mems::GappedAligner Class Reference

#include <GappedAligner.h>

Inheritance diagram for mems::GappedAligner:

[legend]List of all members.

Public Member Functions
virtual boolean	Align (GappedAlignment &cr, Match *r_begin, Match *r_end, std::vector< genome::gnSequence * > &seq_table)=0
	GappedAligner ()
GappedAligner &	operator= (const GappedAligner &ga)
void	SetMaxAlignmentLength (gnSeqI len)
	Set the maximum allowed length for a gapped alignment.
Protected Attributes
gnSeqI	max_alignment_length

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Constructor & Destructor Documentation

mems::GappedAligner::GappedAligner (   )  [inline]

Definition at line 24 of file GappedAligner.h. References max_alignment_length.

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Member Function Documentation

virtual boolean mems::GappedAligner::Align (  GappedAlignment &  cr, Match *  r_begin, Match *  r_end, std::vector< genome::gnSequence * > &  seq_table )  [pure virtual]

Implemented in mems::ClustalInterface, and mems::MuscleInterface. Referenced by mems::Aligner::AlignLCB(), and mems::AlignLCBInParallel().

GappedAligner& mems::GappedAligner::operator= (  const GappedAligner &  ga  )  [inline]

Definition at line 25 of file GappedAligner.h. References max_alignment_length.

void mems::GappedAligner::SetMaxAlignmentLength (  gnSeqI  len  )  [inline]

Set the maximum allowed length for a gapped alignment. Sequences above this length threshold will be ignored. Parameters: max_length  The maximum length Definition at line 35 of file GappedAligner.h. References max_alignment_length. Referenced by mems::Aligner::SetMaxGappedAlignmentLength().

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Member Data Documentation

gnSeqI mems::GappedAligner::max_alignment_length [protected]

Definition at line 38 of file GappedAligner.h. Referenced by GappedAligner(), operator=(), and SetMaxAlignmentLength().

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

• libMems/GappedAligner.h

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