Vall fragment library. More...

#include <VallLibrary.hh>

Inheritance diagram for core::fragment::picking_old::vall::VallLibrary:

Collaboration diagram for core::fragment::picking_old::vall::VallLibrary:

Public Types
typedef Super::Size	Size

typedef Super::BookConstIterator	BookConstIterator
	typedef for Library concept More...

typedef Super::BookIterator	BookIterator
	typedef for Library concept More...

typedef BookConstIterator	VallSectionConstIterator

typedef BookIterator	VallSectionIterator

Public Types inherited from core::fragment::picking_old::concepts::Library< VallSections >
typedef core::Size	Size

typedef VallSections::Book	Book

typedef VallSections::const_iterator	BookConstIterator

typedef VallSections::iterator	BookIterator

Public Member Functions
VallSection const &	operator[] (Size const idx) const
	access a specific VallSection within this section, 1-based indexing More...

void	add_section (VallSection const &section)
	brief add a section to the end of this library More...

VallSection const &	last_section () const
	access the last section in thie library More...

VallSection &	last_section ()
	access the last section in thie library More...

Size	n_residues () const
	total number of residues in the library More...

void	reindex_sections ()
	re-index VallSections within this library so they number 1 .. n More...

void	reserve (Size const n)
	ensure storage currently allocated for VallSections is at least the given size More...

void	tighten_memory (bool const sections_only=true)
	tighten memory usage More...

Public Member Functions inherited from core::fragment::picking_old::concepts::Library< VallSections >
	Library ()
	default constructor More...

	Library (VallSectionsconst &books)
	Books constructor. More...

	~Library ()
	default destructor More...

BookConstIterator	begin () const
	return an iterator that points to the first Book in this library More...

BookIterator	begin ()
	return an iterator that points to the first Book in this library More...

BookConstIterator	end () const
	return an iterator that points beyond the last Book in this library More...

BookIterator	end ()
	return an iterator that points beyond the last Book in this library More...

Size	size () const
	number of books in the library More...

void	clear ()
	clear the library More...

Private Types
typedef core::fragment::picking_old::concepts::Library < VallSections >	Super

Private Member Functions
VallSections const &	sections () const
	return sections container More...

VallSections &	sections ()
	return sections container More...

Additional Inherited Members
Protected Member Functions inherited from core::fragment::picking_old::concepts::Library< VallSections >
VallSectionsconst &	books () const
	return the books in this library More...

VallSections &	books ()
	return the books in this library More...

Detailed Description

Vall fragment library.

Definition at line 37 of file VallLibrary.hh.

Member Typedef Documentation

typedef Super::BookConstIterator core::fragment::picking_old::vall::VallLibrary::BookConstIterator

typedef for Library concept

Definition at line 56 of file VallLibrary.hh.

typedef Super::BookIterator core::fragment::picking_old::vall::VallLibrary::BookIterator

typedef for Library concept

Definition at line 60 of file VallLibrary.hh.

typedef Super::Size core::fragment::picking_old::vall::VallLibrary::Size

Definition at line 49 of file VallLibrary.hh.

typedef core::fragment::picking_old::concepts::Library< VallSections > core::fragment::picking_old::vall::VallLibrary::Super

private

Definition at line 43 of file VallLibrary.hh.

typedef BookConstIterator core::fragment::picking_old::vall::VallLibrary::VallSectionConstIterator

Definition at line 66 of file VallLibrary.hh.

typedef BookIterator core::fragment::picking_old::vall::VallLibrary::VallSectionIterator

Definition at line 67 of file VallLibrary.hh.

Member Function Documentation

void core::fragment::picking_old::vall::VallLibrary::add_section ( VallSection const & section)

inline

brief add a section to the end of this library

Definition at line 85 of file VallLibrary.hh.

References sections(), and core::fragment::picking_old::concepts::Library< VallSections >::size().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

VallSection const& core::fragment::picking_old::vall::VallLibrary::last_section ( ) const

inline

access the last section in thie library

Definition at line 93 of file VallLibrary.hh.

References sections().

VallSection& core::fragment::picking_old::vall::VallLibrary::last_section ( )

inline

access the last section in thie library

Definition at line 100 of file VallLibrary.hh.

References sections().

Size core::fragment::picking_old::vall::VallLibrary::n_residues ( ) const

inline

total number of residues in the library

Definition at line 107 of file VallLibrary.hh.

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), and core::fragment::picking_old::concepts::Library< VallSections >::end().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

VallSection const& core::fragment::picking_old::vall::VallLibrary::operator[] ( Size const idx) const

inline

access a specific VallSection within this section, 1-based indexing

Definition at line 75 of file VallLibrary.hh.

References sections().

void core::fragment::picking_old::vall::VallLibrary::reindex_sections ( )

inline

re-index VallSections within this library so they number 1 .. n

Definition at line 118 of file VallLibrary.hh.

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), and core::fragment::picking_old::concepts::Library< VallSections >::end().

void core::fragment::picking_old::vall::VallLibrary::reserve ( Size const n)

inline

ensure storage currently allocated for VallSections is at least the given size

Definition at line 132 of file VallLibrary.hh.

References sections().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

VallSections const& core::fragment::picking_old::vall::VallLibrary::sections ( ) const

inlineprivate

return sections container

Definition at line 164 of file VallLibrary.hh.

References core::fragment::picking_old::concepts::Library< VallSections >::books().

Referenced by add_section(), last_section(), operator[](), reserve(), and tighten_memory().

VallSections& core::fragment::picking_old::vall::VallLibrary::sections ( )

inlineprivate

return sections container

Definition at line 171 of file VallLibrary.hh.

References core::fragment::picking_old::concepts::Library< VallSections >::books().

void core::fragment::picking_old::vall::VallLibrary::tighten_memory ( bool const sections_only = true)

inline

tighten memory usage

Parameters

sections_only if true, only tightens memory per-section and skips the operation for the whole library

Shrinks the capacity of the library by calling VallSection::tighten_memory() for each section. If 'sections_only' is false, will additionally perform a swap of the library, effectively requiring a similar amount of memory as the current library object.

Warning: The Vall libraries can be very large, so set 'sections_only' false only if you won't be running on a constrained memory platform.

Definition at line 147 of file VallLibrary.hh.

References core::fragment::picking_old::concepts::Library< VallSections >::begin(), core::fragment::picking_old::concepts::Library< VallSections >::end(), and sections().

Referenced by core::fragment::picking_old::vall::vall_library_from_file().

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

src/core/fragment/picking_old/vall/VallLibrary.hh

Public Types

Public Member Functions

Private Types

Private Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Function Documentation