Deprecated Interface for Multiple Sequence Alignment Utilities

Detailed Description

Collaboration diagram for Deprecated Interface for Multiple Sequence Alignment Utilities:

Typedefs
typedef struct vrna_pinfo_s	pair_info
	Old typename of vrna_pinfo_s. More...

Functions
int	get_mpi (char *Alseq[], int n_seq, int length, int *mini)
	Get the mean pairwise identity in steps from ?to?(ident) More...
void	encode_ali_sequence (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ)
	Get arrays with encoded sequence of the alignment. More...
void	alloc_sequence_arrays (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ)
	Allocate memory for sequence array used to deal with aligned sequences. More...
void	free_sequence_arrays (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss)
	Free the memory of the sequence arrays used to deal with aligned sequences. More...

Typedef Documentation

typedef struct vrna_pinfo_s pair_info

#include <ViennaRNA/utils/alignments.h>

Old typename of vrna_pinfo_s.

Deprecated:

Use vrna_pinfo_t instead!

Function Documentation

int get_mpi	(	char *	Alseq[],
		int	n_seq,
		int	length,
		int *	mini
	)

#include <ViennaRNA/utils/alignments.h>

Get the mean pairwise identity in steps from ?to?(ident)

Deprecated:

Use vrna_aln_mpi() as a replacement

Parameters

Alseq
n_seq	The number of sequences in the alignment
length	The length of the alignment
mini

Returns

The mean pairwise identity

void encode_ali_sequence	(	const char *	sequence,
		short *	S,
		short *	s5,
		short *	s3,
		char *	ss,
		unsigned short *	as,
		int	circ
	)

#include <ViennaRNA/utils/alignments.h>

Get arrays with encoded sequence of the alignment.

this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)

Parameters

sequence	The gapped sequence from the alignment
S	pointer to an array that holds encoded sequence
s5	pointer to an array that holds the next base 5' of alignment position i
s3	pointer to an array that holds the next base 3' of alignment position i
ss
as
circ	assume the molecules to be circular instead of linear (circ=0)

void alloc_sequence_arrays	(	const char **	sequences,
		short ***	S,
		short ***	S5,
		short ***	S3,
		unsigned short ***	a2s,
		char ***	Ss,
		int	circ
	)

#include <ViennaRNA/utils/alignments.h>

Allocate memory for sequence array used to deal with aligned sequences.

Note that these arrays will also be initialized according to the sequence alignment given

See also

free_sequence_arrays()

Parameters

sequences	The aligned sequences
S	A pointer to the array of encoded sequences
S5	A pointer to the array that contains the next 5' nucleotide of a sequence position
S3	A pointer to the array that contains the next 3' nucleotide of a sequence position
a2s	A pointer to the array that contains the alignment to sequence position mapping
Ss	A pointer to the array that contains the ungapped sequence
circ	assume the molecules to be circular instead of linear (circ=0)

void free_sequence_arrays	(	unsigned int	n_seq,
		short ***	S,
		short ***	S5,
		short ***	S3,
		unsigned short ***	a2s,
		char ***	Ss
	)

#include <ViennaRNA/utils/alignments.h>

Free the memory of the sequence arrays used to deal with aligned sequences.

This function frees the memory previously allocated with alloc_sequence_arrays()

See also

alloc_sequence_arrays()

Parameters

n_seq	The number of aligned sequences
S	A pointer to the array of encoded sequences
S5	A pointer to the array that contains the next 5' nucleotide of a sequence position
S3	A pointer to the array that contains the next 3' nucleotide of a sequence position
a2s	A pointer to the array that contains the alignment to sequence position mapping
Ss	A pointer to the array that contains the ungapped sequence