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NCBI C++ ToolKit: CDensityMap< CntType

Search Toolkit Book for CDensityMap

class CDensityMap generates a low-resolution view of a set of features. More...

#include <gui/objutils/density_map.hpp>

Inheritance diagram for CDensityMap< CntType >:

Collaboration diagram for CDensityMap< CntType >:

Public Member Functions CDensityMap (TSeqPos start=0, TSeqPos stop=0, double window=1, accum_functor *func=NULL, CntType def=(CntType) 0) CDensityMap (const objects::CBioseq_Handle &handle, double window=1, accum_functor *func=NULL, CntType def=(CntType) 0) CDensityMap (const CDensityMap< CntType > &map) CDensityMap< CntType > & operator= (const CDensityMap< CntType > &map) virtual ~CDensityMap () virtual void AddRange (TSeqRange range, CntType score=1, bool expand=false) virtual void AddRanges (CRangeCollection< TSeqPos > ranges, CntType score=1, bool expand=false) CntType AddLocation (const objects::CSeq_loc &loc) CntType AddFeature (const objects::CSeq_feat &feature) CntType AddFeatures (const objects::CBioseq_Handle &handle, objects::SAnnotSelector sel) All features on this bioseq selected by sel in the range of this. More...
CntType AddAlignments (const objects::CBioseq_Handle &handle, objects::SAnnotSelector sel) All alignments on this bioseq selected by sel in the range of this. More...
CntType AddAlignments (const objects::CBioseq_Handle &handle, const objects::CSeq_annot &seq_annot) All alignments in a given annotation on this bioseq within the range of this. More...
void Clear () TSeqPos GetStart () const TSeqPos GetStop () const TSeqRange GetRange () const double GetWindow () const size_t GetBins () const CntType GetMax () const CntType GetMin () const CntType GetDefVal () const void SetMax (const CntType &max) void SetMin (const CntType &min) const accum_functor * GetAccum () const void ExtendTo (TSeqPos stop) extend our density map to cover the sequence position stop. More...
const_iterator begin () const const_iterator end () const iterator begin () iterator end () runlen_iterator RunLenBegin () const runlen_iterator RunLenIterator (typename container_type::size_type n) const CntType operator[] (typename container_type::size_type n) const CntType & operator[] (typename container_type::size_type n) Protected Member Functions size_t x_CalcNbins () given the range and window size, how many bins should there be? More...
size_t x_BinN (TSeqPos p) convert from sequence coords to a bin number. More...
Detailed Description template<typename CntType>
class CDensityMap< CntType >

class CDensityMap generates a low-resolution view of a set of features.

The features to be processed are defined by the SAnnotSelector object. The return value is a vector of counts, one for each of the bins defined by the window width and spanning the range from start to stop. If start and stop are both zero, then the entire sequence is evaluated.

Definition at line 222 of file density_map.hpp.

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

include/gui/objutils/density_map.hpp

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