mems::MaskedMemHash Class Reference

Finds matches that meet a particular sequence mask, e.g. More...

#include <MaskedMemHash.h>

Inheritance diagram for mems::MaskedMemHash:

[legend]Collaboration diagram for mems::MaskedMemHash:

[legend]List of all members.

Public Member Functions
virtual MaskedMemHash *	Clone () const
	MaskedMemHash (const MaskedMemHash &mh)
	MaskedMemHash ()
MaskedMemHash &	operator= (const MaskedMemHash &mh)
virtual void	SetMask (uint64 seq_mask)
	~MaskedMemHash ()
Protected Member Functions
virtual void	FindSubsets (const Match &mhe, std::vector< Match > &subset_matches)
	Can't find subsets when there is only one permitted sequence mask!
virtual boolean	HashMatch (std::list< idmer > &match_list)
Protected Attributes
uint64	seq_mask

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Detailed Description

Finds matches that meet a particular sequence mask, e.g.

0b11111 for 5-way matches Doesn't filter anything unless a mask is set using SetMask(). The filter can be cleared by calling SetMask(0)

Definition at line 25 of file MaskedMemHash.h.

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Constructor & Destructor Documentation

mems::MaskedMemHash::MaskedMemHash (   )

Definition at line 20 of file MaskedMemHash.cpp. References seq_mask. Referenced by Clone().

mems::MaskedMemHash::~MaskedMemHash (   )  [inline]

Definition at line 28 of file MaskedMemHash.h.

mems::MaskedMemHash::MaskedMemHash (  const MaskedMemHash &  mh  )

Definition at line 25 of file MaskedMemHash.cpp.

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Member Function Documentation

MaskedMemHash * mems::MaskedMemHash::Clone (   )  const [virtual]

Reimplemented from mems::MemHash. Definition at line 34 of file MaskedMemHash.cpp. References MaskedMemHash().

virtual void mems::MaskedMemHash::FindSubsets (  const Match &  mhe, std::vector< Match > &  subset_matches )  [inline, protected, virtual]

Can't find subsets when there is only one permitted sequence mask! Definition at line 37 of file MaskedMemHash.h. References mems::Match.

boolean mems::MaskedMemHash::HashMatch (  std::list< idmer > &  match_list  )  [protected, virtual]

Definition at line 38 of file MaskedMemHash.cpp. References mems::MemHash::AddHashEntry(), mems::MatchHashEntry::CalculateOffset(), mems::MatchFinder::GetSar(), mems::idmer_id_lessthan(), seq_mask, mems::MemHash::SetDirection(), mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), uint, and mems::uint64.

MaskedMemHash & mems::MaskedMemHash::operator= (  const MaskedMemHash &  mh  )

Definition at line 29 of file MaskedMemHash.cpp. References seq_mask.

virtual void mems::MaskedMemHash::SetMask (  uint64  seq_mask  )  [inline, virtual]

Definition at line 32 of file MaskedMemHash.h. References mems::uint64. Referenced by mems::Aligner::align().

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Member Data Documentation

uint64 mems::MaskedMemHash::seq_mask [protected]

Definition at line 39 of file MaskedMemHash.h. Referenced by HashMatch(), MaskedMemHash(), and operator=().

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

• libMems/MaskedMemHash.h
• libMems/MaskedMemHash.cpp

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