orf.cpp File Reference

#include <ncbi_pch.hpp>
#include <algo/sequence/orf.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Na_strand.hpp>
#include <objects/seqfeat/Genetic_code_table.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/general/Int_fuzz.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <algorithm>
#include <algo/sequence/consensus_splice.hpp>

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Typedefs
typedef vector< CRef< CSeq_interval > >	TRangeVec

Functions
	USING_SCOPE (objects)
char	Complement (const char c)
bool	IsGapOrN (const char c)
template<class TSeq >
set< TSeqPos >	FindStarts (const TSeq &seq, TSeqPos from, TSeqPos to, const vector< string > &allowable_starts)
void	AddInterval (TRangeVec &intervals, TSeqPos from, TSeqPos to, bool from_fuzz=false, bool to_fuzz=false)
template<class TSeq >
void	FindForwardOrfs (const TSeq &seq, TRangeVec &ranges, unsigned int min_length_bp, int genetic_code, const vector< string > &allowable_starts, bool longest_orfs, size_t max_seq_gap, bool stop_to_stop)
	Find all ORFs in forward orientation with length in *base pairs* >= min_length_bp. More...
template<class TSeq >
static void	s_FindOrfs (const TSeq &seq, COrf::TLocVec &results, unsigned int min_length_bp, int genetic_code, const vector< string > &allowable_starts_, bool longest_orfs, size_t max_seq_gap)
	Find all ORFs in both orientations that are at least min_length_bp long (not including the stop). More...

Typedef Documentation

TRangeVec

typedef vector<CRef<CSeq_interval> > TRangeVec

Definition at line 50 of file orf.cpp.

Function Documentation

AddInterval()

void AddInterval	(	TRangeVec &	intervals,
		TSeqPos	from,
		TSeqPos	to,
		bool	from_fuzz = false,
		bool	to_fuzz = false
	)

Definition at line 102 of file orf.cpp.

Referenced by FindForwardOrfs().

Complement()

char Complement

(

const char

c

)

Definition at line 53 of file orf.cpp.

Referenced by IsGapOrN().

FindForwardOrfs()

template<class TSeq >

void FindForwardOrfs ( const TSeq &  seq, TRangeVec &  ranges, unsigned int  min_length_bp, int  genetic_code, const vector< string > &  allowable_starts, bool  longest_orfs, size_t  max_seq_gap, bool  stop_to_stop  )

inline

Find all ORFs in forward orientation with length in *base pairs* >= min_length_bp.

seq must be in iupac. Returned range does not include the stop codon.

Definition at line 123 of file orf.cpp.

References _ASSERT, AddInterval(), set< Key, Compare >::begin(), set< Key, Compare >::erase(), f, FindStarts(), i, and IsGapOrN().

Referenced by s_FindOrfs().

FindStarts()

template<class TSeq >

set<TSeqPos> FindStarts	(	const TSeq &	seq,
		TSeqPos	from,
		TSeqPos	to,
		const vector< string > &	allowable_starts
	)

Definition at line 76 of file orf.cpp.

References set< Key, Compare >::insert(), and ITERATE.

Referenced by FindForwardOrfs().

IsGapOrN()

bool IsGapOrN

(

const char

c

)

Definition at line 64 of file orf.cpp.

References Complement().

Referenced by FindForwardOrfs().

s_FindOrfs()

template<class TSeq >

static void s_FindOrfs ( const TSeq &  seq, COrf::TLocVec &  results, unsigned int  min_length_bp, int  genetic_code, const vector< string > &  allowable_starts_, bool  longest_orfs, size_t  max_seq_gap  )

static

Find all ORFs in both orientations that are at least min_length_bp long (not including the stop).

Report results as Seq-locs. seq must be in iupac.

Definition at line 228 of file orf.cpp.

References eExtreme_Positional, eNa_strand_minus, eNa_strand_plus, eSeq_code_type_iupacna, FindForwardOrfs(), i, NON_CONST_ITERATE, and results.

Referenced by COrf::FindOrfs().

USING_SCOPE()

USING_SCOPE

(

objects

)