mems::DenseAbstractMatch< MAX_SEQS > Class Template Reference

The DenseAbstractMatch implements the AbstractMatch interface in a way that is most efficient when Multiplicity and SeqCount are identical or nearly so. More...

#include <DenseAbstractMatch.h>

Inheritance diagram for mems::DenseAbstractMatch< MAX_SEQS >:

[legend]Collaboration diagram for mems::DenseAbstractMatch< MAX_SEQS >:

[legend]List of all members.

Public Member Functions
virtual AbstractMatch *	Clone () const=0
	DenseAbstractMatch (const uint seq_count)
	Creates a new AbstractMatch.
	DenseAbstractMatch ()
virtual uint	FirstStart () const
	Returns the index of the first sequence this match occurs in.
virtual void	Invert ()
	Inverts the coordinates of this match.
virtual gnSeqI	LeftEnd (uint seqI) const
	Returns the left end coordinate of this match at the seqI'th matching position/sequence.
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.
virtual boolean	operator== (const DenseAbstractMatch &dam) const
virtual 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.
virtual void	SetLeftEnd (uint seqI, gnSeqI position)
	sets the left end coordinate of this match in the seqI'th matching position/sequence
virtual 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.
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 Attributes
gnSeqI	leftend [MAX_SEQS]
uint	m_multiplicity
uint	m_seq_count
bool	orient [MAX_SEQS]

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Detailed Description

template<unsigned int MAX_SEQS>
class mems::DenseAbstractMatch< MAX_SEQS >

The DenseAbstractMatch implements the AbstractMatch interface in a way that is most efficient when Multiplicity and SeqCount are identical or nearly so.

It stores all data inline in a fixed size arrays, affording it storage in a contiguous chunk of memory.

Definition at line 29 of file DenseAbstractMatch.h.

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Constructor & Destructor Documentation

template<unsigned int MAX_SEQS> mems::DenseAbstractMatch< MAX_SEQS >::DenseAbstractMatch (   )

Definition at line 89 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, and mems::DenseAbstractMatch< MAX_SEQS >::orient.

template<unsigned int MAX_SEQS> mems::DenseAbstractMatch< MAX_SEQS >::DenseAbstractMatch (  const uint  seq_count  )

Creates a new AbstractMatch. Parameters: seq_count  The total number of sequences in the alignment Definition at line 98 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

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Member Function Documentation

template<unsigned int MAX_SEQS> virtual AbstractMatch* mems::DenseAbstractMatch< MAX_SEQS >::Clone (   )  const [pure virtual]

template<unsigned int MAX_SEQS> uint mems::DenseAbstractMatch< MAX_SEQS >::FirstStart (   )  const [virtual]

Returns the index of the first sequence this match occurs in. Implements mems::AbstractMatch. Definition at line 134 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::SeqCount(), and uint.

template<unsigned int MAX_SEQS> void mems::DenseAbstractMatch< MAX_SEQS >::Invert (   )  [virtual]

Inverts the coordinates of this match. Implements mems::AbstractMatch. Definition at line 127 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> virtual gnSeqI mems::DenseAbstractMatch< MAX_SEQS >::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 58 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, and uint.

template<unsigned int MAX_SEQS> void mems::DenseAbstractMatch< MAX_SEQS >::MoveEnd (  int64  move_amount  )  [virtual]

Shift the left-end coordinates in reverse oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 151 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> void mems::DenseAbstractMatch< MAX_SEQS >::MoveStart (  int64  move_amount  )  [virtual]

Shift the left-end coordinates in forward oriented positions by a given amount. Implements mems::AbstractMatch. Definition at line 143 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> uint mems::DenseAbstractMatch< MAX_SEQS >::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 53 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::m_multiplicity, and uint.

template<unsigned int MAX_SEQS> boolean mems::DenseAbstractMatch< MAX_SEQS >::operator== (  const DenseAbstractMatch< MAX_SEQS > &  dam  )  const [virtual]

Definition at line 107 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> AbstractMatch::orientation mems::DenseAbstractMatch< MAX_SEQS >::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 119 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> uint mems::DenseAbstractMatch< MAX_SEQS >::SeqCount (   )  const [inline, virtual]

Returns the number of sequences in the alignment which contains this match. Implements mems::AbstractMatch. Definition at line 54 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count, and uint. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::FirstStart().

template<unsigned int MAX_SEQS> virtual void mems::DenseAbstractMatch< MAX_SEQS >::SetLeftEnd (  uint  seqI, gnSeqI  position )  [inline, virtual]

sets the left end coordinate of this match in the seqI'th matching position/sequence Implements mems::AbstractMatch. Definition at line 60 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::m_multiplicity, and uint. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::SetStart().

template<unsigned int MAX_SEQS> virtual void mems::DenseAbstractMatch< MAX_SEQS >::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 68 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> void mems::DenseAbstractMatch< MAX_SEQS >::SetStart (  uint  seqI, int64  startI )  [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 48 of file DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::orient, mems::DenseAbstractMatch< MAX_SEQS >::SetLeftEnd(), and uint.

template<unsigned int MAX_SEQS> int64 mems::DenseAbstractMatch< MAX_SEQS >::Start (  uint  seqI  )  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 DenseAbstractMatch.h. References mems::DenseAbstractMatch< MAX_SEQS >::leftend, mems::DenseAbstractMatch< MAX_SEQS >::orient, and uint.

template<unsigned int MAX_SEQS> virtual uint mems::DenseAbstractMatch< MAX_SEQS >::UsedSeq (  uint  seqI  )  const [inline, virtual]

Returns the id of the i-th defined sequence in this match. Implements mems::AbstractMatch. Definition at line 76 of file DenseAbstractMatch.h. References uint.

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Member Data Documentation

template<unsigned int MAX_SEQS> gnSeqI mems::DenseAbstractMatch< MAX_SEQS >::leftend[ MAX_SEQS ] [protected]

Definition at line 83 of file DenseAbstractMatch.h. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::DenseAbstractMatch(), mems::DenseAbstractMatch< MAX_SEQS >::FirstStart(), mems::DenseAbstractMatch< MAX_SEQS >::LeftEnd(), mems::DenseAbstractMatch< MAX_SEQS >::MoveEnd(), mems::DenseAbstractMatch< MAX_SEQS >::MoveStart(), mems::DenseAbstractMatch< MAX_SEQS >::operator==(), mems::DenseAbstractMatch< MAX_SEQS >::Orientation(), mems::DenseAbstractMatch< MAX_SEQS >::SetLeftEnd(), and mems::DenseAbstractMatch< MAX_SEQS >::Start().

template<unsigned int MAX_SEQS> uint mems::DenseAbstractMatch< MAX_SEQS >::m_multiplicity [protected]

Definition at line 85 of file DenseAbstractMatch.h. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::Multiplicity(), and mems::DenseAbstractMatch< MAX_SEQS >::SetLeftEnd().

template<unsigned int MAX_SEQS> uint mems::DenseAbstractMatch< MAX_SEQS >::m_seq_count [protected]

Definition at line 82 of file DenseAbstractMatch.h. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::MoveEnd(), mems::DenseAbstractMatch< MAX_SEQS >::MoveStart(), mems::DenseAbstractMatch< MAX_SEQS >::operator==(), mems::DenseAbstractMatch< MAX_SEQS >::Orientation(), and mems::DenseAbstractMatch< MAX_SEQS >::SeqCount().

template<unsigned int MAX_SEQS> bool mems::DenseAbstractMatch< MAX_SEQS >::orient[ MAX_SEQS ] [protected]

Definition at line 84 of file DenseAbstractMatch.h. Referenced by mems::DenseAbstractMatch< MAX_SEQS >::DenseAbstractMatch(), mems::DenseAbstractMatch< MAX_SEQS >::Invert(), mems::DenseAbstractMatch< MAX_SEQS >::MoveEnd(), mems::DenseAbstractMatch< MAX_SEQS >::MoveStart(), mems::DenseAbstractMatch< MAX_SEQS >::operator==(), mems::DenseAbstractMatch< MAX_SEQS >::Orientation(), mems::DenseAbstractMatch< MAX_SEQS >::SetOrientation(), mems::DenseAbstractMatch< MAX_SEQS >::SetStart(), and mems::DenseAbstractMatch< MAX_SEQS >::Start().

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

• libMems/DenseAbstractMatch.h

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