mems::DNAMemorySML Class Reference

The DNAMemorySML is an implementation of sorted mer lists which creates and stores the sorted mer list entirely in memory. More...

#include <DNAMemorySML.h>

Inheritance diagram for mems::DNAMemorySML:

[legend]Collaboration diagram for mems::DNAMemorySML:

[legend]List of all members.

Public Member Functions
DNAMemorySML *	Clone () const
	DNAMemorySML (const SortedMerList &sa)
	DNAMemorySML (const DNAMemorySML &msa)
	DNAMemorySML (const uint8 *table=SortedMerList::BasicDNATable(), const uint32 alpha_bits=DNA_ALPHA_BITS)
	Create an empty DNAMemorySML Creates an empty DNAMemorySML with the supplied translation table and alphabet bit size.
virtual uint64	GetMer (gnSeqI offset) const
	Get the mer at the specified index in the sorted mer list.
virtual uint64	GetSeedMer (gnSeqI offset) const
	Applies the seed mask to the sequence at the given offset and returns the resulting seed.
DNAMemorySML &	operator= (const DNAMemorySML &msa)
Protected Member Functions
virtual void	FillSML (const genome::gnSequence &seq, std::vector< bmer > &sml_array)

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Detailed Description

The DNAMemorySML is an implementation of sorted mer lists which creates and stores the sorted mer list entirely in memory.

A DNAMemorySML consumes roughly 32 + alpha_bits bits of memory per character in the sequences. For unambiguous DNA sequences 4.25 bytes per base are required. The seed pattern for DNA SMLs must be palindromic

Definition at line 27 of file DNAMemorySML.h.

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Constructor & Destructor Documentation

mems::DNAMemorySML::DNAMemorySML (  const uint8 *  table = SortedMerList::BasicDNATable(), const uint32  alpha_bits = DNA_ALPHA_BITS )

Create an empty DNAMemorySML Creates an empty DNAMemorySML with the supplied translation table and alphabet bit size. Defaults to DNA settings Parameters: table  The array used to translate characters into binary code alpha_bits  The number of bits each character consumes in binary Definition at line 20 of file DNAMemorySML.cpp. References mems::uint32, and mems::uint8. Referenced by Clone().

mems::DNAMemorySML::DNAMemorySML (  const DNAMemorySML &  msa  )

mems::DNAMemorySML::DNAMemorySML (  const SortedMerList &  sa  )

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Member Function Documentation

DNAMemorySML * mems::DNAMemorySML::Clone (   )  const

Reimplemented from mems::MemorySML. Definition at line 29 of file DNAMemorySML.cpp. References DNAMemorySML().

void mems::DNAMemorySML::FillSML (  const genome::gnSequence &  seq, std::vector< bmer > &  sml_array )  [protected, virtual]

Reimplemented from mems::SortedMerList. Definition at line 43 of file DNAMemorySML.cpp. References mems::SortedMerList::FillDnaSML().

uint64 mems::DNAMemorySML::GetMer (  gnSeqI  offset  )  const [virtual]

Get the mer at the specified index in the sorted mer list. Parameters: position  The index of the mer to return. Returns: The specified mer. Reimplemented from mems::SortedMerList. Definition at line 35 of file DNAMemorySML.cpp. References mems::SortedMerList::GetDnaMer(), and mems::uint64.

uint64 mems::DNAMemorySML::GetSeedMer (  gnSeqI  offset  )  const [virtual]

Applies the seed mask to the sequence at the given offset and returns the resulting seed. Reimplemented from mems::SortedMerList. Definition at line 39 of file DNAMemorySML.cpp. References mems::SortedMerList::GetDnaSeedMer(), and mems::uint64.

DNAMemorySML & mems::DNAMemorySML::operator= (  const DNAMemorySML &  msa  )

Definition at line 24 of file DNAMemorySML.cpp.

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

• libMems/DNAMemorySML.h
• libMems/DNAMemorySML.cpp

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