mems::PairwiseMatchAdapter Class Reference

PairwiseMatchAdapter is a wrapper around an AbstractMatch that effectively projects a multi-match to a pairwise match. More...

#include <PairwiseMatchAdapter.h>

Inheritance diagram for mems::PairwiseMatchAdapter:

[legend]Collaboration diagram for mems::PairwiseMatchAdapter:

[legend]List of all members.

Public Member Functions
gnSeqI	AlignmentLength () const
	Returns the total length of this alignment in columns.
PairwiseMatchAdapter *	Clone () const
PairwiseMatchAdapter *	Copy () const
	creates a copy of this using a boost::pool::fast_pool_allocator
void	CropEnd (gnSeqI crop_amount)
	Deprecated: Use CropLeft and CropRight instead Removes the last crop_amount base pairs from the end of the match.
void	CropLeft (gnSeqI crop_amount, uint seqI)
	Crop this match from the left Removes the first crop_amount positions from the left side of the match.
void	CropRight (gnSeqI crop_amount, uint seqI)
	Crop this match from the right Removes the last crop_amount positions from the right side of the match.
void	CropStart (gnSeqI crop_amount)
	Deprecated: Use CropLeft and CropRight instead Removes the first crop_amount base pairs from the beginning of the match.
uint	FirstStart () const
	Returns the index of the first sequence this match occurs in.
void	Free ()
	frees storage used by this object in a boost::pool::fast_pool_allocator
void	GetAlignment (std::vector< mems::bitset_t > &align_matrix) const
void	GetColumn (gnSeqI col, std::vector< gnSeqI > &pos, std::vector< bool > &column) const
	Given an alignment column index, this function returns the corresponding sequence coordinates and whether each sequence is aligned in that column If a given sequence is not represented in the requested column, the position returned in pos should be that of the first nucleotide to the left of the requested column.
void	Invert ()
	Inverts the coordinates of this match.
bool	IsGap (uint seqI, gnSeqI col) const
	returns true if the given row,column of the alignment has a gap character
gnSeqI	LeftEnd (uint seqI) const
	Returns the left end coordinate of this match at the seqI'th matching position/sequence.
gnSeqI	Length (uint seqI) const
	Returns the length of this match.
void	MoveEnd (int64 move_amount)
	Shift the left-end coordinates in reverse oriented positions by a given amount.
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.
orientation	Orientation (uint seqI) const
	Returns the orientation of this match at the startI'th matching position/sequence, either AbstractMatch::forward or AbstractMatch::reverse.
	PairwiseMatchAdapter (AbstractMatch *match, uint seq1, uint seq2)
	PairwiseMatchAdapter ()
uint	SeqCount () const
	Returns the number of sequences in the alignment which contains this match.
void	SetLeftEnd (uint seqI, gnSeqI start)
	sets the left end coordinate of this match in the seqI'th matching position/sequence
void	SetLength (gnSeqI len, uint seqI)
	Sets the length of this match to.
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 start)
	Deprecated: use SetLeftEnd() and SetOrientation instead Sets the start in sequence.
int64	Start (uint startI) const
	Deprecated: use LeftEnd() and Orientation() instead.
uint	UsedSeq (uint seqI) const
	Returns the id of the i-th defined sequence in this match.
Public Attributes
bool	inverted
AbstractMatch *	m
uint	seq [2]
TrackingMatch *	tm

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Detailed Description

PairwiseMatchAdapter is a wrapper around an AbstractMatch that effectively projects a multi-match to a pairwise match.

The adapter class forwards most function calls to the original match class, to which it stores a pointer. Use of non-const functions results in undefined state.

Definition at line 15 of file PairwiseMatchAdapter.h.

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Constructor & Destructor Documentation

mems::PairwiseMatchAdapter::PairwiseMatchAdapter (   )  [inline]

Definition at line 18 of file PairwiseMatchAdapter.h. Referenced by Clone().

mems::PairwiseMatchAdapter::PairwiseMatchAdapter (  AbstractMatch *  match, uint  seq1, uint  seq2 )  [inline]

Definition at line 19 of file PairwiseMatchAdapter.h. References inverted, and uint.

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Member Function Documentation

gnSeqI mems::PairwiseMatchAdapter::AlignmentLength (   )  const [inline, virtual]

Returns the total length of this alignment in columns. Implements mems::AbstractMatch. Definition at line 64 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::AlignmentLength().

PairwiseMatchAdapter* mems::PairwiseMatchAdapter::Clone (   )  const [inline]

Definition at line 27 of file PairwiseMatchAdapter.h. References PairwiseMatchAdapter().

PairwiseMatchAdapter* mems::PairwiseMatchAdapter::Copy (   )  const [inline, virtual]

creates a copy of this using a boost::pool::fast_pool_allocator Implements mems::AbstractMatch. Definition at line 29 of file PairwiseMatchAdapter.h. References mems::m_allocateAndCopy(). Referenced by mems::getPairwiseLCBs().

void mems::PairwiseMatchAdapter::CropEnd (  gnSeqI  crop_amount  )  [inline, virtual]

Deprecated: Use CropLeft and CropRight instead Removes the last crop_amount base pairs from the end of the match. Implements mems::AbstractMatch. Definition at line 67 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::CropEnd().

void mems::PairwiseMatchAdapter::CropLeft (  gnSeqI  crop_amount, uint  seqI )  [inline, virtual]

Crop this match from the left Removes the first crop_amount positions from the left side of the match. Implements mems::AbstractMatch. Definition at line 68 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::CropLeft(), and uint.

void mems::PairwiseMatchAdapter::CropRight (  gnSeqI  crop_amount, uint  seqI )  [inline, virtual]

Crop this match from the right Removes the last crop_amount positions from the right side of the match. Implements mems::AbstractMatch. Definition at line 69 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::CropRight(), and uint.

void mems::PairwiseMatchAdapter::CropStart (  gnSeqI  crop_amount  )  [inline, virtual]

Deprecated: Use CropLeft and CropRight instead Removes the first crop_amount base pairs from the beginning of the match. Implements mems::AbstractMatch. Definition at line 66 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::CropStart().

uint mems::PairwiseMatchAdapter::FirstStart (   )  const [inline, virtual]

Returns the index of the first sequence this match occurs in. Implements mems::AbstractMatch. Definition at line 63 of file PairwiseMatchAdapter.h. References uint.

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

frees storage used by this object in a boost::pool::fast_pool_allocator Implements mems::AbstractMatch. Definition at line 34 of file PairwiseMatchAdapter.h. References mems::m_free().

void mems::PairwiseMatchAdapter::GetAlignment (  std::vector< mems::bitset_t > &  align_matrix  )  const [inline]

Definition at line 70 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::GetAlignment(), mems::AbstractMatch::Invert(), and inverted.

void mems::PairwiseMatchAdapter::GetColumn (  gnSeqI  col, std::vector< gnSeqI > &  pos, std::vector< bool > &  column )  const [inline, virtual]

Given an alignment column index, this function returns the corresponding sequence coordinates and whether each sequence is aligned in that column If a given sequence is not represented in the requested column, the position returned in pos should be that of the first nucleotide to the left of the requested column. If no nucleotides exist to the left of the requested column, then a NO_MATCH is returned in pos for that sequence. Implements mems::AbstractMatch. Definition at line 82 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::GetColumn(), mems::AbstractMatch::Invert(), and inverted.

void mems::PairwiseMatchAdapter::Invert (   )  [inline, virtual]

Inverts the coordinates of this match. Implements mems::AbstractMatch. Definition at line 65 of file PairwiseMatchAdapter.h. References inverted. Referenced by mems::getPairwiseLCBs().

bool mems::PairwiseMatchAdapter::IsGap (  uint  seqI, gnSeqI  col )  const [inline, virtual]

returns true if the given row,column of the alignment has a gap character Implements mems::AbstractMatch. Definition at line 98 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::IsGap(), and uint.

gnSeqI mems::PairwiseMatchAdapter::LeftEnd (  uint  seqI  )  const [inline, virtual]

Returns the left end coordinate of this match at the seqI'th matching position/sequence. Implements mems::AbstractMatch. Definition at line 50 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::LeftEnd(), and uint.

gnSeqI mems::PairwiseMatchAdapter::Length (  uint  seqI  )  const [inline, virtual]

Returns the length of this match. Implements mems::AbstractMatch. Definition at line 42 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::Length(), and uint.

void mems::PairwiseMatchAdapter::MoveEnd (  int64  move_amount  )  [inline, virtual]

Shift the left-end coordinates in reverse oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 60 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::MoveEnd().

void mems::PairwiseMatchAdapter::MoveStart (  int64  move_amount  )  [inline, virtual]

Shift the left-end coordinates in forward oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 59 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::MoveStart().

uint mems::PairwiseMatchAdapter::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 61 of file PairwiseMatchAdapter.h. References uint.

orientation mems::PairwiseMatchAdapter::Orientation (  uint  seqI  )  const [inline, 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 51 of file PairwiseMatchAdapter.h. References inverted, mems::AbstractMatch::Orientation(), and uint. Referenced by mems::getPairwiseLCBs().

uint mems::PairwiseMatchAdapter::SeqCount (   )  const [inline, virtual]

Returns the number of sequences in the alignment which contains this match. Implements mems::AbstractMatch. Definition at line 62 of file PairwiseMatchAdapter.h. References uint.

void mems::PairwiseMatchAdapter::SetLeftEnd (  uint  seqI, gnSeqI  start )  [inline, virtual]

sets the left end coordinate of this match in the seqI'th matching position/sequence Implements mems::AbstractMatch. Definition at line 57 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::SetLeftEnd(), and uint.

void mems::PairwiseMatchAdapter::SetLength (  gnSeqI  len, uint  seqI )  [inline, virtual]

Sets the length of this match to. Parameters: len  Implements mems::AbstractMatch. Definition at line 43 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::SetLength(), and uint.

void mems::PairwiseMatchAdapter::SetOrientation (  uint  seqI, orientation  o )  [inline, virtual]

sets the relative orientation of this match in the seqI'th matching position/sequence Implements mems::AbstractMatch. Definition at line 58 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::SetOrientation(), and uint.

void mems::PairwiseMatchAdapter::SetStart (  uint  seqI, int64  start )  [inline, 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 49 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::SetStart(), and uint.

int64 mems::PairwiseMatchAdapter::Start (  uint  startI  )  const [inline, virtual]

Deprecated: use LeftEnd() and Orientation() instead. Returns the start coordinate of this match in sequence Parameters: startI  Implements mems::AbstractMatch. Definition at line 44 of file PairwiseMatchAdapter.h. References inverted, mems::AbstractMatch::Start(), and uint.

uint mems::PairwiseMatchAdapter::UsedSeq (  uint  seqI  )  const [inline, virtual]

Returns the id of the i-th defined sequence in this match. Implements mems::AbstractMatch. Definition at line 99 of file PairwiseMatchAdapter.h. References mems::AbstractMatch::Start(), and uint.

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Member Data Documentation

bool mems::PairwiseMatchAdapter::inverted

Definition at line 111 of file PairwiseMatchAdapter.h. Referenced by GetAlignment(), GetColumn(), Invert(), Orientation(), PairwiseMatchAdapter(), and Start().

AbstractMatch* mems::PairwiseMatchAdapter::m

Definition at line 108 of file PairwiseMatchAdapter.h.

uint mems::PairwiseMatchAdapter::seq[2]

Definition at line 110 of file PairwiseMatchAdapter.h.

TrackingMatch* mems::PairwiseMatchAdapter::tm

Definition at line 109 of file PairwiseMatchAdapter.h. Referenced by mems::getPairwiseLCBs().

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

• libMems/PairwiseMatchAdapter.h

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