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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sparse__alignment_8hpp_source.html below:

NCBI C++ ToolKit: include/gui/objutils/sparse_alignment.hpp Source File

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1 #ifndef GUI_OBJUTILS___SPARSE_ALIGNMENT__HPP 2 #define GUI_OBJUTILS___SPARSE_ALIGNMENT__HPP 75 void Init

(

const

objects::CSeq_id& master_id,

76

vector<SAlignedSeq*>& aln_seqs,

77

objects::CScope& scope);

89 bool

IsSetAnchor()

const

;

106 bool

try_reverse_dir =

true

)

const

;

109 bool

try_reverse_dir =

true

)

const

;

115 const

objects::CBioseq_Handle& GetBioseqHandle(

TNumrow row

)

const

;

CAlignRange Represents an element of pairwise alignment of two sequences.

CSparseAlignment - an alignment based on CSparse_seg and CAlingRangeCollection classes rather than on...

CConstRef< objects::CSeq_id > m_MasterId

IAlnExplorer::TSignedRange TSignedRange

vector< SRowRec * > TRows

CRef< objects::CScope > m_Scope

SAlignTools::TAlignColl TAlignColl

IAlnExplorer::TNumrow TNumrow

TResidue m_GapChar

the extent of all segments in alignment coords

SAlignTools::TAlignRange TAlignRange

IAlnExplorer::TResidue TResidue

objects::CSeqVector::TResidue TResidue

ESearchDirection

Position search options.

Alignment segment iterator interface.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIOBJUTILS_EXPORT

Defines to provide correct exporting from DLLs in Windows.

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

describes a sequence in the alignment

SAlignedSeq * m_AlignedSeq

objects::CBioseq_Handle * m_BioseqHandle

This is a building block for a Builder represents a Sequence aligned to an Anchor (pairwise alignment...

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