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 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()

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::SeqRange::isNegativeStrand().

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 68 of file SequenceFeatureTools.cpp.

References bpp::SequenceFeatureSet::addFeature().

---

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

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