ViterbiWorkspace Class Reference

#include <viterbi.hpp>

Inheritance diagram for ViterbiWorkspace:

List of all members.

Public Member Functions
	ViterbiWorkspace (size_t n)
int	OptimalAlignment (const Sequence &seq1, const Sequence &seq2, const ScoreMatrix &mat, AlignmentType atype, int gap_open, int gap_extension, bool _allow_DI, bool _allow_ID, Align &a, bool _dangling=true)
int	OptimalScore (const Sequence &seq1, const Sequence &seq2, const ScoreMatrix &mat, AlignmentType atype, int gap_open, int gap_extension, bool _allow_DI, bool _allow_ID)

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Detailed Description

Workspace for optimal alignments (local or global)

Examples:

freescore.cpp.

Definition at line 48 of file viterbi.hpp.

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Constructor & Destructor Documentation

ViterbiWorkspace::ViterbiWorkspace

(

size_t

n

)

Constructor.

Parameters:

n

number of dynamic programming cells to be used.

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Member Function Documentation

int ViterbiWorkspace::OptimalAlignment	(	const Sequence &	seq1,
		const Sequence &	seq2,
		const ScoreMatrix &	mat,
		AlignmentType	atype,
		int	gap_open,
		int	gap_extension,
		bool	_allow_DI,
		bool	_allow_ID,
		Align &	a,
		bool	_dangling = true
	)

Determine optimal score and alignment. Determine optimal alignment of the sequences seq1 and seq2 by SmithWaterman (atype == LocalBounded) or Needleman-Wunsch (atype == Global or atype == GlobalBounded) algorithm.

Parameters:

	seq1	first input sequence
	seq2	second input sequence
	mat	score matrix
	atype	alignment type
	gap_open	gap open parameter
	gap_extension	gap extension parameter
	allow_ID	allow a deletion followed by insertion
	allow_DI	allow an insertion followed by deletion
	a	output alignment
	_dangling	if true fill begin and end of local alignment with gaps (only relevant for atype == LocalBounded)

Returns:

optimal score

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

• src/viterbi.hpp