core::sequence::Aligner Class Reference

#include <Aligner.hh>

Inheritance diagram for core::sequence::Aligner:

Collaboration diagram for core::sequence::Aligner:

Public Member Functions
	Aligner ()
	ctor More...
virtual	~Aligner ()
	dtor More...
virtual SequenceAlignment	align (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)=0
void	validate_input (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)
SequenceAlignment	traceback (SequenceOP seq_x, SequenceOP seq_y, DP_Matrix matrix, CellOP start)

Detailed Description

Definition at line 32 of file Aligner.hh.

Constructor & Destructor Documentation

core::sequence::Aligner::Aligner ( )

inline

ctor

Definition at line 37 of file Aligner.hh.

virtual core::sequence::Aligner::~Aligner ( )

inlinevirtual

dtor

Definition at line 40 of file Aligner.hh.

Member Function Documentation

virtual SequenceAlignment core::sequence::Aligner::align ( SequenceOP  seq_y, SequenceOP  seq_x, ScoringSchemeOP  ss  )

pure virtual

Implemented in core::sequence::MCAligner, core::sequence::ExtendAlignerSW, core::sequence::NWAligner, and core::sequence::SWAligner.

SequenceAlignment core::sequence::Aligner::traceback	(	SequenceOP	seq_x,
		SequenceOP	seq_y,
		DP_Matrix	matrix,
		CellOP	start
	)

Definition at line 54 of file Aligner.cc.

References core::sequence::above, core::sequence::SequenceAlignment::add_sequence(), core::sequence::diagonal, core::sequence::end, core::sequence::left, core::sequence::SequenceAlignment::remove_gapped_positions(), core::sequence::SequenceAlignment::score(), and protocols::loops::start.

Referenced by core::sequence::SWAligner::align(), core::sequence::NWAligner::align(), and core::sequence::MCAligner::align().

void core::sequence::Aligner::validate_input	(	SequenceOP	seq_y,
		SequenceOP	seq_x,
		ScoringSchemeOP	ss
	)

Definition at line 40 of file Aligner.cc.

Referenced by core::sequence::NWAligner::align().

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

• src/core/sequence/Aligner.hh
• src/core/sequence/Aligner.cc