FASTAContainer< TFI_File > Class Reference

FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow. More...

#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>

Collaboration diagram for FASTAContainer< TFI_File >:

Public Member Functions
	FASTAContainer ()=delete
	FASTAContainer (const String &FASTA_file)
	C'tor with FASTA filename. More...
size_t	getChunkOffset () const
	how many entries were read and got swapped out already More...
bool	activateCache ()
	Swaps in the background cache of entries, read previously via cacheChunk() More...
bool	cacheChunk (int suggested_size)
	Prefetch a new cache in the background, with up to suggested_size entries (or fewer upon reaching end-of-file) More...
size_t	chunkSize () const
	number of entries in active cache More...
const FASTAFile::FASTAEntry &	chunkAt (size_t pos) const
	Retrieve a FASTA entry at cache position pos (fast) More...
bool	readAt (FASTAFile::FASTAEntry &protein, size_t pos)
	Retrieve a FASTA entry at global position pos (must not be behind the currently active chunk, but can be smaller) More...
bool	empty ()
	is the FASTA file empty? More...
void	reset ()
	resets reading of the FASTA file, enables fresh reading of the FASTA from the beginning More...
size_t	size () const
	NOT the number of entries in the FASTA file, but merely the number of already read entries (since we do not know how many are still to come) More...

Private Attributes
FASTAFile	f_
	FASTA file connection. More...
std::vector< std::streampos >	offsets_
	internal byte offsets into FASTA file for random access reading of previous entries. More...
std::vector< FASTAFile::FASTAEntry >	data_fg_
	active (foreground) data More...
std::vector< FASTAFile::FASTAEntry >	data_bg_
	prefetched (background) data; will become the next active data More...
size_t	chunk_offset_
	number of entries before the current chunk More...
std::string	filename_
	FASTA file name. More...

Detailed Description

FASTAContainer<TFI_File> will make FASTA entries available chunk-wise from start to end by loading it from a FASTA file. This avoids having to load the full file into memory. While loading, the container will memorize the file offsets of each entry, allowing to read an arbitrary i'th entry again from disk. If possible, only entries from the currently cached chunk should be queried, otherwise access will be slow.

Internally uses FASTAFile class to read single sequences.

Constructor & Destructor Documentation

FASTAContainer() [1/2]

FASTAContainer ( )

delete

FASTAContainer() [2/2]

FASTAContainer ( const String &  FASTA_file )

inline

C'tor with FASTA filename.

Member Function Documentation

activateCache()

bool activateCache ( )

inline

Swaps in the background cache of entries, read previously via cacheChunk()

If you call this function without a prior call to cacheChunk(), the cache will be empty.

Returns

true if cache contains data; false if empty

Note

Should be invoked by a single thread, followed by a barrier to sync access of subsequent calls to chunkAt()

cacheChunk()

bool cacheChunk ( int  suggested_size )

inline

Prefetch a new cache in the background, with up to suggested_size entries (or fewer upon reaching end-of-file)

Call activateCache() afterwards to make the data available via chunkAt() or readAt().

Parameters

suggested_size

Number of FASTA entries to read from disk

Returns

true if new data is available; false if background data is empty

chunkAt()

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

inline

Retrieve a FASTA entry at cache position pos (fast)

Requires prior call to activateCache(). Index pos must be smaller than chunkSize().

Note

: can be used by multiple threads at a time (until activateCache() is called)

chunkSize()

size_t chunkSize ( ) const

inline

number of entries in active cache

empty()

bool empty ( )

inline

is the FASTA file empty?

getChunkOffset()

size_t getChunkOffset ( ) const

inline

how many entries were read and got swapped out already

readAt()

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

inline

Retrieve a FASTA entry at global position pos (must not be behind the currently active chunk, but can be smaller)

This query is fast, if pos contains the currently active chunk, and slow (read from disk) for earlier entries. Can be used before reaching the end of the file, since it will reset the file position after its done reading (if reading from disk is required), but must not be used for entries beyond the active chunk (unseen data).

Parameters

protein	Return value
pos	Absolute entry number in FASTA file

Returns

true if reading was successful; false otherwise (e.g. EOF)

Exceptions

Exception::IndexOverflow

if pos is beyond active chunk

Note

: not multi-threading safe (use chunkAt())!

reset()

void reset ( )

inline

resets reading of the FASTA file, enables fresh reading of the FASTA from the beginning

size()

size_t size ( ) const

inline

NOT the number of entries in the FASTA file, but merely the number of already read entries (since we do not know how many are still to come)

Note

Data in the background cache is included here, i.e. access to size()-1 using readAt() might be slow if activateCache() was not called yet.

Member Data Documentation

chunk_offset_

size_t chunk_offset_

private

number of entries before the current chunk

data_bg_

std::vector<FASTAFile::FASTAEntry> data_bg_

private

prefetched (background) data; will become the next active data

data_fg_

std::vector<FASTAFile::FASTAEntry> data_fg_

private

active (foreground) data

f_

FASTAFile f_

private

FASTA file connection.

filename_

std::string filename_

private

FASTA file name.

offsets_

std::vector<std::streampos> offsets_

private

internal byte offsets into FASTA file for random access reading of previous entries.