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NCBI C++ ToolKit: include/algo/align/mergetree/merge_tree_core.hpp Source File

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set< CRef< CMergeNode > > Children

CMergeNode(CEquivRange Value, int NId)

CRef< CMergeNode > BestChild

set< CRef< CMergeNode > > Parents

TInterruptFnPtr m_Callback

CMergeTree(CTreeAlignMerger &align_merger)

void AddEquiv(CEquivRange NewEquiv)

int Score(const TEquivList &Path) const

CTreeAlignMerger & m_AlignMerger

void SetScoring(SScoring Scoring)

deque< SFindBeforesIterFrame > TFrameBuffer

map< int, TMergeNode > TNodeCache

void x_RemoveParent(TMergeNode Child, TMergeNode Parent)

void x_Dot_Edges(CNcbiOstream &Out, TMergeNode Node, TBitVec &Explored)

bool x_FindBefores_Up_Iter(TMergeNode New, TMergeNode StartCurr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth)

TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr Callback, void *CallbackData)

void x_Dot(CNcbiOstream &Out, TMergeNode Node)

void x_LinkNodes(TMergeNode Parent, TMergeNode Child)

set< TMergeNode > m_Leaves

void Search(TEquivList &Path, bool Once=false)

void Print(CNcbiOstream &Out)

bitvec< unsigned int > TBitVec

void x_Dot_Nodes(CNcbiOstream &Out, TMergeNode Node, TBitVec &Explored)

static const unsigned int kFrameBufSize

bool x_FindBefores(TMergeNode New, TMergeNode Curr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth)

void x_UnLinkNodes(TMergeNode Parent, TMergeNode Child)

SFindBeforesIterFrame * TFrameRef

void x_AddChild(TMergeNode Parent, TMergeNode Child)

void x_AddParent(TMergeNode Child, TMergeNode Parent)

bool x_FindBefores_Up_Recur(TMergeNode New, TMergeNode Curr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth)

void x_Print(CNcbiOstream &Out, TMergeNode Node, int Level, int &Count, TBitVec &Explored)

void AddEquivs(const TEquivList &Equivs)

void x_FindLeafs(TMergeNode Curr, set< TMergeNode > &Leafs, TBitVec &Explored)

TMergeNode x_GetNode(CEquivRange Equiv)

TMergeNode x_Search_Iter(TMergeNode StartNode, TBitVec &Explored, TMergeNode &UnBest)

bool x_FindAfters(TMergeNode New, TMergeNode Curr, set< TMergeNode > &Afters, TBitVec &Explored, TBitVec &Inserted)

size_t x_CountChildLinks(TMergeNode Node, TBitVec &Explored) const

bool x_FindAfters_Up(TMergeNode New, TMergeNode Curr, set< TMergeNode > &Afters, TBitVec &Explored, TBitVec &Inserted)

size_t x_CountChildNodes(TMergeNode Node, TBitVec &Explored) const

void x_RemoveChild(TMergeNode Parent, TMergeNode Child)

void x_CheckInterruptCallback()

bool x_IsEventualChildOf(TMergeNode Parent, TMergeNode ToFind, TBitVec &Explored)

bool(* TInterruptFnPtr)(void *callback_data)

unsigned int m_InterruptCounter

TMergeNode x_Search_Recur(TMergeNode CurrNode, TBitVec &Explored, TMergeNode &UnBest)

static const unsigned int INTERRUPT_CHECK_RATE

void x_EvalGap(const CEquivRange &Early, const CEquivRange &Late, ssize_t &GapOpen, ssize_t &GapExtend) const

static const unsigned int kMaxChildFrames

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

vector< CEquivRange > TEquivList

string Path(const string &dir, const string &file)

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

vector< TMergeNode > TMergeNodeVec

CRef< CMergeNode > TMergeNode

bool operator<(const CMergeNode &A, const CMergeNode &B)

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

Defines NCBI C++ diagnostic APIs, classes, and macros.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

void Out(T t, int w, CNcbiOstream &to=cout)

vector< TFrameRef > ChildFrames

SScoring(int M, int X, int O, int E)

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