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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alignment__smear_8hpp_source.html below:

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

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1 #ifndef GUI_OBJUTILS___ALIGNMENT_SMEAR__HPP 2 #define GUI_OBJUTILS___ALIGNMENT_SMEAR__HPP 71  const

objects::CBioseq_Handle& handle,

80  void

AddAnnot(

const

objects::CSeq_annot& seq_annot,

84  void

AddAlignments(

const

objects::SAnnotSelector& sel,

101  void

SetLabel(

const string

&

label

);

105  static bool

SeparateStrands(

const

objects::CSeq_annot& seq_annot);

109 

{

return

m_AccumSeg.RunLenBegin(); }

111 

{

return

m_AccumGap.RunLenBegin(); }

117  static string

x_GetAnnotName(

const

objects::CSeq_annot& seq_annot);

Run iterator. iterate through runs of equal values in the bins.

Task clients implement this callback interface.

unsigned int TSeqPos

Type for sequence locations and lengths.

score_type GetMaxValue() const

bool AddAlignments(objects::CAlign_CI &align_iter, ISeqTaskProgressCallback *p_cb=NULL)

Smear all the alignments in CAlign_CI.

CDenMapRunIterator< score_type > runlen_iterator

CDensityMap< score_type > TSegMap

CDensityMap< score_type > TGapMap

void AddAlignment(const objects::CAlnMap &align)

Add this one alignment to my smear.

const objects::CBioseq_Handle & m_BioseqHandle

runlen_iterator SmearGapBegin() const

unsigned long m_CntAligns

EAlignSmearStrand GetStrandType() const

EAlignSmearStrand m_StrandType

runlen_iterator SmearSegBegin() const

OUTPUT:

string GetLabel(const CSeq_id &id)

#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.

#define NCBI_GUIOBJUTILS_EXPORT

static const char label[]

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

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