mems::DNAFileSML Class Reference

The seed pattern for DNA SMLs must be palindromic. More...

#include <DNAFileSML.h>

Inheritance diagram for mems::DNAFileSML:

Inheritance graph
[legend]
Collaboration diagram for mems::DNAFileSML:

Collaboration graph
[legend]
List of all members.

Public Member Functions

DNAFileSMLClone () const
 DNAFileSML (const SortedMerList &sa)
 DNAFileSML (const std::string &fname, const uint8 *table=SortedMerList::BasicDNATable(), const uint32 alpha_bits=DNA_ALPHA_BITS)
 Load or create a DNAFileSML () Attempts to load a DNA sorted mer list from the named file if it exists.

 DNAFileSML ()
virtual uint32 FormatVersion ()
virtual uint64 GetMer (gnSeqI position) 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.

DNAFileSMLoperator= (const DNAFileSML &msa)
 ~DNAFileSML ()

Protected Member Functions

virtual uint32 CalculateMaxMerSize () const
virtual void FillSML (const genome::gnSequence &seq, std::vector< bmer > &sml_array)
virtual uint64 GetNeededMemory (gnSeqI len)
 Calculates and returns the amount of memory needed to create a sorted mer list for a sequence of the specified length.


Detailed Description

The seed pattern for DNA SMLs must be palindromic.

Definition at line 23 of file DNAFileSML.h.


Constructor & Destructor Documentation

mems::DNAFileSML::DNAFileSML  ) 
 

Definition at line 21 of file DNAFileSML.cpp.

References FormatVersion().

Referenced by Clone().

mems::DNAFileSML::DNAFileSML const std::string &  fname,
const uint8 table = SortedMerList::BasicDNATable(),
const uint32  alpha_bits = DNA_ALPHA_BITS
 

Load or create a DNAFileSML () Attempts to load a DNA sorted mer list from the named file if it exists.

If the given file does not exist it creates an empty DNAFileSML with the supplied translation table and alphabet bit size.

Parameters:
fname The name of the file to create.
table The array used to translate characters into binary code
alpha_bits The number of bits each character consumes in binary

Definition at line 28 of file DNAFileSML.cpp.

References mems::SMLHeader::alphabet_bits, FormatVersion(), mems::SMLHeader::translation_table, mems::uint32, mems::uint8, UINT8_MAX, and mems::SMLHeader::version.

mems::DNAFileSML::DNAFileSML const SortedMerList sa  ) 
 

mems::DNAFileSML::~DNAFileSML  ) 
 

Definition at line 25 of file DNAFileSML.cpp.


Member Function Documentation

uint32 mems::DNAFileSML::CalculateMaxMerSize  )  const [protected, virtual]
 

Reimplemented from mems::SortedMerList.

Definition at line 54 of file DNAFileSML.cpp.

References mems::SMLHeader::alphabet_bits, and mems::uint32.

DNAFileSML * mems::DNAFileSML::Clone  )  const [virtual]
 

Implements mems::FileSML.

Definition at line 40 of file DNAFileSML.cpp.

References DNAFileSML().

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

Reimplemented from mems::SortedMerList.

Definition at line 66 of file DNAFileSML.cpp.

References mems::SortedMerList::FillDnaSML().

uint32 mems::DNAFileSML::FormatVersion  )  [inline, virtual]
 

Reimplemented from mems::FileSML.

Definition at line 60 of file DNAFileSML.h.

References mems::uint32.

Referenced by DNAFileSML().

uint64 mems::DNAFileSML::GetMer gnSeqI  position  )  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 58 of file DNAFileSML.cpp.

References mems::SortedMerList::GetDnaMer(), and mems::uint64.

uint64 mems::DNAFileSML::GetNeededMemory gnSeqI  len  )  [protected, virtual]
 

Calculates and returns the amount of memory needed to create a sorted mer list for a sequence of the specified length.

Parameters:
len The length of the sequence
Returns:
The amount of memory needed in bytes.

Implements mems::FileSML.

Definition at line 46 of file DNAFileSML.cpp.

References mems::uint64.

uint64 mems::DNAFileSML::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 62 of file DNAFileSML.cpp.

References mems::SortedMerList::GetDnaSeedMer(), and mems::uint64.

DNAFileSML & mems::DNAFileSML::operator= const DNAFileSML msa  ) 
 

Definition at line 35 of file DNAFileSML.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