Rosetta  2020.50
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
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:
Inheritance graph
[legend]

Public Member Functions

 DerivedSequenceMapping ()
 ctor More...
 
 DerivedSequenceMapping (Size s1, Size s2)
 ctor More...
 
 ~DerivedSequenceMapping () override
 dtor More...
 
 DerivedSequenceMapping (DerivedSequenceMapping const &src)
 copy constructor More...
 
DerivedSequenceMappingoperator= (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...
 
SequenceMappingoperator= (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...
 
Sizeoperator[] (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)
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
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
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
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().


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