#include <SequenceMapping.hh>

Inheritance diagram for core::id::SequenceMapping:

Collaboration diagram for core::id::SequenceMapping:

Public Member Functions
	SequenceMapping ()
	ctor More...

	SequenceMapping (Size const s1, Size const s2)
	ctor More...

	SequenceMapping (utility::vector1< Size > const &mapping)
	ctor More...

	SequenceMapping (conformation::signals::LengthEvent const &event)
	convenience constructor from LengthEvent More...

virtual	~SequenceMapping ()
	dtor More...

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

SequenceMapping &	operator= (SequenceMapping const &src)

void	resize (Size const s1, Size const s2)
	resize More...

void	reverse ()
	go from an A->B mapping to a B->A mapping More...

void	downstream_combine (core::id::SequenceMapping const &smap_to_add)
	Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. smap[j] becomes smap_to_add[ smap[j] ]. More...

void	upstream_combine (core::id::SequenceMapping const &smap_to_add)
	Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. smap[j] becomes smap[ smap_to_add[ j ] ]. More...

Size	size1 () const
	size of target sequence More...

Size	size2 () const
	size of aligned sequence ??? More...

void	set_offset (int setting)

bool	all_aligned () const

bool	is_identity () const

bool	is_identity_ignore_gaps () const

void	size2 (Size const s2)

void	push_back (Size const al)

void	delete_source_residue (Size const pos1)

void	show () const

void	show (std::ostream &output) const

void	insert_source_residue (Size const pos1)

void	insert_aligned_residue (Size const pos1, Size const pos2)

void	insert_aligned_residue_safe (Size const pos1, Size const pos2)
	same as insert_aligned_residue, but a couple of extra checks on size1 and size2. More...

void	insert_target_residue (Size const pos)

void	delete_target_residue (Size const pos)

void	clear ()

Size	operator[] (Size const pos1) const

Size &	operator[] (Size const pos1)

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

utility::vector1< core::Size > const &	mapping () const

void	mapping (utility::vector1< core::Size > const &mapping)

std::string	to_string () const

Static Public Member Functions
static SequenceMapping	identity (Size const size)
	Construct an identity mapping, which means that for all positions, i in seq1 maps to i in seq2. More...

Private Attributes
Size	size2_

utility::vector1< Size >	mapping_

Detailed Description

Definition at line 38 of file SequenceMapping.hh.

Constructor & Destructor Documentation

core::id::SequenceMapping::SequenceMapping ( )

inline

ctor

Definition at line 43 of file SequenceMapping.hh.

core::id::SequenceMapping::SequenceMapping	(	Size const	s1,
		Size const	s2
	)

inline

ctor

Definition at line 48 of file SequenceMapping.hh.

core::id::SequenceMapping::SequenceMapping ( utility::vector1< Size > const & mapping)

ctor

Definition at line 34 of file SequenceMapping.cc.

core::id::SequenceMapping::SequenceMapping ( conformation::signals::LengthEvent const & event)

convenience constructor from LengthEvent

Definition at line 39 of file SequenceMapping.cc.

References core::conformation::signals::LengthEvent::INVALIDATE, core::conformation::signals::LengthEvent::length_change, mapping_, core::conformation::signals::LengthEvent::RESIDUE_APPEND, core::conformation::signals::LengthEvent::RESIDUE_DELETE, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, and core::conformation::signals::LengthEvent::tag.

core::id::SequenceMapping::~SequenceMapping ( )

virtual

dtor

Definition at line 93 of file SequenceMapping.cc.

core::id::SequenceMapping::SequenceMapping ( SequenceMapping const & src)

copy constructor

Definition at line 96 of file SequenceMapping.cc.

Member Function Documentation

bool core::id::SequenceMapping::all_aligned ( ) const

Definition at line 177 of file SequenceMapping.cc.

References mapping_, and size1().

Referenced by protocols::loops::apply_sequence_mapping().

void core::id::SequenceMapping::clear ( )

Definition at line 307 of file SequenceMapping.cc.

References mapping_, and size2_.

Referenced by core::sequence::read_alignment_file().

void core::id::SequenceMapping::delete_source_residue ( Size const pos1)

Definition at line 228 of file SequenceMapping.cc.

References mapping_.

Referenced by protocols::loops::apply_sequence_mapping().

void core::id::SequenceMapping::delete_target_residue ( Size const pos)

Definition at line 297 of file SequenceMapping.cc.

References mapping_, size1(), and size2_.

Referenced by core::kinematics::FoldTree::delete_jump_seqpos(), and core::kinematics::FoldTree::delete_seqpos_simple().

void core::id::SequenceMapping::downstream_combine ( core::id::SequenceMapping const & smap_to_add)

Apply a B->C mapping to the current A->B mapping to get an A->C mapping i.e. smap[j] becomes smap_to_add[ smap[j] ].

Definition at line 137 of file SequenceMapping.cc.

References mapping_, size2(), and size2_.

Referenced by core::id::combine_sequence_mappings().

static SequenceMapping core::id::SequenceMapping::identity ( Size const size)

inlinestatic

Construct an identity mapping, which means that for all positions, i in seq1 maps to i in seq2.

Definition at line 135 of file SequenceMapping.hh.

References is_identity(), core::io::serialization::size(), and size1().

Referenced by is_identity(), is_identity_ignore_gaps(), and protocols::relax::RelaxProtocolBase::set_up_constraints().

void core::id::SequenceMapping::insert_aligned_residue	(	Size const	pos1,
		Size const	pos2
	)

Definition at line 267 of file SequenceMapping.cc.

References mapping_.

Referenced by protocols::loops::apply_sequence_mapping(), and protocols::jumping::ResiduePairJumpSetup::generate_jump_frags().

void core::id::SequenceMapping::insert_aligned_residue_safe	(	Size const	pos1,
		Size const	pos2
	)

same as insert_aligned_residue, but a couple of extra checks on size1 and size2.

Definition at line 274 of file SequenceMapping.cc.

References mapping_, size1(), and size2().

Referenced by core::sequence::simple_mapping_from_file().

void core::id::SequenceMapping::insert_source_residue ( Size const pos1)

Definition at line 261 of file SequenceMapping.cc.

References mapping_.

Referenced by protocols::loops::extend_sequence_mapping().

void core::id::SequenceMapping::insert_target_residue ( Size const pos)

Definition at line 288 of file SequenceMapping.cc.

References mapping_, size1(), and size2_.

Referenced by protocols::loops::extend_sequence_mapping().

bool core::id::SequenceMapping::is_identity ( ) const

Definition at line 191 of file SequenceMapping.cc.

References identity(), mapping_, and size1().

Referenced by protocols::loops::apply_sequence_mapping(), and identity().

bool core::id::SequenceMapping::is_identity_ignore_gaps ( ) const

Definition at line 203 of file SequenceMapping.cc.

References identity(), mapping_, and size1().

utility::vector1< core::Size > const& core::id::SequenceMapping::mapping ( ) const

inline

Definition at line 145 of file SequenceMapping.hh.

References mapping_.

Referenced by mapping(), core::sequence::DerivedSequenceMapping::operator=(), operator=(), protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache::remap_residues(), and upstream_combine().

void core::id::SequenceMapping::mapping ( utility::vector1< core::Size > const & mapping)

inline

Definition at line 149 of file SequenceMapping.hh.

References mapping(), and mapping_.

SequenceMapping & core::id::SequenceMapping::operator= ( SequenceMapping const & src)

Definition at line 103 of file SequenceMapping.cc.

References mapping(), mapping_, size2(), and size2_.

bool core::id::SequenceMapping::operator== ( SequenceMapping const & other) const

Equality operator.

Definition at line 325 of file SequenceMapping.cc.

References mapping_, and size1().

Size core::id::SequenceMapping::operator[] ( Size const pos1) const

Definition at line 314 of file SequenceMapping.cc.

References mapping_.

Size & core::id::SequenceMapping::operator[] ( Size const pos1)

Definition at line 320 of file SequenceMapping.cc.

References mapping_.

void core::id::SequenceMapping::push_back ( Size const al)

Definition at line 222 of file SequenceMapping.cc.

References mapping_.

Referenced by protocols::loops::extend_sequence_mapping(), and core::sequence::read_alignment_file().

void core::id::SequenceMapping::resize	(	Size const	s1,
		Size const	s2
	)

resize

Definition at line 111 of file SequenceMapping.cc.

References mapping_, and size2_.

Referenced by protocols::rbsegment_relax::setup_pose_from_rbsegs().

void core::id::SequenceMapping::reverse ( )

go from an A->B mapping to a B->A mapping

Definition at line 120 of file SequenceMapping.cc.

References mapping_, size1(), and size2_.

Referenced by core::pack::task::PackerTask_::remap_residue_level_tasks(), protocols::relax::RelaxProtocolBase::set_up_constraints(), protocols::abinitio::Template::Template(), and protocols::loops::trim_back_sequence_mapping().

void core::id::SequenceMapping::set_offset ( int setting)

Definition at line 250 of file SequenceMapping.cc.

References mapping_, and size1().

Referenced by protocols::abinitio::Template::Template().

void core::id::SequenceMapping::show ( ) const

Definition at line 234 of file SequenceMapping.cc.

References core::pack::interaction_graph::T().

Referenced by protocols::loops::apply_sequence_mapping(), and core::id::operator<<().

void core::id::SequenceMapping::show ( std::ostream & output) const

Definition at line 240 of file SequenceMapping.cc.

References mapping_, and size1().

Size core::id::SequenceMapping::size1 ( ) const

Size core::id::SequenceMapping::size2 ( ) const

size of aligned sequence ???

Definition at line 170 of file SequenceMapping.cc.

References size2_.

Referenced by protocols::loops::apply_sequence_mapping(), downstream_combine(), protocols::loops::extend_sequence_mapping(), insert_aligned_residue_safe(), core::sequence::DerivedSequenceMapping::operator=(), operator=(), core::sequence::read_alignment_file(), core::sequence::transitive_map(), and protocols::loops::trim_back_sequence_mapping().

void core::id::SequenceMapping::size2 ( Size const s2)

Definition at line 216 of file SequenceMapping.cc.

References size2_.

std::string core::id::SequenceMapping::to_string ( ) const

Definition at line 335 of file SequenceMapping.cc.

References mapping_, and size1().

void core::id::SequenceMapping::upstream_combine ( core::id::SequenceMapping const & smap_to_add)

Apply a C->A mapping to the current A->B mapping to get a C->B mapping i.e. smap[j] becomes smap[ smap_to_add[ j ] ].

Definition at line 148 of file SequenceMapping.cc.

References mapping(), and mapping_.

Member Data Documentation

utility::vector1< Size > core::id::SequenceMapping::mapping_

private

Size core::id::SequenceMapping::size2_

private

Definition at line 156 of file SequenceMapping.hh.

Referenced by clear(), delete_target_residue(), downstream_combine(), insert_target_residue(), operator=(), resize(), reverse(), and size2().

The documentation for this class was generated from the following files:

src/core/id/SequenceMapping.hh
src/core/id/SequenceMapping.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation