core::sequence::DerivedSequenceMapping Class Reference

This is quite possibly the laziest form of class naming ever. What does the name of this class tell you about it? It's a SequenceMapping, and it's derived from SequenceMapping. Oops, it said it twice. What is different about this sequence mapping from the parent class? Who knows! When should you use it? Who knows!</snark> More...

#include <DerivedSequenceMapping.hh>

Inheritance diagram for core::sequence::DerivedSequenceMapping:

Public Member Functions
	DerivedSequenceMapping ()
	ctor More...
	DerivedSequenceMapping (Size s1, Size s2)
	ctor More...
	~DerivedSequenceMapping () override
	dtor More...
	DerivedSequenceMapping (DerivedSequenceMapping const &src)
	copy constructor More...
DerivedSequenceMapping &	operator= (DerivedSequenceMapping const &src)
bool	operator== (SequenceMapping const &rhs) const override
bool	same_type_as_me (SequenceMapping const &other) const override
std::string &	seq1 ()
std::string &	seq2 ()
std::string const &	seq1 () const
std::string const &	seq2 () const
Size const &	start_seq2 () const
void	seq1 (std::string const &s)
void	seq2 (std::string const &s)
void	start_seq2 (Size s)
Public Member Functions inherited from core::id::SequenceMapping
	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...
	~SequenceMapping () override
	dtor More...
	SequenceMapping (SequenceMapping const &src)
	copy constructor More...
SequenceMapping &	operator= (SequenceMapping const &src)
Size	get_corresponding_residue_in_current (Size original_resnum) const
	A->B; Get the corresponding (new) resnum (B) from the old (A). More...
Size	operator[] (Size const pos1) const
	A->B; Get a list of the old residues contained in this class (all A residues). More...
Size &	operator[] (Size const pos1)
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 ()
virtual bool	operator== (SequenceMapping const &rhs) const
	Equality operator. More...
virtual bool	same_type_as_me (SequenceMapping const &other) const
	virtual function for ensuring both sequence mappings are the same type; essential for a valid equality operator. More...
utility::vector1< core::Size > const &	mapping () const
void	mapping (utility::vector1< core::Size > const &mapping)
std::string	to_string () const

Private Attributes
std::string	seq1_
std::string	seq2_
Size	start_seq2_

Additional Inherited Members
Static Public Member Functions inherited from core::id::SequenceMapping
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...

Detailed Description

This is quite possibly the laziest form of class naming ever. What does the name of this class tell you about it? It's a SequenceMapping, and it's derived from SequenceMapping. Oops, it said it twice. What is different about this sequence mapping from the parent class? Who knows! When should you use it? Who knows!</snark>

Constructor & Destructor Documentation

core::sequence::DerivedSequenceMapping::DerivedSequenceMapping ( )

inline

ctor

core::sequence::DerivedSequenceMapping::DerivedSequenceMapping ( Size  s1, Size  s2  )

inline

ctor

core::sequence::DerivedSequenceMapping::~DerivedSequenceMapping ( )

overridedefault

dtor

core::sequence::DerivedSequenceMapping::DerivedSequenceMapping

(

DerivedSequenceMapping const &

src

)

copy constructor

Member Function Documentation

DerivedSequenceMapping & core::sequence::DerivedSequenceMapping::operator=

(

DerivedSequenceMapping const &

src

)

References core::id::SequenceMapping::mapping(), seq1(), seq1_, seq2(), seq2_, core::id::SequenceMapping::size2(), start_seq2(), and start_seq2_.

bool core::sequence::DerivedSequenceMapping::operator== ( SequenceMapping const &  rhs ) const

override

References seq1_, seq2_, and start_seq2_.

bool core::sequence::DerivedSequenceMapping::same_type_as_me ( SequenceMapping const &  other ) const

override

std::string& core::sequence::DerivedSequenceMapping::seq1 ( )

inline

References seq1_.

Referenced by operator=(), protocols::abinitio::Template::query_sequence(), and core::sequence::simple_mapping_from_file().

std::string const& core::sequence::DerivedSequenceMapping::seq1 ( ) const

inline

References seq1_.

void core::sequence::DerivedSequenceMapping::seq1 ( std::string const &  s )

inline

References seq1_.

std::string& core::sequence::DerivedSequenceMapping::seq2 ( )

inline

References seq2_.

Referenced by operator=(), core::sequence::simple_mapping_from_file(), and protocols::abinitio::Template::Template().

std::string const& core::sequence::DerivedSequenceMapping::seq2 ( ) const

inline

References seq2_.

void core::sequence::DerivedSequenceMapping::seq2 ( std::string const &  s )

inline

References seq2_.

Size const& core::sequence::DerivedSequenceMapping::start_seq2 ( ) const

inline

References start_seq2_.

Referenced by operator=(), core::sequence::simple_mapping_from_file(), and protocols::abinitio::Template::Template().

void core::sequence::DerivedSequenceMapping::start_seq2 ( Size  s )

inline

References start_seq2_.

Member Data Documentation

std::string core::sequence::DerivedSequenceMapping::seq1_

private

Referenced by operator=(), operator==(), and seq1().

std::string core::sequence::DerivedSequenceMapping::seq2_

private

Referenced by operator=(), operator==(), and seq2().

Size core::sequence::DerivedSequenceMapping::start_seq2_

private

Referenced by operator=(), operator==(), and start_seq2().

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

• src/core/sequence/DerivedSequenceMapping.hh
• src/core/sequence/DerivedSequenceMapping.cc