core::sequence::NWAligner Class Reference

#include <NWAligner.hh>

Inheritance diagram for core::sequence::NWAligner:

Collaboration diagram for core::sequence::NWAligner:

Public Member Functions
	NWAligner ()
	ctor More...
virtual	~NWAligner ()
	dtor More...
virtual SequenceAlignment	align (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)
Public Member Functions inherited from core::sequence::Aligner
	Aligner ()
	ctor More...
virtual	~Aligner ()
	dtor More...
void	validate_input (SequenceOP seq_y, SequenceOP seq_x, ScoringSchemeOP ss)
SequenceAlignment	traceback (SequenceOP seq_x, SequenceOP seq_y, DP_Matrix matrix, CellOP start)

Static Public Member Functions
static void	init_matrix (Size y_len, Size x_len, ScoringSchemeOP ss, DP_Matrix &scores)

Detailed Description

Definition at line 30 of file NWAligner.hh.

Constructor & Destructor Documentation

core::sequence::NWAligner::NWAligner ( )

inline

ctor

Definition at line 35 of file NWAligner.hh.

virtual core::sequence::NWAligner::~NWAligner ( )

inlinevirtual

dtor

Definition at line 38 of file NWAligner.hh.

Member Function Documentation

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

virtual

Implements core::sequence::Aligner.

Definition at line 65 of file NWAligner.cc.

References core::sequence::above, core::sequence::diagonal, init_matrix(), core::sequence::left, core::sequence::Aligner::traceback(), and core::sequence::Aligner::validate_input().

void core::sequence::NWAligner::init_matrix ( Size  y_len, Size  x_len, ScoringSchemeOP  ss, DP_Matrix &  scores  )

static

Definition at line 35 of file NWAligner.cc.

References core::sequence::end.

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

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

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