#include <SequenceAlignment.hh>

Inheritance diagram for core::sequence::SequenceAlignment:

Collaboration 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)

Detailed Description

Definition at line 45 of file SequenceAlignment.hh.

Constructor & Destructor Documentation

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

inline

ctor

Definition at line 48 of file SequenceAlignment.hh.

Referenced by clone().

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

virtual

dtor

moving from .cc file

Definition at line 39 of file SequenceAlignment.cc.

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

copy constructor

Definition at line 439 of file SequenceAlignment.cc.

Member Function Documentation

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

Definition at line 45 of file SequenceAlignment.cc.

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

Definition at line 115 of file SequenceAlignment.cc.

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.

Definition at line 241 of file SequenceAlignment.cc.

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.

Definition at line 223 of file SequenceAlignment.cc.

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

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

inline

Definition at line 62 of file SequenceAlignment.hh.

References comments_, and sequences_.

Referenced by operator=().

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

inline

Definition at line 58 of file SequenceAlignment.hh.

References SequenceAlignment().

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

getter/setters for comments

Definition at line 366 of file SequenceAlignment.cc.

References comments_.

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

Definition at line 370 of file SequenceAlignment.cc.

References comments_.

Referenced by operator=().

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

Definition at line 285 of file SequenceAlignment.cc.

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.

Definition at line 314 of file SequenceAlignment.cc.

References is_gapped(), and length().

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

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

Returns the number of positions at which all.

Definition at line 296 of file SequenceAlignment.cc.

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.

Definition at line 391 of file SequenceAlignment.cc.

References sequences_, and size().

Referenced by gapped_positions().

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

Returns the length of all sequences in this SequenceAlignment.

Definition at line 53 of file SequenceAlignment.cc.

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.

Definition at line 374 of file SequenceAlignment.cc.

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

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

assignment operator

Definition at line 448 of file SequenceAlignment.cc.

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

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

inline

Equality operator.

Definition at line 161 of file SequenceAlignment.hh.

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

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

Definition at line 484 of file SequenceAlignment.cc.

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)

Definition at line 138 of file SequenceAlignment.cc.

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.

Definition at line 121 of file SequenceAlignment.cc.

References add_sequence().

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

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

Definition at line 193 of file SequenceAlignment.cc.

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.

Definition at line 84 of file SequenceAlignment.cc.

References score().

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

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

Definition at line 79 of file SequenceAlignment.cc.

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

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

Definition at line 88 of file SequenceAlignment.cc.

References scores_.

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

Definition at line 98 of file SequenceAlignment.cc.

References scores_.

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

Definition at line 71 of file SequenceAlignment.cc.

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)

Definition at line 75 of file SequenceAlignment.cc.

References scores_.

SequenceOP core::sequence::SequenceAlignment::sequence ( Size idx) const

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.

Definition at line 347 of file SequenceAlignment.cc.

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.

Definition at line 161 of file SequenceAlignment.cc.

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::ExtraThreadingMover::get_qt_mapping(), protocols::comparative_modeling::ThreadingMover::get_qt_mapping(), protocols::comparative_modeling::loops_from_alignment(), protocols::comparative_modeling::loops_from_transitive_alignments(), core::sequence::map_seq1_seq2(), core::sequence::n_correctly_aligned_positions(), and operator==().

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.

Definition at line 323 of file SequenceAlignment.cc.

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

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

Returns the number of sequences.

Definition at line 49 of file SequenceAlignment.cc.

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().