Rosetta Core  2014.35
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
core::id::SequenceMapping Class Reference

#include <SequenceMapping.hh>

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...
 
SequenceMappingoperator= (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
 
Sizeoperator[] (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< Sizemapping_
 

Constructor & Destructor Documentation

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

ctor

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

ctor

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

ctor

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

dtor

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

copy constructor

Member Function Documentation

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

References mapping_, and size1().

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

References mapping_, and size2_.

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

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

References mapping_.

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

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.

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

Referenced by is_identity(), and is_identity_ignore_gaps().

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

References mapping_.

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.

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

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

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

References mapping_.

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

References mapping_, size1(), and size2_.

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

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

Referenced by identity().

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

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

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

References mapping(), and mapping_.

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

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

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

Equality operator.

References mapping_, and size1().

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

References mapping_.

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

References mapping_.

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

References mapping_.

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

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

resize

References mapping_, and size2_.

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

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

References mapping_, size1(), and size2_.

Referenced by core::pack::task::PackerTask_::remap_residue_level_tasks().

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

References mapping_, and size1().

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

References basic::T().

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

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

References mapping_, and size1().

Size core::id::SequenceMapping::size1 ( ) const
Size core::id::SequenceMapping::size2 ( ) const
void core::id::SequenceMapping::size2 ( Size const  s2)

References size2_.

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

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 ] ].

References mapping(), and mapping_.

Member Data Documentation

utility::vector1< Size > core::id::SequenceMapping::mapping_
private
Size core::id::SequenceMapping::size2_
private

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