mems::SMLHeader Struct Reference

#include <SortedMerList.h>

List of all members.

Public Attributes
uint32	alphabet_bits
	Bits per character in the alphabet - 4 bytes.
boolean	circular
	Circularity of sequence - 1 byte.
char	description [DESCRIPTION_SIZE]
	Freeform text description of sequence data -- 2048 bytes.
sarID_t	id
	Obsolete ID value - 1 byte, eaten by alignment?
uint64	length
	length of the sequence before circularity - 8 bytes
boolean	little_endian
	Is the byte order little endian? 0==no, !0==yes.
uint64	seed
	The pattern used in each seed.
uint32	seed_length
	The length of the seed mask.
uint32	seed_weight
	The weight of the seed mask.
uint8	translation_table [UINT8_MAX]
	Translation table for ascii characters to binary values -- 256 bytes.
uint32	unique_mers
	Number of unique mers in the sequence 4 bytes.
uint32	version
	Format version - 4 bytes.
uint32	word_size
	Word size on the machine the sequence was translated.

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Member Data Documentation

uint32 mems::SMLHeader::alphabet_bits

Bits per character in the alphabet - 4 bytes. Definition at line 55 of file SortedMerList.h. Referenced by mems::MatchFinder::AddSequence(), mems::SortedMerList::CalculateMaxMerSize(), mems::DNAFileSML::CalculateMaxMerSize(), mems::SortedMerList::Clear(), mems::DNAFileSML::DNAFileSML(), mems::SortedMerList::Find(), mems::SortedMerList::FindAll(), mems::MatchFinder::FindSubsets(), mems::FileSML::LoadFile(), mems::MemorySML::MemorySML(), mems::SortedMerList::SetMerMaskSize(), mems::SortedMerList::SetSequence(), and mems::SortedMerList::SortedMerList().

boolean mems::SMLHeader::circular

Circularity of sequence - 1 byte. Definition at line 65 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::Create(), mems::SortedMerList::FindAll(), mems::SortedMerList::FindMer(), mems::SortedMerList::IsCircular(), mems::FileSML::LoadFile(), mems::SortedMerList::SMLLength(), and mems::SortedMerList::SortedMerList().

char mems::SMLHeader::description[DESCRIPTION_SIZE]

Freeform text description of sequence data -- 2048 bytes. Definition at line 67 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::Description(), mems::SortedMerList::SetDescription(), mems::FileSML::SetDescription(), and mems::SortedMerList::SortedMerList().

sarID_t mems::SMLHeader::id

Obsolete ID value - 1 byte, eaten by alignment? Definition at line 64 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::GetID(), mems::SortedMerList::SetID(), mems::FileSML::SetID(), and mems::SortedMerList::SortedMerList().

uint64 mems::SMLHeader::length

length of the sequence before circularity - 8 bytes Definition at line 60 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::Create(), mems::SortedMerList::GetBSequence(), mems::SortedMerList::Length(), mems::FileSML::LoadFile(), mems::SortedMerList::SMLLength(), mems::SortedMerList::SortedMerList(), and mems::SortedMerList::UniqueMerCount().

boolean mems::SMLHeader::little_endian

Is the byte order little endian? 0==no, !0==yes. Definition at line 63 of file SortedMerList.h.

uint64 mems::SMLHeader::seed

The pattern used in each seed. Definition at line 57 of file SortedMerList.h. Referenced by mems::SortedMerList::Create(), mems::SortedMerList::GetSeedMer(), and mems::SortedMerList::Seed().

uint32 mems::SMLHeader::seed_length

The length of the seed mask. Definition at line 58 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::Create(), mems::MemorySML::Create(), mems::SortedMerList::FillDnaSeedSML(), mems::SortedMerList::FillDnaSML(), mems::SortedMerList::FillSML(), mems::SortedMerList::FindAll(), mems::SortedMerList::FindMer(), mems::SortedMerList::GetDnaMer(), mems::SortedMerList::GetSeedMer(), mems::FileSML::LoadFile(), mems::SortedMerList::SeedLength(), mems::SortedMerList::SetMerMaskSize(), mems::SortedMerList::SMLLength(), and mems::SortedMerList::SortedMerList().

uint32 mems::SMLHeader::seed_weight

The weight of the seed mask. Definition at line 59 of file SortedMerList.h. Referenced by mems::SortedMerList::Create(), mems::MemorySML::Create(), mems::SortedMerList::GetDnaSeedMer(), mems::SortedMerList::GetSeedMer(), mems::FileSML::LoadFile(), and mems::SortedMerList::SeedWeight().

uint8 mems::SMLHeader::translation_table[UINT8_MAX]

Translation table for ascii characters to binary values -- 256 bytes. Definition at line 66 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::DNAFileSML::DNAFileSML(), mems::SortedMerList::FillSML(), mems::MemorySML::MemorySML(), mems::SortedMerList::SortedMerList(), mems::SortedMerList::translate(), and mems::SortedMerList::translate32().

uint32 mems::SMLHeader::unique_mers

Number of unique mers in the sequence 4 bytes. Definition at line 61 of file SortedMerList.h. Referenced by mems::SortedMerList::Clear(), mems::SortedMerList::SortedMerList(), mems::SortedMerList::UniqueMerCount(), and mems::FileSML::UniqueMerCount().

uint32 mems::SMLHeader::version

Format version - 4 bytes. Definition at line 54 of file SortedMerList.h. Referenced by mems::DNAFileSML::DNAFileSML(), and mems::MemorySML::MemorySML().

uint32 mems::SMLHeader::word_size

Word size on the machine the sequence was translated. Definition at line 62 of file SortedMerList.h.

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

• libMems/SortedMerList.h

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