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NCBI C++ ToolKit: src/algo/structure/struct_util/su_alignment_set.hpp Source File

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std::list< ncbi::CRef< ncbi::objects::CSeq_annot > >

;

std::list < ncbi::CRef < MasterSlaveAlignment > >

;

& sequenceSet,

std::vector < unsigned int > *rowOrder =

);

AlignmentSet(SequenceSet *seqSet, const SeqAnnotList &seqAnnots, bool ignoreBadPairwiseAlignments=false)

SeqAnnotList * newAsnAlignmentData

vector< const MasterSlaveAlignment * > AlignmentList

std::list< ncbi::CRef< MasterSlaveAlignment > > AlignmentList

AlignmentList m_alignments

std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList

const Sequence * m_master

static AlignmentSet * CreateFromMultiple(const BlockMultipleAlignment *multiple, SeqAnnotList *newAsnAlignmentData, const SequenceSet &sequenceSet, const std::vector< unsigned int > *rowOrder=NULL)

ResidueVector m_blockStructure

MasterSlaveAlignment(const SequenceSet *sequenceSet, const Sequence *masterSequence, const objects::CSeq_align &seqAlign)

vector< int > ResidueVector

std::vector< unsigned int > ResidueVector

const Sequence * m_master

ResidueVector m_masterToSlave

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

The NCBI C++/STL use hints.

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