter/setters for comments More...

utility::vector1< std::string >	comments () const

void	data_integrity_check () const

Size	identities () const
	Returns the number of positions at which all. More...

Size	gapped_positions () const
	Returns the number of positions in the SequenceAlignment with at least one gap. More...

Real	max_gap_percentage () const
	Returns the number of gaps contained by the sequence in the alignment with the most gaps. More...

bool	is_gapped (Size const col_idx) const
	Returns true if the given alignment column index is gapped, false otherwise. More...

std::string	alignment_id () const
	this gives the id of the second sequence — in a typical alignment it is 1) query, 2) template More...

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

SequenceAlignment &	operator= (SequenceAlignment const &src)
	assignment operator More...

bool	operator== (const SequenceAlignment &other) const
	Equality operator. More...

void	printGrishinFormat (std::ostream &out) const

Private Attributes
utility::vector1< SequenceOP >	sequences_

utility::vector1< std::string >	comments_

std::map< std::string, core::Real >	scores_

Friends
bool	operator< (SequenceAlignment const &lhs, SequenceAlignment const &rhs)
	Less-than operator. Usd for storing SequenceAlignment objects in a std::set. More...

std::ostream &	operator<< (std::ostream &out, const SequenceAlignment &sa)
	Print SequenceAlignment object to the given std::ostream. More...

std::istream &	operator>> (std::istream &in, SequenceAlignment &aln)

Constructor & Destructor Documentation

core::sequence::SequenceAlignment::SequenceAlignment ( )

inline

ctor

Referenced by clone().

core::sequence::SequenceAlignment::~SequenceAlignment ( )

virtual

dtor

moving from .cc file

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

copy constructor

Member Function Documentation

void core::sequence::SequenceAlignment::add_sequence ( SequenceOP myseq )

References sequences_.

Referenced by core::sequence::alignment_from_pose(), core::sequence::mapping_to_alignment(), operator=(), read_data(), read_from_file(), core::sequence::steal_alignment(), and core::sequence::Aligner::traceback().

std::string core::sequence::SequenceAlignment::alignment_id ( ) const

this gives the id of the second sequence — in a typical alignment it is 1) query, 2) template

References sequence().

Referenced by protocols::comparative_modeling::ThreadingJob::alignment_id(), and operator==().

utility::vector1< Real > core::sequence::SequenceAlignment::calculate_per_position_scores ( ScoringSchemeOP ss ) const

calculates pairwise scores similar to calculate_score_sum_of_pairs.

References length(), scores(), sequence(), sequences_, size(), and core::sequence::tr().

Referenced by calculate_score_sum_of_pairs().

Real core::sequence::SequenceAlignment::calculate_score_sum_of_pairs ( ScoringSchemeOP ss ) const

calculates the score of this alignment under the given ScoringScheme by summing up all of pairwise alignment scores between all pairs of sequence.

References calculate_per_position_scores(), core::sequence::end, score(), and scores().

void core::sequence::SequenceAlignment::clear ( )

inline

References comments_, and sequences_.

Referenced by protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), and operator=().

SequenceAlignmentOP core::sequence::SequenceAlignment::clone ( ) const

inline

References SequenceAlignment().

Referenced by core::sequence::MCAligner::align(), and core::sequence::Aligner::traceback().

void core::sequence::SequenceAlignment::comment ( std::string const & comment )

getter/setters for comments

References comments_.

utility::vector1< std::string > core::sequence::SequenceAlignment::comments ( ) const

References comments_.

Referenced by operator=().

void core::sequence::SequenceAlignment::data_integrity_check ( ) const

References length(), sequences_, size(), and to_string().

Referenced by identities().

Size core::sequence::SequenceAlignment::gapped_positions ( ) const

Returns the number of positions in the SequenceAlignment with at least one gap.

References is_gapped(), and length().

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

Size core::sequence::SequenceAlignment::identities ( ) const

Returns the number of positions at which all.

References data_integrity_check(), length(), and sequences_.

Referenced by core::sequence::map_seq1_seq2(), and core::sequence::operator<<().

bool core::sequence::SequenceAlignment::is_gapped ( Size const col_idx ) const

Returns true if the given alignment column index is gapped, false otherwise.

References sequences_, and size().

Referenced by gapped_positions().

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

Returns the length of all sequences in this SequenceAlignment.

References sequences_, and size().

Referenced by calculate_per_position_scores(), data_integrity_check(), protocols::nonlocal::find_regions_with_minimum_size(), gapped_positions(), identities(), core::sequence::map_seq1_seq2(), max_gap_percentage(), core::sequence::n_correctly_aligned_positions(), core::sequence::operator<<(), remove_gapped_positions(), sequence_indices(), sequence_mapping(), sequences_are_in_frame(), and core::sequence::steal_alignment().

Real core::sequence::SequenceAlignment::max_gap_percentage ( ) const

Returns the number of gaps contained by the sequence in the alignment with the most gaps.

References core::sequence::end, length(), and sequences_.

SequenceAlignment & core::sequence::SequenceAlignment::operator= ( SequenceAlignment const & src )

assignment operator

References add_sequence(), clear(), comments(), comments_, scores(), scores_, sequence(), and size().

bool core::sequence::SequenceAlignment::operator== ( const SequenceAlignment & other ) const

inline

Equality operator.

References alignment_id(), core::sequence::end, sequence(), sequence_mapping(), and size().

void core::sequence::SequenceAlignment::printGrishinFormat ( std::ostream & out ) const

References core::sequence::end, score(), scores_, sequence(), and size().

Referenced by protocols::comparative_modeling::AlignmentCluster::output().

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

References add_sequence(), and score().

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

void core::sequence::SequenceAlignment::read_from_file ( std::string const & filename )

initialize this SequenceAlignment object from the given file.

super-general alignment format reader. This will never ever ever have to be improved or extended.

References add_sequence().

void core::sequence::SequenceAlignment::remove_gapped_positions ( )

Removes positions that are gapped in all columns of the alignment.

References core::sequence::end, length(), and sequences_.

Referenced by core::sequence::Aligner::traceback().

void core::sequence::SequenceAlignment::score ( Real const & sc )

Accessors for the score of this SequenceAlignment.

References score().

Referenced by core::sequence::operator<<(), and core::sequence::Aligner::traceback().

Real core::sequence::SequenceAlignment::score ( ) const

References score().

Referenced by calculate_score_sum_of_pairs(), printGrishinFormat(), read_data(), score(), and to_string().

Real core::sequence::SequenceAlignment::score ( std::string const & name ) const

References scores_.

void core::sequence::SequenceAlignment::score	(	std::string const &	name,
		Real const	value
	)

References scores_.

std::map< std::string, core::Real > core::sequence::SequenceAlignment::scores ( ) const

References scores_.

Referenced by calculate_per_position_scores(), calculate_score_sum_of_pairs(), and operator=().

void core::sequence::SequenceAlignment::scores ( std::map< std::string, core::Real > new_scores )

References scores_.

utility::vector1< core::Size > core::sequence::SequenceAlignment::sequence_indices ( core::Size const column ) const

Returns a vector1 of the sequence indices in the given column of the SequenceAlignment that are calculated using the Sequence resnum() method.

References core::sequence::end, length(), and sequences_.

core::id::SequenceMapping core::sequence::SequenceAlignment::sequence_mapping	(	core::Size const	idx1,
		core::Size const	idx2
	)		const

returns a SequenceMapping of the sequence at index idx1 mapped to the sequence at idx2.

References length(), sequences_, and size().

Referenced by protocols::medal::alignment_probabilities(), protocols::relax::MiniRelax::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), protocols::comparative_modeling::bounded_loops_from_alignment(), protocols::relax::coordinate_constrain_selection(), protocols::comparative_modeling::gather_coords(), protocols::comparative_modeling::get_qt_mapping_general(), protocols::comparative_modeling::loops_from_alignment(), protocols::comparative_modeling::loops_from_transitive_alignments(), core::sequence::map_seq1_seq2(), core::sequence::n_correctly_aligned_positions(), operator==(), and protocols::frag_picker::scores::sequencealign().

bool core::sequence::SequenceAlignment::sequences_are_in_frame ( ) const

Returns true if all of the sequences are "in-frame," which means that residue x in the first sequence maps to residue x in all other sequences. This method intentionally ignores any sequence at the position where that sequence has a gap.

References core::sequence::end, length(), and sequences_.

Size core::sequence::SequenceAlignment::size ( ) const

Returns the number of sequences.

References sequences_.

Referenced by calculate_per_position_scores(), protocols::relax::coordinate_constrain_selection(), data_integrity_check(), is_gapped(), length(), core::sequence::n_correctly_aligned_positions(), core::sequence::SequenceAlignmentHasher::operator()(), core::sequence::operator<(), core::sequence::operator<<(), operator=(), operator==(), printGrishinFormat(), sequence(), sequence_mapping(), core::sequence::steal_alignment(), and to_string().