NCBI C++ ToolKit
Classes | Functions
merge_tree.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <algo/align/mergetree/equiv_range.hpp>
#include <algo/align/mergetree/merge_tree_core.hpp>
#include <algo/align/mergetree/merge_tree.hpp>
#include <algo/align/nw/align_exception.hpp>
+ Include dependency graph for merge_tree.cpp:

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Classes

class  CAlignDistGraph
 

Functions

 USING_SCOPE (objects)
 
set< ints_AlignIdsFromEquivList (const TEquivList &Equivs)
 
size_t s_ScoreFromEquivList (const TEquivList &Equivs)
 
size_t s_LengthFromEquivList (const TEquivList &Equivs)
 
bool s_SortSeqAlignByQuery_Subjt (CRef< CSeq_align > A, CRef< CSeq_align > B)
 
bool s_SortSeqAlignByQueryMinus_Subjt (CRef< CSeq_align > A, CRef< CSeq_align > B)
 
TSignedSeqPos s_SeqAlignIntercept (const CSeq_align &A)
 
bool s_SortSeqAlignByIntercept (CRef< CSeq_align > A, CRef< CSeq_align > B)
 
bool s_SortSeqAlignByLength (CRef< CSeq_align > A, CRef< CSeq_align > B)
 
void s_EquivDiff (const TEquivList &A, const TEquivList &B)
 
TSeqPos s_AlignDist (const CSeq_align &A, const CSeq_align &B)
 
void s_FindBestSubRange (const CMergeTree &Tree, const TEquivList &Path)
 
int s_UniformAlignId (const TEquivList &Equivs)
 

Function Documentation

◆ s_AlignDist()

TSeqPos s_AlignDist ( const CSeq_align A,
const CSeq_align B 
)

◆ s_AlignIdsFromEquivList()

set<int> s_AlignIdsFromEquivList ( const TEquivList Equivs)

◆ s_EquivDiff()

void s_EquivDiff ( const TEquivList A,
const TEquivList B 
)

Definition at line 140 of file merge_tree.cpp.

Referenced by CTreeAlignMerger::Merge_Pairwise().

◆ s_FindBestSubRange()

void s_FindBestSubRange ( const CMergeTree Tree,
const TEquivList Path 
)

Definition at line 257 of file merge_tree.cpp.

References BF, F, int, max(), min(), Path(), and CMergeTree::Score().

◆ s_LengthFromEquivList()

size_t s_LengthFromEquivList ( const TEquivList Equivs)

Definition at line 76 of file merge_tree.cpp.

References ITERATE.

Referenced by CTreeAlignMerger::x_Merge_Dist_Impl().

◆ s_ScoreFromEquivList()

size_t s_ScoreFromEquivList ( const TEquivList Equivs)

Definition at line 67 of file merge_tree.cpp.

References ITERATE.

◆ s_SeqAlignIntercept()

TSignedSeqPos s_SeqAlignIntercept ( const CSeq_align A)

◆ s_SortSeqAlignByIntercept()

bool s_SortSeqAlignByIntercept ( CRef< CSeq_align A,
CRef< CSeq_align B 
)

Definition at line 126 of file merge_tree.cpp.

References s_SeqAlignIntercept().

◆ s_SortSeqAlignByLength()

bool s_SortSeqAlignByLength ( CRef< CSeq_align A,
CRef< CSeq_align B 
)

Definition at line 135 of file merge_tree.cpp.

References CSeq_align::GetAlignLength().

Referenced by CTreeAlignMerger::Merge_Pairwise().

◆ s_SortSeqAlignByQuery_Subjt()

bool s_SortSeqAlignByQuery_Subjt ( CRef< CSeq_align A,
CRef< CSeq_align B 
)

◆ s_SortSeqAlignByQueryMinus_Subjt()

bool s_SortSeqAlignByQueryMinus_Subjt ( CRef< CSeq_align A,
CRef< CSeq_align B 
)

◆ s_UniformAlignId()

int s_UniformAlignId ( const TEquivList Equivs)

Definition at line 1239 of file merge_tree.cpp.

References ITERATE.

Referenced by CTreeAlignMerger::x_Merge_Dist_Impl().

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Wed Jul 17 13:22:10 2024 by modify_doxy.py rev. 669887