mems::DNAFileSML Class Reference

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

#include <DNAFileSML.h>

Inheritance diagram for mems::DNAFileSML:

[legend]Collaboration diagram for mems::DNAFileSML:

[legend]List of all members.

Public Member Functions
DNAFileSML *	Clone () 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.
DNAFileSML &	operator= (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.

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Detailed Description

The seed pattern for DNA SMLs must be palindromic.

Definition at line 23 of file DNAFileSML.h.

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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.

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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.

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

• libMems/DNAFileSML.h
• libMems/DNAFileSML.cpp

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