Classes
class	Aligner

class	AlignerFactory

class	AnnotatedSequence

class	CacheableSequenceProfile

class	Cell

class	ChemicalShiftScoringScheme

class	ChemicalShiftSequence

class	ChemicalShiftSequenceCreator

class	CompassScoringScheme

class	CompositeScoringScheme

class	CompositeSequence

class	CompositeSequenceCreator

class	DerivedSequenceMapping

class	DP_Matrix

class	DPScoringScheme

class	ExtendAlignerSW

class	L1ScoringScheme

class	MatrixScoringScheme

class	MCAligner

class	NWAligner

class	PairScoringScheme

class	ProfSimScoringScheme

class	ScoringScheme

class	ScoringSchemeFactory

class	Sequence

class	SequenceAlignment

struct	SequenceAlignmentHasher

class	SequenceCoupling

class	SequenceCouplingCreator

class	SequenceCreator
	Abstract base class for a Mover factory; the Creator class is responsible for creating a particular mover class. More...

class	SequenceFactory

class	SequenceProfile

class	SequenceProfileCreator

class	SequenceRegistrator
	This templated class will register an instance of an SequenceCreator (class T) with the SequenceFactory. It will ensure that no SequenceCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...

class	SimpleScoringScheme

class	SimpleSequenceCreator

class	SWAligner

Typedefs
typedef utility::pointer::owning_ptr < Aligner >	AlignerOP

typedef utility::pointer::owning_ptr < Aligner const >	AlignerCOP

typedef utility::pointer::owning_ptr < CacheableSequenceProfile >	CacheableSequenceProfileOP

typedef utility::pointer::owning_ptr < CacheableSequenceProfile const >	CacheableSequenceProfileCOP

typedef utility::pointer::access_ptr < CacheableSequenceProfile >	CacheableSequenceProfileAP

typedef utility::pointer::access_ptr < CacheableSequenceProfile const >	CacheableSequenceProfileCAP

typedef utility::pointer::owning_ptr < ChemicalShiftSequence >	ChemicalShiftSequenceOP

typedef utility::pointer::owning_ptr < ChemicalShiftSequence const >	ChemicalShiftSequenceCOP

typedef utility::pointer::owning_ptr < CompositeScoringScheme >	CompositeScoringSchemeOP

typedef utility::pointer::owning_ptr < CompositeSequence >	CompositeSequenceOP

typedef utility::pointer::owning_ptr < CompositeSequence const >	CompositeSequenceCOP

typedef utility::pointer::owning_ptr < DerivedSequenceMapping >	DerivedSequenceMappingOP

typedef utility::pointer::owning_ptr < DerivedSequenceMapping const >	DerivedSequenceMappingCOP

typedef utility::pointer::owning_ptr < Cell >	CellOP

typedef utility::pointer::owning_ptr < NWAligner >	NWAlignerOP

typedef utility::pointer::owning_ptr < NWAligner const >	NWAlignerCOP

typedef utility::pointer::owning_ptr < PairScoringScheme >	PairScoringSchemeOP

typedef utility::pointer::owning_ptr < ScoringScheme >	ScoringSchemeOP

typedef utility::pointer::owning_ptr < Sequence >	SequenceOP

typedef utility::pointer::owning_ptr < Sequence const >	SequenceCOP

typedef utility::pointer::owning_ptr < SequenceAlignment >	SequenceAlignmentOP

typedef utility::pointer::owning_ptr < SequenceAlignment const >	SequenceAlignmentCOP

typedef utility::pointer::owning_ptr < SequenceCoupling >	SequenceCouplingOP

typedef utility::pointer::owning_ptr < SequenceCoupling const >	SequenceCouplingCOP

typedef utility::pointer::owning_ptr < SequenceCreator >	SequenceCreatorOP

typedef utility::pointer::owning_ptr < SequenceCreator const >	SequenceCreatorCOP

typedef utility::pointer::owning_ptr < SequenceProfile >	SequenceProfileOP

typedef utility::pointer::owning_ptr < SequenceProfile const >	SequenceProfileCOP

typedef utility::pointer::owning_ptr < SWAligner >	SWAlignerOP

typedef utility::pointer::owning_ptr < SWAligner const >	SWAlignerCOP

Enumerations
enum	AlignMove { diagonal = 1, left, above, end }

Functions
std::ostream &	operator<< (std::ostream &out, const ChemicalShiftSequence &p)

std::ostream &	operator<< (std::ostream &out, const CompositeSequence &p)

std::ostream &	operator<< (std::ostream &out, const DP_Matrix &m)

std::ostream &	operator<< (std::ostream &out, const Sequence &seq)

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

std::ostream &	operator<< (std::ostream &out, const SequenceAlignment &sa)

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

bool	operator< (SequenceAlignment const &lhs, SequenceAlignment const &rhs)

std::ostream &	operator<< (std::ostream &out, const SequenceProfile &p)

void	read_all_alignments (const std::string &format, const utility::vector1< std::string > &files, utility::vector1< SequenceAlignment > *alignments)
	Populates the non-null vector <alignments> with all of the sequence alignments found in <files>. Each alignment is required to have format <format>. More...

void	read_alignment_file (std::string const &filename, std::string &seq1, std::string &seq2, core::sequence::DerivedSequenceMapping &mapping)
	helper function for reading a SequenceMapping from an alignment file. More...

vector1< string >	read_fasta_file_str (std::string const &filename)

vector1< SequenceOP >	read_fasta_file (std::string const &filename)
	Read in sequences from a fasta-formatted file. More...

std::string	read_fasta_file_return_str (std::string const &filename)

core::sequence::DerivedSequenceMapping	simple_mapping_from_file (std::string const &filename)
	Read in a SequenceMapping from a file. File format is super-simple, it just contains single lines like this that claim that residue resi and resj are aligned: resi resj. More...

utility::vector1< SequenceOP >	seqs_from_cmd_lines ()

utility::vector1 < SequenceAlignment >	read_aln (std::string const &format, std::string const &filename)

utility::vector1 < SequenceAlignment >	read_general_aln (std::istream &input)
	read generalized alignment format. More...

utility::vector1 < SequenceAlignment >	read_general_aln_file (std::string const &filename)

utility::vector1 < SequenceAlignment >	read_grishin_aln_file (std::string const &filename)

Size	n_correctly_aligned_positions (SequenceAlignment &candidate_aln, SequenceAlignment &true_aln)

SequenceAlignment	steal_alignment (SequenceAlignment aln_to_steal, utility::vector1< SequenceOP > seqs)
	takes the sequences in the provided vector1 and makes them match the alignment in aln_to_steal by matching gaps. This assumes that the ungapped sequences at index j in the vector1< SequenceOP > match the ungapped sequences at index j in aln_to_steal. More...

SequenceAlignment	mapping_to_alignment (core::id::SequenceMapping const &mapping, SequenceOP seq1, SequenceOP seq2)
	Constructs a SequenceAlignment from the given SequenceMapping and the two sequences. More...

core::id::SequenceMapping	transitive_map (core::id::SequenceMapping const &map1, core::id::SequenceMapping const &map2)
	Assuming that map1 maps sequence A to sequence B, and map2 maps sequence B to sequence C, this function returns the SequenceMapping representing the direct map of sequence A to sequence C. More...

core::id::SequenceMapping	map_seq1_seq2 (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2)
	Generates a mapping of sequence 1 onto sequence 2 using dynamic programming with a simple scoring framework. More...

core::sequence::SequenceAlignment	align_naive (core::sequence::SequenceOP seq1, core::sequence::SequenceOP seq2)
	Generate a naive sequence alignment between two sequences. More...

core::sequence::SequenceAlignment	align_poses_naive (core::pose::Pose &pose1, core::pose::Pose &pose2)

utility::vector1< Real >	get_maximum_scores (core::sequence::ScoringSchemeOP ss, core::sequence::SequenceOP seq)

core::sequence::SequenceAlignment	alignment_from_pose (core::pose::Pose &pose)

void	alignment_into_pose (core::sequence::SequenceAlignment const &aln, core::pose::Pose &pose)

core::Real	calpha_superimpose_with_mapping (core::pose::Pose &mod_pose, core::pose::Pose const &ref_pose, core::id::SequenceMapping const &mapping)

Variables
static basic::Tracer	tr ("core.sequence.ChemicalShiftSequence")

static basic::Tracer	tr ("core.sequence.CompositeSequence")

static basic::Tracer	tr ("core.sequence.MatrixScoringScheme")

static numeric::random::RandomGenerator	align_RG (31882)

static basic::Tracer	tr ("core.sequence.SequenceAlignment")

static basic::Tracer	tr ("core.sequence.SequenceCoupling")

static basic::Tracer	tr ("core.sequence.SequenceFactory")

static basic::Tracer	tr ("core.sequence.SequenceProfile")

static basic::Tracer	tr ("core.sequence")

Typedef Documentation

typedef utility::pointer::owning_ptr< Aligner const > core::sequence::AlignerCOP

typedef utility::pointer::owning_ptr< Aligner > core::sequence::AlignerOP

typedef utility::pointer::access_ptr< CacheableSequenceProfile > core::sequence::CacheableSequenceProfileAP

typedef utility::pointer::access_ptr< CacheableSequenceProfile const > core::sequence::CacheableSequenceProfileCAP

typedef utility::pointer::owning_ptr< CacheableSequenceProfile const > core::sequence::CacheableSequenceProfileCOP

typedef utility::pointer::owning_ptr< CacheableSequenceProfile > core::sequence::CacheableSequenceProfileOP

typedef utility::pointer::owning_ptr< Cell > core::sequence::CellOP

typedef utility::pointer::owning_ptr< ChemicalShiftSequence const > core::sequence::ChemicalShiftSequenceCOP

typedef utility::pointer::owning_ptr< ChemicalShiftSequence > core::sequence::ChemicalShiftSequenceOP

typedef utility::pointer::owning_ptr< CompositeScoringScheme > core::sequence::CompositeScoringSchemeOP

typedef utility::pointer::owning_ptr< CompositeSequence const > core::sequence::CompositeSequenceCOP

typedef utility::pointer::owning_ptr< CompositeSequence > core::sequence::CompositeSequenceOP

typedef utility::pointer::owning_ptr< DerivedSequenceMapping const > core::sequence::DerivedSequenceMappingCOP

typedef utility::pointer::owning_ptr< DerivedSequenceMapping > core::sequence::DerivedSequenceMappingOP

typedef utility::pointer::owning_ptr< NWAligner const > core::sequence::NWAlignerCOP

typedef utility::pointer::owning_ptr< NWAligner > core::sequence::NWAlignerOP

typedef utility::pointer::owning_ptr< PairScoringScheme > core::sequence::PairScoringSchemeOP

typedef utility::pointer::owning_ptr< ScoringScheme > core::sequence::ScoringSchemeOP

typedef utility::pointer::owning_ptr< SequenceAlignment const > core::sequence::SequenceAlignmentCOP

typedef utility::pointer::owning_ptr< SequenceAlignment > core::sequence::SequenceAlignmentOP

typedef utility::pointer::owning_ptr< Sequence const > core::sequence::SequenceCOP

typedef utility::pointer::owning_ptr< SequenceCoupling const > core::sequence::SequenceCouplingCOP

typedef utility::pointer::owning_ptr< SequenceCoupling > core::sequence::SequenceCouplingOP

typedef utility::pointer::owning_ptr< SequenceCreator const > core::sequence::SequenceCreatorCOP

typedef utility::pointer::owning_ptr< SequenceCreator > core::sequence::SequenceCreatorOP

typedef utility::pointer::owning_ptr< Sequence > core::sequence::SequenceOP

typedef utility::pointer::owning_ptr< SequenceProfile const > core::sequence::SequenceProfileCOP

typedef utility::pointer::owning_ptr< SequenceProfile > core::sequence::SequenceProfileOP

typedef utility::pointer::owning_ptr< SWAligner const > core::sequence::SWAlignerCOP

typedef utility::pointer::owning_ptr< SWAligner > core::sequence::SWAlignerOP

Enumeration Type Documentation

enum core::sequence::AlignMove

Enumerator
diagonal
left
above
end

Function Documentation

core::sequence::SequenceAlignment core::sequence::align_naive	(	core::sequence::SequenceOP	seq1,
		core::sequence::SequenceOP	seq2
	)

Generate a naive sequence alignment between two sequences.

References ss.

Referenced by align_poses_naive().

core::sequence::SequenceAlignment core::sequence::align_poses_naive	(	core::pose::Pose &	pose1,
		core::pose::Pose &	pose2
	)

References align_naive(), and core::pose::Pose::sequence().

core::sequence::SequenceAlignment core::sequence::alignment_from_pose ( core::pose::Pose & pose )

References core::sequence::SequenceAlignment::add_sequence(), core::pose::get_comment(), and tr.

void core::sequence::alignment_into_pose	(	core::sequence::SequenceAlignment const &	aln,
		core::pose::Pose &	pose
	)

References core::pose::add_comment(), and core::sequence::SequenceAlignment::sequence().

core::Real core::sequence::calpha_superimpose_with_mapping	(	core::pose::Pose &	mod_pose,
		core::pose::Pose const &	ref_pose,
		core::id::SequenceMapping const &	mapping
	)

References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), core::scoring::superimpose_pose(), and core::pose::Pose::total_residue().

utility::vector1< Real > core::sequence::get_maximum_scores	(	core::sequence::ScoringSchemeOP	ss,
		core::sequence::SequenceOP	seq
	)

core::id::SequenceMapping core::sequence::map_seq1_seq2	(	core::sequence::SequenceOP	seq1,
		core::sequence::SequenceOP	seq2
	)

Generates a mapping of sequence 1 onto sequence 2 using dynamic programming with a simple scoring framework.

References core::sequence::SequenceAlignment::identities(), core::sequence::SequenceAlignment::length(), core::sequence::SequenceAlignment::sequence_mapping(), ss, and tr.

Referenced by core::pose::sequence_map_from_pdbinfo().

SequenceAlignment core::sequence::mapping_to_alignment	(	core::id::SequenceMapping const &	mapping,
		SequenceOP	seq1_orig,
		SequenceOP	seq2_orig
	)

Constructs a SequenceAlignment from the given SequenceMapping and the two sequences.

References core::sequence::SequenceAlignment::add_sequence(), length, runtime_assert, and core::id::SequenceMapping::size1().

core::Size core::sequence::n_correctly_aligned_positions	(	SequenceAlignment &	candidate_aln,
		SequenceAlignment &	true_aln
	)

References core::sequence::SequenceAlignment::length(), runtime_assert, core::sequence::SequenceAlignment::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), and core::sequence::SequenceAlignment::size().

bool core::sequence::operator<	(	SequenceAlignment const &	lhs,
		SequenceAlignment const &	rhs
	)

References core::sequence::SequenceAlignment::sequence(), and core::sequence::SequenceAlignment::size().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const CompositeSequence &	p
	)

References core::sequence::CompositeSequence::to_string().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const DP_Matrix &	m
	)

References core::sequence::DP_Matrix::cols(), j, core::io::raw_data::precision, core::sequence::DP_Matrix::rows(), score, core::sequence::DP_Matrix::xlab(), and core::sequence::DP_Matrix::ylab().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const ChemicalShiftSequence &	p
	)

References j, core::sequence::Sequence::length(), core::io::raw_data::precision, core::sequence::SequenceProfile::prof_row(), core::sequence::Sequence::to_string(), and core::sequence::SequenceProfile::width().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const Sequence &	seq
	)

References core::sequence::Sequence::to_string().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const SequenceAlignment &	sa
	)

References core::sequence::SequenceAlignment::gapped_positions(), core::sequence::SequenceAlignment::identities(), core::sequence::SequenceAlignment::length(), core::sequence::SequenceAlignment::score(), core::sequence::SequenceAlignment::sequence(), and core::sequence::SequenceAlignment::size().

std::ostream& core::sequence::operator<<	(	std::ostream &	out,
		const SequenceProfile &	p
	)

References j, core::sequence::Sequence::length(), core::io::raw_data::precision, core::sequence::SequenceProfile::prof_row(), core::sequence::Sequence::to_string(), and core::sequence::SequenceProfile::width().

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

References core::sequence::Sequence::read_data().

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

References core::sequence::SequenceAlignment::read_data().

void core::sequence::read_alignment_file	(	std::string const &	filename,
		std::string &	seq1,
		std::string &	seq2,
		sequence::DerivedSequenceMapping &	mapping
	)

helper function for reading a SequenceMapping from an alignment file.

if position i in seq1 is aligned with position j in seq2, mapping[ i ] == j if position i in seq1 is unaligned, mapping[ i ] == 0

References core::id::SequenceMapping::clear(), getline(), core::id::SequenceMapping::push_back(), runtime_assert, core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and basic::T().

void core::sequence::read_all_alignments	(	const std::string &	format,
		const utility::vector1< std::string > &	files,
		utility::vector1< SequenceAlignment > *	alignments
	)

Populates the non-null vector <alignments> with all of the sequence alignments found in <files>. Each alignment is required to have format <format>.

References read_aln().

utility::vector1< SequenceAlignment > core::sequence::read_aln	(	std::string const &	format,
		std::string const &	filename
	)

References read_general_aln_file(), read_grishin_aln_file(), tr, and utility_exit_with_message.

Referenced by read_all_alignments().

utility::vector1< SequenceOP > core::sequence::read_fasta_file ( std::string const & filename )

Read in sequences from a fasta-formatted file.

References getline(), strip_whitespace(), and utility_exit_with_message.

Referenced by read_fasta_file_str(), seqs_from_cmd_lines(), and core::import_pose::pose_stream::streams_from_cmd_line().

std::string core::sequence::read_fasta_file_return_str ( std::string const & filename )

References getline(), and utility_exit_with_message.

utility::vector1< std::string > core::sequence::read_fasta_file_str ( std::string const & filename )

References end, and read_fasta_file().

utility::vector1< SequenceAlignment > core::sequence::read_general_aln ( std::istream & input )

read generalized alignment format.

References getline(), score, and tr.

Referenced by read_general_aln_file().

utility::vector1< SequenceAlignment > core::sequence::read_general_aln_file ( std::string const & filename )

References read_general_aln(), and utility_exit_with_message.

Referenced by read_aln().

utility::vector1< SequenceAlignment > core::sequence::read_grishin_aln_file ( std::string const & filename )

References getline(), method, score, start, and utility_exit_with_message.

Referenced by read_aln().

utility::vector1< SequenceOP > core::sequence::seqs_from_cmd_lines ( )

References end, in::file::fasta, option, in::file::pssm, read_fasta_file(), and user.

core::sequence::DerivedSequenceMapping core::sequence::simple_mapping_from_file ( std::string const & filename )

Read in a SequenceMapping from a file. File format is super-simple, it just contains single lines like this that claim that residue resi and resj are aligned: resi resj.

References end, getline(), core::id::SequenceMapping::insert_aligned_residue_safe(), resi, resj, core::sequence::DerivedSequenceMapping::seq1(), core::sequence::DerivedSequenceMapping::seq2(), core::io::serialization::size(), core::sequence::DerivedSequenceMapping::start_seq2(), tag, tr, type, and utility_exit_with_message.

SequenceAlignment core::sequence::steal_alignment	(	SequenceAlignment	aln_to_steal,
		utility::vector1< SequenceOP >	seqs
	)

takes the sequences in the provided vector1 and makes them match the alignment in aln_to_steal by matching gaps. This assumes that the ungapped sequences at index j in the vector1< SequenceOP > match the ungapped sequences at index j in aln_to_steal.

References core::sequence::SequenceAlignment::add_sequence(), j, length, core::sequence::SequenceAlignment::length(), runtime_assert, sequence, core::sequence::SequenceAlignment::sequence(), core::sequence::SequenceAlignment::size(), start, and utility_exit_with_message.

core::id::SequenceMapping core::sequence::transitive_map	(	core::id::SequenceMapping const &	map1,
		core::id::SequenceMapping const &	map2
	)

Assuming that map1 maps sequence A to sequence B, and map2 maps sequence B to sequence C, this function returns the SequenceMapping representing the direct map of sequence A to sequence C.

References core::id::SequenceMapping::size1(), and core::id::SequenceMapping::size2().