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/*
* rnamat.h
*
* Header file for API for RNA matrix routines. Used in parsing alignment
* into matrix and later reading in matrix.
*
* Robert J. Klein
* February 25, 2002
*/
#ifndef _RNAMAT_H
#define _RNAMAT_H
#include "esl_config.h"
#include "config.h"
#include "easel.h"
#include "esl_msa.h"
#include "structs.h"
#define RNAPAIR_ALPHABET "AAAACCCCGGGGUUUU"
#define RNAPAIR_ALPHABET2 "ACGUACGUACGUACGU"
/*
* Matrix type
*
* Contains array in one dimension (to be indexed later), matrix size,
* H, and E.
*/
typedef struct _matrix_t {
double *matrix;
int edge_size; /* Size of one edge, e.g. 4 for 4x4 matrix */
int full_size; /* Num of elements, e.g. 10 for 4x4 matirx */
double H;
double E;
} matrix_t;
/*
* Full matrix definition, includes the g background freq vector (added by EPN).
*/
typedef struct _fullmat_t {
const ESL_ALPHABET *abc;/* alphabet, we enforce it's eslRNA */
matrix_t *unpaired;
matrix_t *paired;
char *name;
float *g; /* EPN: the background distro, g vector in RSEARCH paper
* this now appears in the RIBOSUM matrix files */
int scores_flag; /* TRUE if matrix values are log odds scores, FALSE if
* they're target probs, or unfilled */
int probs_flag; /* TRUE if matrix values are target probs, FALSE if
* they're log odds scores, or unfilled */
} fullmat_t;
/* Returns true if pos. C of seq B of msa A is a gap */
#define is_rna_gap(A, B, C) (esl_abc_CIsGap(A->abc, A->aseq[B][C]))
/* Returns true if position C of digitized sequence B of msa A is a canonical */
#define is_defined_rna_nucleotide(A, B, C) (esl_abc_CIsCanonical(A->abc, A->aseq[B][C]))
/*
* Maps c as follows
*
* A->0
* C->1
* G->2
* T->3
* U->3
* else -> 4
*/
int numbered_nucleotide (char c);
/*
* Maps base pair c,d as follows:
*
* AA -> 0
* AC -> 1
* ....
* TG -> 15
* TT -> 16 (T==U)
* Anything else maps to -1
*/
int numbered_basepair (char c, char d);
/*
* Maps to index of matrix, using binary representation of
* nucleotides (unsorted).
*
* See lab book 7, p. 3-4 for details of mapping function
*/
#define matrix_index(X,Y) ((X>Y) ? X*(X+1)/2+Y: Y*(Y+1)/2+X)
#define unpairedmat_size (matrix_index(3,3) + 1)
#define pairedmat_size (matrix_index (15,15) + 1)
/*
* Setup the matrix by allocating matrix in two dimensions as triangle.
* Initialize to 0.0
*/
matrix_t *setup_matrix (int size);
/*
* Actually count the basepairs and gaps into the fullmat simply by summing
* to existing values there. Also counts nt counts to background_nt
*/
void count_matrix (ESL_MSA *msa, fullmat_t *fullmat, double *background_nt,
int cutoff_perc, int product_weights);
/*
* Prints the matrix
*/
void print_matrix (FILE *fp, fullmat_t *fullmat);
/*
* Read the matrix from a file
*/
fullmat_t *ReadMatrix(const ESL_ALPHABET *abc, FILE *matfp);
/*
* Opens matrix file
*/
FILE *MatFileOpen (char *matfile);
/*
* Reports minium allowed sum of alpha + beta for matrix
*/
float get_min_alpha_beta_sum (fullmat_t *fullmat);
/* Free a fullmat_t object */
void FreeMat(fullmat_t *fullmat);
/* convert a matrix with log odds scores to target freqs */
int ribosum_calc_targets(fullmat_t *fullmat);
/* resolve degeneracies in a single seq MSA by replacing
* with most likely target residue within degenerate alphabet */
int ribosum_MSA_resolve_degeneracies(fullmat_t *fullmat, ESL_MSA *msa);
/*
* Maps i as follows:
* 0->A
* 1->C
* 2->G
* 3->U
* else->-1
*/
int unpaired_res (int i);
#endif
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