adRevCompl.cxx File Reference

#include "arbdbt.h"
#include <cctype>

Include dependency graph for adRevCompl.cxx:

Go to the source code of this file.

Functions
static char	GBT_complementNucleotide (char c, char T_or_U)
char *	GBT_reverseNucSequence (const char *s, int len)
char *	GBT_complementNucSequence (const char *s, int len, char T_or_U)
NOT4PERL GB_ERROR	GBT_determine_T_or_U (GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target)
NOT4PERL void	GBT_reverseComplementNucSequence (char *seq, long length, char T_or_U)

Function Documentation

static char GBT_complementNucleotide ( char  c, char  T_or_U  )

static

Definition at line 15 of file adRevCompl.cxx.

Referenced by GBT_complementNucSequence(), and GBT_reverseComplementNucSequence().

char* GBT_reverseNucSequence	(	const char *	s,
		int	len
	)

Definition at line 66 of file adRevCompl.cxx.

Referenced by revcomp_op::operate(), and SearchTree::SearchTree().

char* GBT_complementNucSequence	(	const char *	s,
		int	len,
		char	T_or_U
	)

Definition at line 78 of file adRevCompl.cxx.

References GBT_complementNucleotide().

Referenced by modify_target_string(), revcomp_op::operate(), PV_ComplementarySequence(), and SearchTree::SearchTree().

NOT4PERL GB_ERROR GBT_determine_T_or_U	(	GB_alignment_type	alignment_type,
		char *	T_or_U,
		const char *	supposed_target
	)

Definition at line 90 of file adRevCompl.cxx.

References GB_AT_DNA, GB_AT_RNA, GBS_global_string(), and NULp.

Referenced by alignToNextRelative(), GBT_read_gene_sequence_and_length(), modify_target_string(), PV_ComplementarySequence(), revcomp_op::revcomp_op(), reverseComplement(), SearchTree::SearchTree(), and track_ali_change_cb().

NOT4PERL void GBT_reverseComplementNucSequence	(	char *	seq,
		long	length,
		char	T_or_U
	)

Definition at line 102 of file adRevCompl.cxx.

References GBT_complementNucleotide().

Referenced by alignToNextRelative(), GBT_read_gene_sequence_and_length(), modify_target_string(), mp_file2list(), ProbeMatchParser::ProbeMatchParser(), and reverseComplement().