ClustalV.hxx File Reference

#include <arb_error.h>

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Functions
ARB_ERROR	ClustalV_align (int is_dna, int weighted, const char *seq1, int length1, const char *seq2, int length2, const int *gapsBefore1, int max_seq_length, const char *&result1, const char *&result2, int &result_len, int &score)
void	ClustalV_exit ()
int	baseMatch (char c1, char c2)

Function Documentation

ARB_ERROR ClustalV_align	(	int	is_dna,
		int	weighted,
		const char *	seq1,
		int	length1,
		const char *	seq2,
		int	length2,
		const int *	gapsBefore1,
		int	max_seq_length,
		const char *&	result1,
		const char *&	result2,
		int &	result_len,
		int &	score
	)

Definition at line 971 of file ClustalV.cxx.

References add_ggaps(), ckalloc(), do_align(), iupac::encode(), error(), fill_pam(), init_myers(), init_show_pair(), make_pamo(), max, module_initialized, n_encode(), p_encode(), and seq_array.

Referenced by cannot_fast_align().

void ClustalV_exit

(

)

Definition at line 1049 of file ClustalV.cxx.

References exit_myers(), exit_show_pair(), module_initialized, and seq_array.

Referenced by Aligner::run().

int baseMatch	(	char	c1,
		char	c2
	)

Definition at line 249 of file ClustalV.cxx.

References baseCmp(), and fa_assert().

Referenced by relatedBases().