Rosetta Core  2014.35
Public Member Functions | Private Attributes | List of all members
core::sequence::DerivedSequenceMapping Class Reference

#include <DerivedSequenceMapping.hh>

Public Member Functions

 DerivedSequenceMapping ()
 ctor More...
 DerivedSequenceMapping (Size s1, Size s2)
 ctor More...
 ~DerivedSequenceMapping ()
 dtor More...
 DerivedSequenceMapping (DerivedSequenceMapping const &src)
 copy constructor More...
DerivedSequenceMappingoperator= (DerivedSequenceMapping const &src)
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...
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

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...

Constructor & Destructor Documentation

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


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


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


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

copy constructor

Member Function Documentation

DerivedSequenceMapping & core::sequence::DerivedSequenceMapping::operator= ( DerivedSequenceMapping const &  src)
std::string& core::sequence::DerivedSequenceMapping::seq1 ( )
std::string const& core::sequence::DerivedSequenceMapping::seq1 ( ) const

References seq1_.

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

References seq1_.

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

References seq2_.

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

References seq2_.

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

References start_seq2_.

Member Data Documentation

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

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

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

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

Size core::sequence::DerivedSequenceMapping::start_seq2_

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

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