mems::MatchHashEntry Class Reference

The Match class stores the location of an equal size (inexact or exactly) matching region between several sequences. More...

#include <MatchHashEntry.h>

Inheritance diagram for mems::MatchHashEntry:

[legend]Collaboration diagram for mems::MatchHashEntry:

[legend]List of all members.


Public Types
enum	MemType { seed, extended }
Public Member Functions
virtual void	CalculateOffset ()
	Calculates the generalized offset and other bookkeeping information for this mem.
MatchHashEntry *	Clone () const
boolean	Contains (const MatchHashEntry &mhe) const
	Will return true if this match contains mhe Containment implies that a match has a length >= the contained match, it has coordinates in every genome the contained match has, the difference in start positions in each genome is the same.
MatchHashEntry *	Copy () const
boolean	Extended () const
virtual void	Free ()
	MatchHashEntry (const MatchHashEntry &mhe)
	MatchHashEntry (const uint seq_count, const gnSeqI mersize, const MemType m_type=seed)
	Creates a new Match.
	MatchHashEntry ()
uint	MerSize () const
int64	Offset () const
	Returns the generalized offset of this match.
MatchHashEntry &	operator= (const MatchHashEntry &mhe)
boolean	operator== (const MatchHashEntry &mhe) const
	comparison operator, compares two matches to see if they are the same
void	SetExtended (boolean extended)
	Sets this match to be extended if the value passed in "extended" is true.
void	SetOffset (int64 offset)
	Sets the generalized offset of this match to "offset".
Static Public Member Functions
int64	end_to_start_compare (const MatchHashEntry &a, const MatchHashEntry &b)
	compare the end of a to the start of b
boolean	offset_lessthan (const MatchHashEntry &a, const MatchHashEntry &b)
int64	start_compare (const MatchHashEntry &a, const MatchHashEntry &b)
bool	start_lessthan (const MatchHashEntry &a, const MatchHashEntry &b)
boolean	start_lessthan_ptr (const MatchHashEntry a, const MatchHashEntry b)
boolean	strict_start_lessthan_ptr (const MatchHashEntry a, const MatchHashEntry b)
Private Attributes
boolean	m_extended
gnSeqI	m_mersize
int64	m_offset

Detailed Description

The Match class stores the location of an equal size (inexact or exactly) matching region between several sequences.

There are numerous functions in this class which can be used to compare and manipulate this match.

Definition at line 30 of file MatchHashEntry.h.

Member Enumeration Documentation

enum mems::MatchHashEntry::MemType

Enumeration values:

seed

extended

Definition at line 33 of file MatchHashEntry.h.

Constructor & Destructor Documentation

mems::MatchHashEntry::MatchHashEntry ( )

Definition at line 98 of file MatchHashEntry.cpp.
References mems::Match.
Referenced by Clone().

mems::MatchHashEntry::MatchHashEntry ( const uint seq_count,

const gnSeqI mersize,

const MemType m_type = seed

)

Creates a new Match.

Parameters:

seq_count The total number of sequences in the alignment

mersize The size of the mers used in the sorted mer lists.

m_type The type of mem to create, can either be a seed or already extended.

See also:
MemType

mems::MatchHashEntry::MatchHashEntry ( const MatchHashEntry & mhe ) [inline]

Definition at line 52 of file MatchHashEntry.h.

Member Function Documentation

void mems::MatchHashEntry::CalculateOffset ( ) [virtual]

Calculates the generalized offset and other bookkeeping information for this mem.
This should always be called after changing the start positions of the mem.
Definition at line 141 of file MatchHashEntry.cpp.
References mems::UngappedLocalAlignment< AbstractMatchImpl >::Length(), m_offset, and uint.
Referenced by mems::RepeatHash::HashMatch(), mems::MemHash::HashMatch(), mems::MaskedMemHash::HashMatch(), mems::MemHash::LoadFile(), and mems::RepeatMatchList::ReadList().

MatchHashEntry * mems::MatchHashEntry::Clone ( ) const

Reimplemented from mems::UngappedLocalAlignment< AbstractMatchImpl >.
Definition at line 114 of file MatchHashEntry.cpp.
References MatchHashEntry().

boolean mems::MatchHashEntry::Contains ( const MatchHashEntry & mhe ) const

Will return true if this match contains mhe Containment implies that a match has a length >= the contained match, it has coordinates in every genome the contained match has, the difference in start positions in each genome is the same.

Parameters:

mhe The match to check for containment.

Returns:
True if this match contains mhe.

Definition at line 164 of file MatchHashEntry.cpp.
References mems::UngappedLocalAlignment< AbstractMatchImpl >::Length(), m_offset, and uint.
Referenced by mems::MheCompare::operator()().

MatchHashEntry * mems::MatchHashEntry::Copy ( ) const [inline]

Reimplemented from mems::UngappedLocalAlignment< AbstractMatchImpl >.
Definition at line 106 of file MatchHashEntry.h.
References mems::m_allocateAndCopy().
Referenced by mems::RepeatMatchList::ReadList().

int64 mems::MatchHashEntry::end_to_start_compare ( const MatchHashEntry & a,

const MatchHashEntry & b

) [static]

compare the end of a to the start of b

Definition at line 91 of file MatchHashEntry.cpp.
References mems::UngappedLocalAlignment< AbstractMatchImpl >::CropStart(), and mems::UngappedLocalAlignment< AbstractMatchImpl >::Length().

boolean mems::MatchHashEntry::Extended ( ) const [inline]

Returns:
true if this match has already been extended

Definition at line 60 of file MatchHashEntry.h.
References m_extended.
Referenced by mems::MemHash::AddHashEntry().

void mems::MatchHashEntry::Free ( ) [inline, virtual]

Reimplemented from mems::UngappedLocalAlignment< AbstractMatchImpl >.
Definition at line 111 of file MatchHashEntry.h.
References mems::m_free().

uint mems::MatchHashEntry::MerSize ( ) const [inline]

Returns:
the mer size of the sorted mer lists used to find this match

Definition at line 64 of file MatchHashEntry.h.
References m_mersize, and uint.

int64 mems::MatchHashEntry::Offset ( ) const [inline]

Returns the generalized offset of this match.

Definition at line 74 of file MatchHashEntry.h.
References m_offset.
Referenced by mems::MemHash::AddHashEntry().

boolean mems::MatchHashEntry::offset_lessthan ( const MatchHashEntry & a,

const MatchHashEntry & b

) [static]

Definition at line 21 of file MatchHashEntry.cpp.
References m_offset.

MatchHashEntry & mems::MatchHashEntry::operator= ( const MatchHashEntry & mhe )

Definition at line 118 of file MatchHashEntry.cpp.
References m_extended, m_mersize, and m_offset.

boolean mems::MatchHashEntry::operator== ( const MatchHashEntry & mhe ) const

comparison operator, compares two matches to see if they are the same

Definition at line 128 of file MatchHashEntry.cpp.
References m_extended, m_mersize, and m_offset.

void mems::MatchHashEntry::SetExtended ( boolean extended ) [inline]

Sets this match to be extended if the value passed in "extended" is true.

Definition at line 62 of file MatchHashEntry.h.
References m_extended.

void mems::MatchHashEntry::SetOffset ( int64 offset ) [inline]

Sets the generalized offset of this match to "offset".

Definition at line 77 of file MatchHashEntry.h.
References m_offset.

int64 mems::MatchHashEntry::start_compare ( const MatchHashEntry & a,

const MatchHashEntry & b

) [static]

Definition at line 71 of file MatchHashEntry.cpp.
References mems::UngappedLocalAlignment< AbstractMatchImpl >::Length(), m_mersize, and uint.

bool mems::MatchHashEntry::start_lessthan ( const MatchHashEntry & a,

const MatchHashEntry & b

) [inline, static]

Definition at line 117 of file MatchHashEntry.h.
References start_lessthan_ptr().