FASTAContainer< TFI_Vector > Class Template Reference

FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory. More...

#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>

Collaboration diagram for FASTAContainer< TFI_Vector >:

Public Member Functions
	FASTAContainer ()=delete
	FASTAContainer (const std::vector< FASTAFile::FASTAEntry > &data)
	C'tor for already existing data (by reference). More...
size_t	getChunkOffset () const
	always 0, since this specialization requires/supports no chunking More...
bool	activateCache ()
	no-op (since data is already fully available as vector) More...
bool	cacheChunk (int)
	no-op (since data is already fully available as vector) More...
size_t	chunkSize () const
	active data spans the full range, i.e. size of container More...
const FASTAFile::FASTAEntry &	chunkAt (size_t pos) const
	fast access to chunked (i.e. all) entries More...
bool	readAt (FASTAFile::FASTAEntry &protein, size_t pos) const
	fast access to an entry More...
bool	empty () const
	calls empty() on underlying vector More...
size_t	size () const
	calls size() on underlying vector More...
void	reset ()
	required for template parameters! More...

Private Attributes
const std::vector< FASTAFile::FASTAEntry > &	data_
	reference to existing data More...
int	activate_count_ = 0
int	cache_count_ = 0

Detailed Description

template<>
class OpenMS::FASTAContainer< TFI_Vector >

FASTAContainer<TFI_Vector> simply takes an existing vector of FASTAEntries and provides the same interface with a potentially huge speed benefit over FASTAContainer<TFI_File> since it does not need disk access, but at the cost of memory.

Constructor & Destructor Documentation

FASTAContainer() [1/2]

FASTAContainer ( )

delete

FASTAContainer() [2/2]

FASTAContainer ( const std::vector< FASTAFile::FASTAEntry > &  data )

inline

C'tor for already existing data (by reference).

An internal reference will be kept. Make sure the data is not deleted during the lifetime of FASTAContainer

Member Function Documentation

activateCache()

bool activateCache ( )

inline

no-op (since data is already fully available as vector)

Returns

true only on the first call; false on subsequent calls

cacheChunk()

bool cacheChunk ( int  )

inline

no-op (since data is already fully available as vector)

Returns

true only on the first call; false on subsequent calls

chunkAt()

const FASTAFile::FASTAEntry& chunkAt ( size_t  pos ) const

inline

fast access to chunked (i.e. all) entries

chunkSize()

size_t chunkSize ( ) const

inline

active data spans the full range, i.e. size of container

Returns

the size of the underlying vector

empty()

bool empty ( ) const

inline

calls empty() on underlying vector

getChunkOffset()

size_t getChunkOffset ( ) const

inline

always 0, since this specialization requires/supports no chunking

readAt()

bool readAt ( FASTAFile::FASTAEntry &  protein, size_t  pos  ) const

inline

fast access to an entry

reset()

void reset ( )

inline

required for template parameters!

size()

size_t size ( ) const

inline

calls size() on underlying vector

Member Data Documentation

activate_count_

int activate_count_ = 0

private

cache_count_

int cache_count_ = 0

private

data_

const std::vector<FASTAFile::FASTAEntry>& data_

private

reference to existing data