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:

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Collaboration diagram for mems::DNAMemorySML:

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List of all members.

Public Member Functions

DNAMemorySMLClone () 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.

DNAMemorySMLoperator= (const DNAMemorySML &msa)

Protected Member Functions

virtual void FillSML (const genome::gnSequence &seq, std::vector< bmer > &sml_array)

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.


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  ) 
 


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.


The documentation for this class was generated from the following files:
Generated on Fri Mar 14 06:01:40 2008 for libMems by doxygen 1.3.6