mems::AbstractGappedAlignment< AbstractMatchImpl > Class Template Reference

#include <AbstractGappedAlignment.h>

List of all members.

Public Member Functions
	AbstractGappedAlignment (uint seq_count, gnSeqI align_length)
	AbstractGappedAlignment ()
gnSeqI	AlignmentLength () const
gnSeqI	Length (uint seqI=UINT_MAX) const
virtual void	SetAlignment (const std::vector< std::string > &seq_align)=0
	Sets the alignment.
void	SetAlignmentLength (gnSeqI len)
virtual void	SetLength (gnSeqI len, uint seqI)
Protected Member Functions
void	swap (AbstractGappedAlignment *other)
Private Attributes
gnSeqI	align_length
std::vector< gnSeqI >	length

template<class AbstractMatchImpl>
class mems::AbstractGappedAlignment< AbstractMatchImpl >

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Constructor & Destructor Documentation

template<class AbstractMatchImpl> mems::AbstractGappedAlignment< AbstractMatchImpl >::AbstractGappedAlignment (   )

Definition at line 51 of file AbstractGappedAlignment.h. References mems::AbstractGappedAlignment< AbstractMatchImpl >::align_length.

template<class AbstractMatchImpl> mems::AbstractGappedAlignment< AbstractMatchImpl >::AbstractGappedAlignment (  uint  seq_count, gnSeqI  align_length )

Definition at line 57 of file AbstractGappedAlignment.h. References mems::AbstractGappedAlignment< AbstractMatchImpl >::length, and uint.

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Member Function Documentation

template<class AbstractMatchImpl> gnSeqI mems::AbstractGappedAlignment< AbstractMatchImpl >::AlignmentLength (   )  const [inline]

Definition at line 38 of file AbstractGappedAlignment.h.

template<class AbstractMatchImpl> gnSeqI mems::AbstractGappedAlignment< AbstractMatchImpl >::Length (  uint  seqI = UINT_MAX  )  const

Definition at line 72 of file AbstractGappedAlignment.h. References mems::AbstractGappedAlignment< AbstractMatchImpl >::align_length, mems::AbstractGappedAlignment< AbstractMatchImpl >::length, and uint.

template<class AbstractMatchImpl> virtual void mems::AbstractGappedAlignment< AbstractMatchImpl >::SetAlignment (  const std::vector< std::string > &  seq_align  )  [pure virtual]

Sets the alignment. Parameters: seq_align  should be in row/column format, e.g. one string per sequence (row) Implemented in mems::GappedAlignment.

template<class AbstractMatchImpl> void mems::AbstractGappedAlignment< AbstractMatchImpl >::SetAlignmentLength (  gnSeqI  len  )  [inline]

Definition at line 39 of file AbstractGappedAlignment.h.

template<class AbstractMatchImpl> virtual void mems::AbstractGappedAlignment< AbstractMatchImpl >::SetLength (  gnSeqI  len, uint  seqI )  [inline, virtual]

Definition at line 36 of file AbstractGappedAlignment.h.

template<class AbstractMatchImpl> void mems::AbstractGappedAlignment< AbstractMatchImpl >::swap (  AbstractGappedAlignment< AbstractMatchImpl > *  other  )  [protected]

Definition at line 64 of file AbstractGappedAlignment.h. References mems::AbstractGappedAlignment< AbstractMatchImpl >::align_length, mems::AbstractGappedAlignment< AbstractMatchImpl >::length, and std::swap().

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Member Data Documentation

template<class AbstractMatchImpl> gnSeqI mems::AbstractGappedAlignment< AbstractMatchImpl >::align_length [private]

Definition at line 46 of file AbstractGappedAlignment.h. Referenced by mems::AbstractGappedAlignment< AbstractMatchImpl >::AbstractGappedAlignment(), mems::AbstractGappedAlignment< AbstractMatchImpl >::Length(), and mems::AbstractGappedAlignment< AbstractMatchImpl >::swap().

template<class AbstractMatchImpl> std::vector< gnSeqI > mems::AbstractGappedAlignment< AbstractMatchImpl >::length [private]

Definition at line 45 of file AbstractGappedAlignment.h. Referenced by mems::AbstractGappedAlignment< AbstractMatchImpl >::AbstractGappedAlignment(), mems::AbstractGappedAlignment< AbstractMatchImpl >::Length(), and mems::AbstractGappedAlignment< AbstractMatchImpl >::swap().

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

• libMems/AbstractGappedAlignment.h

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