NCBI C++ ToolKit
Typedefs | Functions
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>
+ Include dependency graph for orf.cpp:

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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< TSeqPosFindStarts (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, and NON_CONST_ITERATE.

Referenced by COrf::FindOrfs().

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Thu Feb 29 12:23:49 2024 by modify_doxy.py rev. 669887