bpp::Fasta::FileIndex Class Reference

The SequenceFileIndex class for Fasta format. More...

#include <Bpp/Seq/Io/Fasta.h>

Inheritance diagram for bpp::Fasta::FileIndex:

Collaboration diagram for bpp::Fasta::FileIndex:

Public Member Functions
	FileIndex ()
	~FileIndex ()
void	build (const std::string &path)
	Build the index given a path to the file. More...
void	build (const std::string &path, const bool strictSequenceNames)
	Constructor. More...
std::streampos	getSequencePosition (const std::string &id) const
	Get the position of a Sequence given its ID. More...
size_t	getNumberOfSequences () const
	Get the number of sequences. More...
void	read (const std::string &path)
	Read the index from a file. More...
void	write (const std::string &path)
	Write the index to a file. More...
void	getSequence (const std::string &seqid, Sequence &seq, const std::string &path) const
	Get a sequence given its ID. More...
void	getSequence (const std::string &seqid, Sequence &seq, const std::string &path, const bool strictSequenceNames) const

Private Attributes
std::map< std::string, std::streampos >	index_
std::streampos	fileSize_

Detailed Description

The SequenceFileIndex class for Fasta format.

Author

Sylvain Gaillard

Definition at line 146 of file Fasta.h.

Constructor & Destructor Documentation

FileIndex()

bpp::Fasta::FileIndex::FileIndex ( )

inline

Definition at line 149 of file Fasta.h.

~FileIndex()

bpp::Fasta::FileIndex::~FileIndex ( )

inline

Definition at line 150 of file Fasta.h.

Member Function Documentation

build() [1/2]

void bpp::Fasta::FileIndex::build ( const std::string &  path )

inlinevirtual

Build the index given a path to the file.

Implements bpp::SequenceFileIndex.

Definition at line 151 of file Fasta.h.

build() [2/2]

void Fasta::FileIndex::build	(	const std::string &	path,
		const bool	strictSequenceNames
	)

Constructor.

Parameters

path	The path to the file.
strictSequenceNames	Tells if the sequence names should be restricted to the characters between '>' and the first blank one.

Definition at line 205 of file Fasta.cpp.

getNumberOfSequences()

size_t bpp::Fasta::FileIndex::getNumberOfSequences ( ) const

inlinevirtual

Get the number of sequences.

Implements bpp::SequenceFileIndex.

Definition at line 163 of file Fasta.h.

References index_.

getSequence() [1/2]

void Fasta::FileIndex::getSequence	(	const std::string &	seqid,
		Sequence &	seq,
		const std::string &	path
	)		const

Get a sequence given its ID.

Definition at line 270 of file Fasta.cpp.

getSequence() [2/2]

void Fasta::FileIndex::getSequence	(	const std::string &	seqid,
		Sequence &	seq,
		const std::string &	path,
		const bool	strictSequenceNames
	)		const

Definition at line 275 of file Fasta.cpp.

References bpp::Fasta::nextSequence(), and bpp::Fasta::strictNames().

getSequencePosition()

streampos Fasta::FileIndex::getSequencePosition ( const std::string &  id ) const

virtual

Get the position of a Sequence given its ID.

Implements bpp::SequenceFileIndex.

Definition at line 233 of file Fasta.cpp.

read()

void Fasta::FileIndex::read

(

const std::string &

path

)

Read the index from a file.

Definition at line 243 of file Fasta.cpp.

References bpp::StringTokenizer::getToken(), bpp::TextTools::isEmpty(), bpp::TextTools::removeSurroundingWhiteSpaces(), and bpp::TextTools::toInt().

write()

void Fasta::FileIndex::write

(

const std::string &

path

)

Write the index to a file.

Definition at line 260 of file Fasta.cpp.

References bpp::TextTools::toString().

Member Data Documentation

fileSize_

std::streampos bpp::Fasta::FileIndex::fileSize_

private

Definition at line 183 of file Fasta.h.

index_

std::map<std::string, std::streampos> bpp::Fasta::FileIndex::index_

private

Definition at line 182 of file Fasta.h.

Referenced by getNumberOfSequences().

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

• Bpp/Seq/Io/Fasta.h
• Bpp/Seq/Io/Fasta.cpp