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core::fragment::picking_old::vall::gen::SecStructGen Class Reference

Generator that requires fragments to have a specific secondary structure string. More...

#include <SecStructGen.hh>

Inheritance diagram for core::fragment::picking_old::vall::gen::SecStructGen:
Inheritance graph
[legend]

Public Types

typedef Super::Size Size
 
typedef std::string String
 
typedef Super::Extent Extent
 typedef for ExtentGenerator concept More...
 
typedef Super::PageIterator PageIterator
 typedef for ExtentGenerator concept More...
 
typedef PageIterator VallResidueIterator
 
- Public Types inherited from core::fragment::picking_old::vall::gen::VallFragmentGen
typedef core::Size Size
 
typedef
core::fragment::picking_old::concepts::Extent
< VallSection::PageConstIterator
Extent
 typedef for ExtentGenerator concept More...
 
typedef Extent::PageIterator PageIterator
 typedef for ExtentGenerator concept More...
 
typedef PageIterator VallResidueIterator
 

Public Member Functions

 SecStructGen ()
 default constructor More...
 
 SecStructGen (String const &ss)
 secondary structure string constructor More...
 
 SecStructGen (SecStructGen const &rval)
 copy constructor More...
 
 ~SecStructGen () override
 default destructor More...
 
SecStructGenoperator= (SecStructGen const &rval)
 copy assignment More...
 
VallFragmentGenOP clone () const override
 clone this object More...
 
Extent operator() (VallResidueIterator extent_begin, VallResidueIterator section_end) const override
 return the desired fragment extent w/ length equal to the secondary structure string More...
 
- Public Member Functions inherited from core::fragment::picking_old::vall::gen::VallFragmentGen
 VallFragmentGen ()
 default constructor More...
 
 VallFragmentGen (VallFragmentGen const &rval)
 copy constructor More...
 
 ~VallFragmentGen () override
 default destructor More...
 
VallFragmentGenoperator= (VallFragmentGen const &rval)
 copy assignment More...
 

Private Types

typedef VallFragmentGen Super
 

Private Attributes

String ss_
 the required secondary structure of desired fragment More...
 

Detailed Description

Generator that requires fragments to have a specific secondary structure string.

Remarks
assumes that Pages in the Book are stored in a container capable of returning a RandomAccessIterator, such as std::vector

Member Typedef Documentation

typedef for ExtentGenerator concept

typedef for ExtentGenerator concept

Constructor & Destructor Documentation

core::fragment::picking_old::vall::gen::SecStructGen::SecStructGen ( )

default constructor

core::fragment::picking_old::vall::gen::SecStructGen::SecStructGen ( String const &  ss)

secondary structure string constructor

fragment size constructor

Parameters
[in]ssthe required secondary structure string of the fragment
core::fragment::picking_old::vall::gen::SecStructGen::SecStructGen ( SecStructGen const &  rval)
default

copy constructor

core::fragment::picking_old::vall::gen::SecStructGen::~SecStructGen ( )
overridedefault

default destructor

Member Function Documentation

VallFragmentGenOP core::fragment::picking_old::vall::gen::SecStructGen::clone ( ) const
overridevirtual
SecStructGen::Extent core::fragment::picking_old::vall::gen::SecStructGen::operator() ( VallResidueIterator  extent_begin,
VallResidueIterator  section_end 
) const
overridevirtual

return the desired fragment extent w/ length equal to the secondary structure string

Returns
Valid (true) extent if the extent has exactly the required secondary structure string and the end of the extent does not go past section_end. Invalid (false) extent otherwise.
Remarks
we assume VallResidueIterator is a type of RandomAccessIterator, such as those used in std::vector

Implements core::fragment::picking_old::vall::gen::VallFragmentGen.

References core::fragment::picking_old::concepts::Extent< PageIterator >::begin, core::fragment::picking_old::concepts::Extent< PageIterator >::end, ss_, and core::fragment::picking_old::concepts::Extent< PageIterator >::valid.

SecStructGen & core::fragment::picking_old::vall::gen::SecStructGen::operator= ( SecStructGen const &  rval)

Member Data Documentation

String core::fragment::picking_old::vall::gen::SecStructGen::ss_
private

the required secondary structure of desired fragment

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


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