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CAlignCleanup Class Reference

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class CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager. More...

#include <algo/sequence/align_cleanup.hpp>

+ Collaboration diagram for CAlignCleanup:

Public Types

enum  EMode { eAlignVec , eAnchoredAlign , eDefault = eAnchoredAlign }
 
typedef list< CConstRef< CSeq_align > > TConstAligns
 
typedef list< CRef< CSeq_align > > TAligns
 

Public Member Functions

 CAlignCleanup ()
 
 CAlignCleanup (CScope &scope)
 
void Cleanup (const TAligns &aligns_in, TAligns &aligns_out, EMode mode=eDefault)
 
void Cleanup (const TConstAligns &aligns_in, TAligns &aligns_out, EMode mode=eDefault)
 
void SortInputsByScore (bool b)
 flags these primarity affect the CAlnVec implementation More...
 
void AllowTranslocations (bool)
 Permit off-diagonal high-scoring items (particularly ones on the opposite strand) More...
 
void PreserveRows (bool b)
 Assume that the alignments contains alignments of a sequence to itself. More...
 
void FillUnaligned (bool b)
 Fill any unaligned regions with explicit gaps. More...
 

Static Public Member Functions

static void CreatePairwiseFromMultiple (const CSeq_align &multiple, TAligns &pairwise)
 

Private Member Functions

void x_Cleanup_AlignVec (const TConstAligns &aligns_in, TAligns &aligns_out)
 
void x_Cleanup_AnchoredAln (const TConstAligns &aligns_in, TAligns &aligns_out)
 

Private Attributes

CRef< CScopem_Scope
 
bool m_SortByScore
 
bool m_PreserveRows
 
bool m_FillUnaligned
 

Detailed Description

class CAlignCleanup implements an alignment cleanup utility based on the C++ alignment manager.

The primary goal is to remove redundancies from any given set of alignment, and generate a cleaned up version of these alignments

Definition at line 48 of file align_cleanup.hpp.

Member Typedef Documentation

◆ TAligns

Definition at line 55 of file align_cleanup.hpp.

◆ TConstAligns

Definition at line 54 of file align_cleanup.hpp.

Member Enumeration Documentation

◆ EMode

Enumerator
eAlignVec 
eAnchoredAlign 
eDefault 

Definition at line 57 of file align_cleanup.hpp.

Constructor & Destructor Documentation

◆ CAlignCleanup() [1/2]

CAlignCleanup::CAlignCleanup ( )

Definition at line 207 of file align_cleanup.cpp.

◆ CAlignCleanup() [2/2]

CAlignCleanup::CAlignCleanup ( CScope scope)

Definition at line 214 of file align_cleanup.cpp.

Member Function Documentation

◆ AllowTranslocations()

void CAlignCleanup::AllowTranslocations ( bool  )
inline

Permit off-diagonal high-scoring items (particularly ones on the opposite strand)

NB: this is a no-op, as it is no longer necessary

Definition at line 89 of file align_cleanup.hpp.

◆ Cleanup() [1/2]

void CAlignCleanup::Cleanup ( const TAligns aligns_in,
TAligns aligns_out,
EMode  mode = eDefault 
)

◆ Cleanup() [2/2]

void CAlignCleanup::Cleanup ( const TConstAligns aligns_in,
TAligns aligns_out,
EMode  mode = eDefault 
)

◆ CreatePairwiseFromMultiple()

void CAlignCleanup::CreatePairwiseFromMultiple ( const CSeq_align multiple,
TAligns pairwise 
)
static

◆ FillUnaligned()

void CAlignCleanup::FillUnaligned ( bool  b)
inline

Fill any unaligned regions with explicit gaps.

Definition at line 95 of file align_cleanup.hpp.

References b.

Referenced by CInversionMergeAligner::x_MergeSeqAlignSet(), and CMergeAligner::x_MergeSeqAlignSet().

◆ PreserveRows()

void CAlignCleanup::PreserveRows ( bool  b)
inline

Assume that the alignments contains alignments of a sequence to itself.

Definition at line 92 of file align_cleanup.hpp.

References b.

◆ SortInputsByScore()

void CAlignCleanup::SortInputsByScore ( bool  b)
inline

flags these primarity affect the CAlnVec implementation

Sort input alignments by score before evaluating

Definition at line 83 of file align_cleanup.hpp.

References b.

Referenced by BOOST_AUTO_TEST_CASE(), and CInversionMergeAligner::x_MergeSeqAlignSet().

◆ x_Cleanup_AlignVec()

void CAlignCleanup::x_Cleanup_AlignVec ( const TConstAligns aligns_in,
TAligns aligns_out 
)
private

◆ x_Cleanup_AnchoredAln()

void CAlignCleanup::x_Cleanup_AnchoredAln ( const TConstAligns aligns_in,
TAligns aligns_out 
)
private

Member Data Documentation

◆ m_FillUnaligned

bool CAlignCleanup::m_FillUnaligned
private

Definition at line 104 of file align_cleanup.hpp.

Referenced by x_Cleanup_AnchoredAln().

◆ m_PreserveRows

bool CAlignCleanup::m_PreserveRows
private

Definition at line 103 of file align_cleanup.hpp.

Referenced by x_Cleanup_AlignVec(), and x_Cleanup_AnchoredAln().

◆ m_Scope

CRef<CScope> CAlignCleanup::m_Scope
private

Definition at line 101 of file align_cleanup.hpp.

Referenced by x_Cleanup_AlignVec().

◆ m_SortByScore

bool CAlignCleanup::m_SortByScore
private

Definition at line 102 of file align_cleanup.hpp.

Referenced by x_Cleanup_AlignVec(), and x_Cleanup_AnchoredAln().


The documentation for this class was generated from the following files:
Modified on Sat May 18 11:39:18 2024 by modify_doxy.py rev. 669887