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:

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...
SecStructGen &	operator= (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...
VallFragmentGen &	operator= (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 Super::Extent core::fragment::picking_old::vall::gen::SecStructGen::Extent

typedef for ExtentGenerator concept

typedef Super::PageIterator core::fragment::picking_old::vall::gen::SecStructGen::PageIterator

typedef for ExtentGenerator concept

typedef Super::Size core::fragment::picking_old::vall::gen::SecStructGen::Size

typedef std::string core::fragment::picking_old::vall::gen::SecStructGen::String

typedef VallFragmentGen core::fragment::picking_old::vall::gen::SecStructGen::Super

private

typedef PageIterator core::fragment::picking_old::vall::gen::SecStructGen::VallResidueIterator

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]

ss

the 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

clone this object

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

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

)

copy assignment

References core::fragment::picking_old::vall::gen::VallFragmentGen::operator=(), and ss_.

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=().

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

• src/core/fragment/picking_old/vall/gen/SecStructGen.hh
• src/core/fragment/picking_old/vall/gen/SecStructGen.cc