mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc > Class Template Reference

The SparseAbstractMatch implements the AbstractMatch interface in a way that allows matches with a large SeqCount and low Multiplicity to be stored efficiently. More...

#include <SparseAbstractMatch.h>

Inheritance diagram for mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >:

[legend]Collaboration diagram for mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >:

[legend]List of all members.

Public Member Functions
uint	FirstStart () const
	Returns the index of the first sequence this match occurs in.
virtual void	Invert ()
	Inverts the coordinates of this match.
gnSeqI	LeftEnd (uint seqI) const
	Returns the left end coordinate of this match at the seqI'th matching position/sequence.
virtual void	MoveEnd (int64 move_amount)
	Shift the left-end coordinates in reverse oriented positions by a given amount.
virtual void	MoveStart (int64 move_amount)
	Shift the left-end coordinates in forward oriented positions by a given amount.
uint	Multiplicity () const
	Returns the multiplicity of the match.
virtual boolean	operator== (const SparseAbstractMatch &sam) const
orientation	Orientation (uint seqI) const
	Returns the orientation of this match at the startI'th matching position/sequence, either AbstractMatch::forward or AbstractMatch::reverse.
uint	SeqCount () const
	Returns the number of sequences in the alignment which contains this match.
void	SetLeftEnd (uint seqI, gnSeqI position)
	sets the left end coordinate of this match in the seqI'th matching position/sequence
void	SetOrientation (uint seqI, orientation o)
	sets the relative orientation of this match in the seqI'th matching position/sequence
void	SetStart (uint seqI, int64 startI)
	Deprecated: use SetLeftEnd() and SetOrientation instead Sets the start in sequence.
	SparseAbstractMatch (const uint seq_count)
	Creates a new SparseAbstractMatch.
	SparseAbstractMatch ()
int64	Start (uint seqI) const
	Deprecated: use LeftEnd() and Orientation() instead.
virtual uint	UsedSeq (uint seqI) const
	Returns the id of the i-th defined sequence in this match.
Protected Member Functions
uint	SeqToIndex (uint seqI) const
void	swap (SparseAbstractMatch *other)
Protected Attributes
std::vector< gnSeqI, gnSeqIAlloc >	leftend
uint	m_seq_count
bitset_t	orient
std::vector< uint, uintAlloc >	seq_ids

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Detailed Description

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>>
class mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >

The SparseAbstractMatch implements the AbstractMatch interface in a way that allows matches with a large SeqCount and low Multiplicity to be stored efficiently.

Definition at line 30 of file SparseAbstractMatch.h.

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Constructor & Destructor Documentation

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SparseAbstractMatch (   )  [inline]

Definition at line 32 of file SparseAbstractMatch.h.

template<class gnSeqIAlloc, class uintAlloc> mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SparseAbstractMatch (  const uint  seq_count  )

Creates a new SparseAbstractMatch. Parameters: seq_count  The total number of sequences in the alignment Definition at line 76 of file SparseAbstractMatch.h. References uint.

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Member Function Documentation

template<class gnSeqIAlloc, class uintAlloc> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::FirstStart (   )  const [virtual]

Returns the index of the first sequence this match occurs in. Implements mems::AbstractMatch. Definition at line 90 of file SparseAbstractMatch.h. References uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Invert (   )  [virtual]

Inverts the coordinates of this match. Implements mems::AbstractMatch. Reimplemented in mems::GappedAlignment. Definition at line 148 of file SparseAbstractMatch.h.

template<class gnSeqIAlloc, class uintAlloc> gnSeqI mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::LeftEnd (  uint  seqI  )  const [virtual]

Returns the left end coordinate of this match at the seqI'th matching position/sequence. Implements mems::AbstractMatch. Definition at line 156 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::MoveEnd (  int64  move_amount  )  [virtual]

Shift the left-end coordinates in reverse oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 216 of file SparseAbstractMatch.h. References uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::MoveStart (  int64  move_amount  )  [virtual]

Shift the left-end coordinates in forward oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 208 of file SparseAbstractMatch.h. References uint.

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Multiplicity (   )  const [inline, virtual]

Returns the multiplicity of the match. e.g. the number of sequences this match occurs in Implements mems::AbstractMatch. Definition at line 45 of file SparseAbstractMatch.h.

template<class gnSeqIAlloc, class uintAlloc> boolean mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::operator== (  const SparseAbstractMatch< gnSeqIAlloc, uintAlloc > &  sam  )  const [virtual]

Definition at line 224 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::leftend, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::orient, and uint.

template<class gnSeqIAlloc, class uintAlloc> AbstractMatch::orientation mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Orientation (  uint  seqI  )  const [virtual]

Returns the orientation of this match at the startI'th matching position/sequence, either AbstractMatch::forward or AbstractMatch::reverse. Implements mems::AbstractMatch. Definition at line 164 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqCount (   )  const [inline, virtual]

Returns the number of sequences in the alignment which contains this match. Implements mems::AbstractMatch. Definition at line 46 of file SparseAbstractMatch.h.

template<class gnSeqIAlloc, class uintAlloc> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex (  uint  seqI  )  const [protected]

Definition at line 99 of file SparseAbstractMatch.h. References uint. Referenced by mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::LeftEnd(), mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Orientation(), mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetLeftEnd(), mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetOrientation(), mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetStart(), and mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Start().

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetLeftEnd (  uint  seqI, gnSeqI  position )  [virtual]

sets the left end coordinate of this match in the seqI'th matching position/sequence Implements mems::AbstractMatch. Definition at line 174 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetOrientation (  uint  seqI, orientation  o )  [virtual]

sets the relative orientation of this match in the seqI'th matching position/sequence Implements mems::AbstractMatch. Definition at line 198 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SetStart (  uint  seqI, int64  startI )  [virtual]

Deprecated: use SetLeftEnd() and SetOrientation instead Sets the start in sequence. Parameters: seqI  of this match to start  Implements mems::AbstractMatch. Definition at line 121 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc, class uintAlloc> int64 mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::Start (  uint  seqI  )  const [virtual]

Deprecated: use LeftEnd() and Orientation() instead. Returns the start coordinate of this match in sequence Parameters: startI  Implements mems::AbstractMatch. Definition at line 110 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::SeqToIndex(), and uint.

template<class gnSeqIAlloc, class uintAlloc> void mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::swap (  SparseAbstractMatch< gnSeqIAlloc, uintAlloc > *  other  )  [protected]

Definition at line 81 of file SparseAbstractMatch.h. References mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::leftend, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::m_seq_count, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::orient, mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::seq_ids, and std::swap().

template<class gnSeqIAlloc, class uintAlloc> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::UsedSeq (  uint  seqI  )  const [virtual]

Returns the id of the i-th defined sequence in this match. Implements mems::AbstractMatch. Definition at line 235 of file SparseAbstractMatch.h. References uint.

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Member Data Documentation

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> std::vector<gnSeqI, gnSeqIAlloc > mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::leftend [protected]

Definition at line 66 of file SparseAbstractMatch.h. Referenced by mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::operator==(), and mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::swap().

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> uint mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::m_seq_count [protected]

Definition at line 65 of file SparseAbstractMatch.h. Referenced by mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::swap().

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> bitset_t mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::orient [protected]

Definition at line 67 of file SparseAbstractMatch.h. Referenced by mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::operator==(), and mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::swap().

template<class gnSeqIAlloc = std::allocator<gnSeqI>, class uintAlloc = std::allocator<uint>> std::vector<uint, uintAlloc > mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::seq_ids [protected]

Definition at line 64 of file SparseAbstractMatch.h. Referenced by mems::SparseAbstractMatch< gnSeqIAlloc, uintAlloc >::swap().

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

• libMems/SparseAbstractMatch.h

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