bpp::SequenceFeatureTools Class Reference

#include <Bpp/Seq/Feature/SequenceFeatureTools.h>

Static Public Member Functions
static Sequence *	extract (const Sequence &seq, const SeqRange &range)
	Extract a sub-sequence given a SeqRange. More...
static void	extract (const Sequence &seq, const SeqRange &range, Sequence &output)
	Extract a sub-sequence given a SeqRange. More...
static unsigned int	getOrfs (const Sequence &seq, SequenceFeatureSet &featSet, const GeneticCode &gCode)
	Get ORF features for a Sequence. More...

Detailed Description

Definition at line 51 of file SequenceFeatureTools.h.

Member Function Documentation

extract() [1/2]

Sequence * SequenceFeatureTools::extract ( const Sequence &  seq, const SeqRange &  range  )

static

Extract a sub-sequence given a SeqRange.

The sub-sequence is revese-complemented if SeqRange is in negative strand.

Parameters

seq	The Sequence to trunc.
range	The SeqRange to extract.

Returns

A new Sequence object with the given subsequence oriented according to the SeqRange.

Author

Sylvain Gaillard

Definition at line 55 of file SequenceFeatureTools.cpp.

References bpp::Range< class >::begin(), bpp::Range< class >::end(), bpp::SequenceTools::invertComplement(), bpp::SeqRange::isNegativeStrand(), bpp::Sequence::size(), and bpp::SequenceTools::subseq().

extract() [2/2]

void SequenceFeatureTools::extract ( const Sequence &  seq, const SeqRange &  range, Sequence &  output  )

static

Extract a sub-sequence given a SeqRange.

The sub-sequence is revese-complemented if SeqRange is in negative strand.

Parameters

seq	The Sequence to trunc.
range	The SeqRange to extract.
output	The Sequence object to be filled with the given subsequence oriented according to the SeqRange.

Author

Sylvain Gaillard

Definition at line 68 of file SequenceFeatureTools.cpp.

References bpp::Range< class >::begin(), bpp::Range< class >::end(), bpp::SequenceTools::invertComplement(), bpp::SeqRange::isNegativeStrand(), bpp::Sequence::size(), and bpp::SequenceTools::subseq().

getOrfs()

unsigned int SequenceFeatureTools::getOrfs ( const Sequence &  seq, SequenceFeatureSet &  featSet, const GeneticCode &  gCode  )

static

Get ORF features for a Sequence.

Parameters

seq	The Sequence where to find ORF. Must be a nucleic sequence.
featSet	A SequenceFeatureSet to fill with the annotations.
gCode	The genetic code to use.

Returns

The number of ORF found.

Author

Sylvain Gaillard

Definition at line 79 of file SequenceFeatureTools.cpp.

References bpp::SequenceFeatureSet::addFeature(), bpp::Sequence::getAlphabet(), bpp::CodonAlphabet::getCodon(), bpp::Sequence::getName(), bpp::GeneticCode::getSourceAlphabet(), bpp::Sequence::getValue(), bpp::AlphabetTools::isNucleicAlphabet(), bpp::GeneticCode::isStart(), bpp::GeneticCode::isStop(), and bpp::Sequence::size().

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

• Bpp/Seq/Feature/SequenceFeatureTools.h
• Bpp/Seq/Feature/SequenceFeatureTools.cpp