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:

Collaboration 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...

virtual	~SecStructGen ()
	default destructor More...

SecStructGen &	operator= (SecStructGen const &rval)
	copy assignment More...

virtual VallFragmentGenOP	clone () const
	clone this object More...

virtual Extent	operator() (VallResidueIterator extent_begin, VallResidueIterator section_end) const
	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...

virtual	~VallFragmentGen ()
	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

Definition at line 39 of file SecStructGen.hh.

Member Typedef Documentation

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

typedef for ExtentGenerator concept

Definition at line 59 of file SecStructGen.hh.

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

typedef for ExtentGenerator concept

Definition at line 63 of file SecStructGen.hh.

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

Definition at line 51 of file SecStructGen.hh.

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

Definition at line 52 of file SecStructGen.hh.

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

private

Definition at line 45 of file SecStructGen.hh.

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

Definition at line 69 of file SecStructGen.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 29 of file SecStructGen.cc.

Referenced by clone().

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

Definition at line 36 of file SecStructGen.cc.

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

copy constructor

Definition at line 43 of file SecStructGen.cc.

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

virtual

default destructor

Definition at line 50 of file SecStructGen.cc.

Member Function Documentation

VallFragmentGenOP core::fragment::picking_old::vall::gen::SecStructGen::clone ( ) const

virtual

clone this object

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

Definition at line 65 of file SecStructGen.cc.

References SecStructGen().

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

virtual

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.