NCBI C++ ToolKit
Classes | Typedefs | Functions
genomic_compart.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <util/range.hpp>
#include <algo/align/util/genomic_compart.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqalign/Dense_seg.hpp>
+ Include dependency graph for genomic_compart.cpp:

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Classes

struct  SRangesByStart
 
struct  SRangesBySize
 
struct  SRangesByScore
 
struct  SRangesByPctIdent
 
struct  SSeqAlignsBySize
 
struct  SSeqAlignsByScore
 
struct  SSeqAlignsByPctIdent
 
struct  SRangeIteratorsByAddress
 
struct  SCompartScore
 

Typedefs

typedef pair< TSeqRange, TSeqRangeTRange
 
typedef pair< TRange, CRef< CSeq_align > > TAlignRange
 
typedef multiset< TAlignRange, SRangesByStartTAlignRangeMultiSet
 

Functions

bool IsIntersectingQuery (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)
 
bool IsIntersectingSubject (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2)
 
bool IsConsistent (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)
 
TSeqPos Difference (const pair< TSeqRange, TSeqRange > &r1, const pair< TSeqRange, TSeqRange > &r2, ENa_strand s1, ENa_strand s2)
 
void FindCompartments (const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options, float diff_len_filter)
 
void JoinCompartment (const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns)
 

Typedef Documentation

◆ TAlignRange

typedef pair<TRange, CRef<CSeq_align> > TAlignRange

Definition at line 177 of file genomic_compart.cpp.

◆ TAlignRangeMultiSet

Definition at line 200 of file genomic_compart.cpp.

◆ TRange

typedef pair<TSeqRange, TSeqRange> TRange

Definition at line 176 of file genomic_compart.cpp.

Function Documentation

◆ Difference()

TSeqPos Difference ( const pair< TSeqRange, TSeqRange > &  r1,
const pair< TSeqRange, TSeqRange > &  r2,
ENa_strand  s1,
ENa_strand  s2 
)

Definition at line 120 of file genomic_compart.cpp.

Referenced by FindCompartments().

◆ FindCompartments()

void FindCompartments ( const list< CRef< CSeq_align > > &  aligns,
list< CRef< CSeq_align_set > > &  align_sets,
TCompartOptions  options,
float  diff_len_filter 
)

◆ IsConsistent()

bool IsConsistent ( const pair< TSeqRange, TSeqRange > &  r1,
const pair< TSeqRange, TSeqRange > &  r2,
ENa_strand  s1,
ENa_strand  s2 
)

Definition at line 82 of file genomic_compart.cpp.

References eNa_strand_minus, and SameOrientation().

Referenced by FindCompartments().

◆ IsIntersectingQuery()

bool IsIntersectingQuery ( const pair< TSeqRange, TSeqRange > &  r1,
const pair< TSeqRange, TSeqRange > &  r2 
)

Definition at line 46 of file genomic_compart.cpp.

Referenced by FindCompartments().

◆ IsIntersectingSubject()

bool IsIntersectingSubject ( const pair< TSeqRange, TSeqRange > &  r1,
const pair< TSeqRange, TSeqRange > &  r2 
)

Definition at line 64 of file genomic_compart.cpp.

Referenced by FindCompartments().

◆ JoinCompartment()

void JoinCompartment ( const CRef< CSeq_align_set > &  compartment,
float  gap_ratio,
list< CRef< CSeq_align > > &  aligns 
)
Modified on Fri Mar 01 10:09:05 2024 by modify_doxy.py rev. 669887