mems::SeedOccurrenceList Class Reference

#include <SeedOccurrenceList.h>

List of all members.

Public Types
typedef float32	frequency_type
Public Member Functions
template<typename SMLType> void	construct (SMLType &sml)
frequency_type	getFrequency (gnSeqI position)
SeedOccurrenceList &	operator= (const SeedOccurrenceList &sol)
	SeedOccurrenceList (const SeedOccurrenceList &sol)
	SeedOccurrenceList ()
	~SeedOccurrenceList ()
Protected Member Functions
template<typename SMLType> void	smoothFrequencies (const SMLType &sml, frequency_type *count)
	converts position freqs to the average freq of all k-mers containing that position
Protected Attributes
boost::iostreams::mapped_file_source	data
std::string	tmpfile

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Member Typedef Documentation

typedef float32 mems::SeedOccurrenceList::frequency_type

Definition at line 17 of file SeedOccurrenceList.h. Referenced by construct(), getFrequency(), mems::GetPairwiseAnchorScore(), and smoothFrequencies().

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Constructor & Destructor Documentation

mems::SeedOccurrenceList::SeedOccurrenceList (   )  [inline]

Definition at line 19 of file SeedOccurrenceList.h.

mems::SeedOccurrenceList::~SeedOccurrenceList (   )  [inline]

Definition at line 81 of file SeedOccurrenceList.h. References tmpfile.

mems::SeedOccurrenceList::SeedOccurrenceList (  const SeedOccurrenceList &  sol  )  [inline]

Definition at line 91 of file SeedOccurrenceList.h.

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Member Function Documentation

template<typename SMLType> void mems::SeedOccurrenceList::construct (  SMLType &  sml  )  [inline]

Definition at line 22 of file SeedOccurrenceList.h. References CreateTempFileName(), frequency_type, mems::bmer::mer, mems::bmer::position, smoothFrequencies(), tmpfile, and mems::uint64.

frequency_type mems::SeedOccurrenceList::getFrequency (  gnSeqI  position  )  [inline]

Definition at line 77 of file SeedOccurrenceList.h. References frequency_type. Referenced by mems::GetPairwiseAnchorScore().

SeedOccurrenceList& mems::SeedOccurrenceList::operator= (  const SeedOccurrenceList &  sol  )  [inline]

Definition at line 92 of file SeedOccurrenceList.h.

template<typename SMLType> void mems::SeedOccurrenceList::smoothFrequencies (  const SMLType &  sml, frequency_type *  count )  [inline, protected]

converts position freqs to the average freq of all k-mers containing that position Definition at line 99 of file SeedOccurrenceList.h. References frequency_type. Referenced by construct().

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Member Data Documentation

boost::iostreams::mapped_file_source mems::SeedOccurrenceList::data [protected]

Definition at line 117 of file SeedOccurrenceList.h.

std::string mems::SeedOccurrenceList::tmpfile [protected]

Definition at line 118 of file SeedOccurrenceList.h. Referenced by construct(), and ~SeedOccurrenceList().

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

• libMems/SeedOccurrenceList.h

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