libMems/SeedMasks.h File Reference

#include <math.h>
#include "libGenome/gnDefs.h"

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Functions
uint	getDefaultSeedWeight (gnSeqI avg_sequence_length)
	Calculate the default seed weight based on sequence length.
int64	getSeed (int weight, int seed_rank)
	returns a seed of a given weight.
int	getSeedLength (int64 seed)
	calculates the length of a seed pattern
int	getSeedWeight (int64 seed)
	calculates the weight of a seed pattern
int64	getSolidSeed (int weight)
	Returns a solid seed of a given weight.
uint32 **	seedMasks ()
	returns the array of default seed mask patterns Each seed is represented by a pair of 32 bit integers
Variables
const int	CODING_SEED = 3
const uint	MAX_DNA_SEED_WEIGHT = 31
const uint	MIN_DNA_SEED_WEIGHT = 5
const int	SOLID_SEED = INT_MAX

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Function Documentation

uint getDefaultSeedWeight (  gnSeqI  avg_sequence_length  )

Calculate the default seed weight based on sequence length. Definition at line 389 of file SeedMasks.h. References MAX_DNA_SEED_WEIGHT, MIN_DNA_SEED_WEIGHT, and uint. Referenced by mems::GenericMatchList< MatchPtrType >::GetDefaultMerSize(), mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::Aligner::Recursion(), and mems::SearchLCBGaps().

int64 getSeed (  int  weight, int  seed_rank )

returns a seed of a given weight. Setting seed_rank > 0 will select a seed of a lower sensitivity rank according to Choi et. al. 2004 Definition at line 298 of file SeedMasks.h. References getSolidSeed(), seedMasks(), and SOLID_SEED. Referenced by mems::GenericMatchList< MatchPtrType >::CreateMemorySMLs(), mems::GenericMatchList< MatchPtrType >::LoadSMLs(), mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::Aligner::Recursion(), and mems::SearchLCBGaps().

int getSeedLength (  int64  seed  )

calculates the length of a seed pattern Definition at line 335 of file SeedMasks.h. References uint. Referenced by mems::SortedMerList::Create().

int getSeedWeight (  int64  seed  )

calculates the weight of a seed pattern Definition at line 363 of file SeedMasks.h. References uint. Referenced by mems::SortedMerList::Create().

int64 getSolidSeed (  int  weight  )

Returns a solid seed of a given weight. Definition at line 276 of file SeedMasks.h. Referenced by getSeed(), and mems::RepeatMatchList::LoadSMLs().

uint32 ** seedMasks (   )

returns the array of default seed mask patterns Each seed is represented by a pair of 32 bit integers Definition at line 44 of file SeedMasks.h. Referenced by getSeed().

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Variable Documentation

const int CODING_SEED = 3 [static]

Definition at line 262 of file SeedMasks.h.

const uint MAX_DNA_SEED_WEIGHT = 31

Definition at line 376 of file SeedMasks.h. Referenced by getDefaultSeedWeight().

const uint MIN_DNA_SEED_WEIGHT = 5

Definition at line 375 of file SeedMasks.h. Referenced by getDefaultSeedWeight(), mems::ProgressiveAligner::pairwiseAnchorSearch(), mems::Aligner::Recursion(), and mems::SearchLCBGaps().

const int SOLID_SEED = INT_MAX [static]

Definition at line 263 of file SeedMasks.h. Referenced by getSeed().

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