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NCBI C++ ToolKit: CMergeTree Class Reference

#include <algo/align/mergetree/merge_tree_core.hpp>

void x_AddChild (TMergeNode Parent, TMergeNode Child) void x_RemoveChild (TMergeNode Parent, TMergeNode Child) void x_AddParent (TMergeNode Child, TMergeNode Parent) void x_RemoveParent (TMergeNode Child, TMergeNode Parent) void x_LinkNodes (TMergeNode Parent, TMergeNode Child) void x_UnLinkNodes (TMergeNode Parent, TMergeNode Child) void x_CheckInterruptCallback () TMergeNode x_GetNode (CEquivRange Equiv) void x_FindLeafs (TMergeNode Curr, set< TMergeNode > &Leafs, TBitVec &Explored) bool x_FindBefores (TMergeNode New, TMergeNode Curr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth) bool x_FindAfters (TMergeNode New, TMergeNode Curr, set< TMergeNode > &Afters, TBitVec &Explored, TBitVec &Inserted) bool x_FindBefores_Up_Recur (TMergeNode New, TMergeNode Curr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth) bool x_FindBefores_Up_Iter (TMergeNode New, TMergeNode StartCurr, set< TMergeNode > &Befores, TBitVec &Explored, TBitVec &Inserted, int &Depth) bool x_FindAfters_Up (TMergeNode New, TMergeNode Curr, set< TMergeNode > &Afters, TBitVec &Explored, TBitVec &Inserted) TMergeNode x_Search_Recur (TMergeNode CurrNode, TBitVec &Explored, TMergeNode &UnBest) TMergeNode x_Search_Iter (TMergeNode StartNode, TBitVec &Explored, TMergeNode &UnBest) void x_EvalGap (const CEquivRange &Early, const CEquivRange &Late, ssize_t &GapOpen, ssize_t &GapExtend) const bool x_IsEventualChildOf (TMergeNode Parent, TMergeNode ToFind, TBitVec &Explored) void x_Print (CNcbiOstream &Out, TMergeNode Node, int Level, int &Count, TBitVec &Explored) void x_Dot (CNcbiOstream &Out, TMergeNode Node) void x_Dot_Nodes (CNcbiOstream &Out, TMergeNode Node, TBitVec &Explored) void x_Dot_Edges (CNcbiOstream &Out, TMergeNode Node, TBitVec &Explored) size_t x_CountChildNodes (TMergeNode Node, TBitVec &Explored) const size_t x_CountChildLinks (TMergeNode Node, TBitVec &Explored) const

Definition at line 111 of file merge_tree_core.hpp.

◆ TBitVec ◆ TFrameBuffer ◆ TFrameRef ◆ TInterruptFnPtr ◆ TNodeCache ◆ CMergeTree() ◆ ~CMergeTree() CMergeTree::~CMergeTree ( )

Definition at line 72 of file merge_tree_core.cpp.

References CMergeNode::BestChild, CMergeNode::Children, map_checker< Container >::clear(), set< Key, Compare >::clear(), ITERATE, m_Leaves, m_NodeCache, m_Root, NON_CONST_ITERATE, NULL, CMergeNode::Parents, and CRef< C, Locker >::Reset().

◆ AddEquiv()

Definition at line 206 of file merge_tree_core.cpp.

References CMergeNode::Children, bitvec< T >::clear(), CEquivRange::eAfter, set< Key, Compare >::empty(), CMergeNode::Equiv, set< Key, Compare >::insert(), ITERATE, m_AlignMerger, CTreeAlignMerger::m_Explored, CTreeAlignMerger::m_Inserted, m_Leaves, m_Root, max(), CMergeNode::Parents, x_FindBefores(), x_FindBefores_Up_Iter(), x_GetNode(), x_LinkNodes(), and x_UnLinkNodes().

Referenced by AddEquivs().

◆ AddEquivs()

Definition at line 307 of file merge_tree_core.cpp.

References AddEquiv(), eNa_strand_minus, eNa_strand_plus, ITERATE, PS(), s_SortMergeNodeByQuery(), s_SortMergeNodeByQuery_Minus(), s_SortMergeNodeBySubjt(), ct::sort(), and x_GetNode().

Referenced by CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), and CTreeAlignMerger::x_Merge_Dist_Impl().

◆ GetInterrupted() bool CMergeTree::GetInterrupted ( ) inline ◆ IsEmpty() bool CMergeTree::IsEmpty ( ) const ◆ Links() size_t CMergeTree::Links ( ) const ◆ Print() ◆ Score() ◆ Search()

Definition at line 701 of file merge_tree_core.cpp.

References CMergeNode::BestChild, CMergeNode::ChainScore, CMergeNode::Children, bitvec< T >::clear(), CMergeNode::Equiv, ERASE_ITERATE, INTERRUPT_CHECK_RATE, CRef< C, Locker >::IsNull(), m_InterruptCounter, m_Interrupted, m_Root, min(), NON_CONST_ITERATE, CRef< C, Locker >::NotNull(), NULL, CMergeNode::Parents, Path(), CRef< C, Locker >::Reset(), x_CheckInterruptCallback(), x_IsEventualChildOf(), x_LinkNodes(), x_Search_Iter(), and x_UnLinkNodes().

Referenced by CTreeAlignMerger::Merge_AllAtOnce(), CTreeAlignMerger::Merge_Pairwise(), and CTreeAlignMerger::x_Merge_Dist_Impl().

◆ SetInterruptCallback() ◆ SetScoring() void CMergeTree::SetScoring ( SScoring Scoring ) inline ◆ Size() size_t CMergeTree::Size ( ) const ◆ x_AddChild() ◆ x_AddParent() ◆ x_CheckInterruptCallback() void CMergeTree::x_CheckInterruptCallback ( ) private ◆ x_CountChildLinks() ◆ x_CountChildNodes() ◆ x_Dot() ◆ x_Dot_Edges() ◆ x_Dot_Nodes()

Definition at line 1292 of file merge_tree_core.cpp.

References CEquivRange::AlignId, CMergeNode::ChainScore, CMergeNode::Children, eNa_strand_plus, CMergeNode::Equiv, bitvec< T >::get(), CRange_Base::GetFrom(), CMergeNode::Id, ITERATE, CEquivRange::Matches, Out(), CEquivRange::Query, bitvec< T >::set(), CEquivRange::Strand, and CEquivRange::Subjt.

Referenced by x_Dot().

◆ x_EvalGap() ◆ x_FindAfters()

Definition at line 430 of file merge_tree_core.cpp.

References CEquivRange::CalcRelative(), CMergeNode::Children, CEquivRange::eAfter, CEquivRange::eBefore, CEquivRange::Empty(), set< Key, Compare >::empty(), CMergeNode::Equiv, bitvec< T >::get(), CMergeNode::Id, set< Key, Compare >::insert(), ITERATE, and bitvec< T >::set().

◆ x_FindAfters_Up()

Definition at line 645 of file merge_tree_core.cpp.

References CEquivRange::CalcRelative(), CEquivRange::eAfter, CEquivRange::eBefore, CEquivRange::Empty(), CMergeNode::Equiv, bitvec< T >::get(), CMergeNode::Id, set< Key, Compare >::insert(), ITERATE, CMergeNode::Parents, and bitvec< T >::set().

◆ x_FindBefores()

Definition at line 387 of file merge_tree_core.cpp.

References CEquivRange::CalcRelative(), CMergeNode::Children, CEquivRange::eAfter, CEquivRange::eBefore, CEquivRange::Empty(), CMergeNode::Equiv, bitvec< T >::get(), CMergeNode::Id, set< Key, Compare >::insert(), ITERATE, and bitvec< T >::set().

Referenced by AddEquiv().

◆ x_FindBefores_Up_Iter()

Definition at line 521 of file merge_tree_core.cpp.

References CEquivRange::CalcRelative(), CMergeTree::SFindBeforesIterFrame::ChildFrames, CMergeTree::SFindBeforesIterFrame::Curr, CEquivRange::eAfter, CEquivRange::eBefore, CEquivRange::Empty(), CMergeNode::Equiv, set< Key, Compare >::erase(), ERASE_ITERATE, bitvec< T >::get(), CMergeNode::Id, set< Key, Compare >::insert(), CRef< C, Locker >::IsNull(), ITERATE, m_AlignMerger, CTreeAlignMerger::m_FrameBuffer, CMergeNode::Parents, CMergeTree::SFindBeforesIterFrame::Returned, bitvec< T >::set(), and CMergeTree::SFindBeforesIterFrame::VisitCount.

Referenced by AddEquiv().

◆ x_FindBefores_Up_Recur()

Definition at line 468 of file merge_tree_core.cpp.

References CEquivRange::CalcRelative(), CEquivRange::eAfter, CEquivRange::eBefore, CEquivRange::Empty(), CMergeNode::Equiv, set< Key, Compare >::erase(), ERASE_ITERATE, bitvec< T >::get(), CMergeNode::Id, set< Key, Compare >::insert(), ITERATE, CMergeNode::Parents, and bitvec< T >::set().

◆ x_FindLeafs() ◆ x_GetNode() ◆ x_IsEventualChildOf() ◆ x_LinkNodes() ◆ x_Print()

Definition at line 1258 of file merge_tree_core.cpp.

References CMergeNode::BestChild, CMergeNode::ChainScore, CMergeNode::Children, set< Key, Compare >::empty(), CMergeNode::Equiv, bitvec< T >::get(), i, CMergeNode::Id, ITERATE, CRef< C, Locker >::NotNull(), Out(), CMergeNode::SelfScore, and bitvec< T >::set().

Referenced by Print().

◆ x_RemoveChild() ◆ x_RemoveParent() ◆ x_Search_Iter()

Definition at line 927 of file merge_tree_core.cpp.

References CEquivRange::AlignId, CMergeNode::ChainScore, CMergeNode::Equiv, CMergeTree::SScoring::GapExtend, CMergeTree::SScoring::GapOpen, bitvec< T >::get(), CMergeNode::Id, INTERRUPT_CHECK_RATE, CRef< C, Locker >::IsNull(), ITERATE, m_InterruptCounter, m_Interrupted, m_Scoring, CMergeTree::SScoring::Match, min(), CMergeTree::SScoring::MisMatch, NULL, CRef< C, Locker >::Reset(), REVERSE_ITERATE, bitvec< T >::set(), x_CheckInterruptCallback(), and x_EvalGap().

Referenced by Search().

◆ x_Search_Recur()

Definition at line 783 of file merge_tree_core.cpp.

References CMergeNode::BestChild, CMergeNode::ChainScore, CMergeNode::Children, CMergeNode::Equiv, CMergeTree::SScoring::GapExtend, CMergeTree::SScoring::GapOpen, bitvec< T >::get(), CMergeNode::Id, INTERRUPT_CHECK_RATE, CRef< C, Locker >::IsNull(), m_InterruptCounter, m_Interrupted, m_Scoring, CMergeTree::SScoring::Match, CEquivRange::Matches, min(), CMergeTree::SScoring::MisMatch, CEquivRange::MisMatches, NON_CONST_ITERATE, CRef< C, Locker >::NotNull(), NULL, CRef< C, Locker >::Reset(), CMergeNode::SelfScore, bitvec< T >::set(), x_CheckInterruptCallback(), and x_EvalGap().

◆ x_UnLinkNodes() ◆ INTERRUPT_CHECK_RATE const unsigned int CMergeTree::INTERRUPT_CHECK_RATE = 100 staticprivate ◆ kFrameBufSize ◆ kMaxChildFrames const unsigned int CMergeTree::kMaxChildFrames = 2 static ◆ m_AlignMerger ◆ m_Callback ◆ m_CallbackData void* CMergeTree::m_CallbackData private ◆ m_InterruptCounter unsigned int CMergeTree::m_InterruptCounter private ◆ m_Interrupted bool CMergeTree::m_Interrupted private ◆ m_Leaves ◆ m_NodeCache ◆ m_NodeIdCounter int CMergeTree::m_NodeIdCounter private ◆ m_Root ◆ m_Scoring

The documentation for this class was generated from the following files:

include/algo/align/mergetree/merge_tree_core.hpp
src/algo/align/mergetree/merge_tree_core.cpp

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