bpp-seq
2.2.0
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The SequenceFileIndex class for Fasta format. More...
#include <Bpp/Seq/Io/Fasta.h>
Public Member Functions | |
FileIndex () | |
~FileIndex () | |
void | build (const std::string &path) throw (Exception) |
Build the index given a path to the file. More... | |
std::streampos | getSequencePosition (const std::string &id) const throw (Exception) |
Get the position of a Sequence given its ID. More... | |
size_t | getNumberOfSequences () const throw (Exception) |
Get the number of sequences. More... | |
void | read (const std::string &path) throw (Exception) |
Read the index from a file. More... | |
void | write (const std::string &path) throw (Exception) |
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... | |
Private Attributes | |
std::map< std::string, std::streampos > | index_ |
std::streampos | fileSize_ |
The SequenceFileIndex class for Fasta format.
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virtual |
Build the index given a path to the file.
Implements bpp::SequenceFileIndex.
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inlinevirtual |
Get the number of sequences.
Implements bpp::SequenceFileIndex.
Definition at line 190 of file Fasta.h.
References index_.
void Fasta::FileIndex::getSequence | ( | const std::string & | seqid, |
Sequence & | seq, | ||
const std::string & | path | ||
) | const |
Get a sequence given its ID.
Definition at line 282 of file Fasta.cpp.
References bpp::Fasta::nextSequence().
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virtual |
Get the position of a Sequence given its ID.
Implements bpp::SequenceFileIndex.
void Fasta::FileIndex::read | ( | const std::string & | path | ) | |
throw | ( | Exception | |||
) |
void Fasta::FileIndex::write | ( | const std::string & | path | ) | |
throw | ( | Exception | |||
) |
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private |
Definition at line 206 of file Fasta.h.
Referenced by getNumberOfSequences().