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/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* convert.h: functions for different methods of converting a block into a */
/* matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef CONVERT_H_
#define CONVERT_H_
/* Defaults for Altschul's substitution probability pseudo-count
conversion method (3) */
#define LOCAL_QIJ_FILE "default.qij"
#define LOCAL_QIJ_RTOT 5.0
#define AAS 21
/*
* Exported variables and data structures
*/
extern double RTot; /* total number of pseudo-counts */
struct float_qij { /* qij matrix and marginal frequencies */
double value[AAS][AAS];
double marg[AAS];
};
extern struct float_qij *Qij;
struct pb_counts { /* for pb_weights() */
double diffaas; /* # of different aas in position */
double naas[MATRIX_AA_WIDTH]; /* # of each aa in position */
};
/* Pauline Ng's definitions (renamed) */
/* Dirichlet stuff */
#define MAXDIRI 40 /* max # of Dirichlet components (was MAXCOMP) */
/* Dirichlet mixtures (was struct dirichlet) */
struct diri {
int ncomp; /* number of components */
double q[MAXDIRI];
double altot[MAXDIRI];
double alpha[MAXDIRI][AAS];
double alpha_normalized[MAXDIRI][AAS]; /* Pauline, relative freq. of amino
acid to component (normalized against
component length*/
double frequency_to_background_ratio[MAXDIRI][AAS];
/* frequency to background ratio as calculated
in TableII of Sjolander's 1996 CABIOS paper*/
};
#define SIFT_TOLERANCE .05 /* was TOLERANCE_PROB_THRESHOLD */
/*
* Exported functions
*/
extern struct float_qij *load_qij( FILE *fin);
extern void pb_weights();
extern void normalize();
/*
* block_to_matrix
* converts a block into a matrix (possition specific matrix?) according
* to the rule specified in BlockToMatrixConversionType. The block field
* of the matrix is set in this function.
* Parameters:
* Block *block: the block to convert
* Return codes: Returns the pointer to the new Matrix.
* Error codes:
*/
extern Matrix *block_to_matrix();
/*
* original_conversion_method
* The original conversion method. This is done by weighted average of the
* clusters. This follows the method in patmat.
* Parameters:
* Block *block: the block to be converted
* Matrix *matrix: where the resulting matrix will be put
* Error codes: none
*/
extern void original_conversion_method();
/*
* original_conversion_method_cleaned_up
* The original conversion method. This is done by weighted average of the
* clusters. This follows the method in patmat but has been written in
* a more legible manner and has the following changes:
* no more reliance on flag values for B, Z, and X
* X, '-', '*', & non-code scores are read straight from the frequencies
* the frequencies for B and Z are ignored, when a B or Z is encountered
* it is partitioned between D & N or E & Q.
* the matrix scores for B and Z are computed from the matrix scores of
* D & N and E & Q.
* Parameters:
* Block *block: the block to be converted
* Matrix *matrix: where the resulting matrix will be put
* Error codes: none
*/
extern void original_conversion_method_cleaned_up();
/*
* pre_weighted_conversion_method
* This conversion method uses the pre-weighted sequence scores and
* uses the basic matrix construction method. This method has the
* following properties:
* X, '-', '*', & non-code scores are read straight from the frequencies
* the frequencies for B and Z are ignored, when a B or Z is encountered
* it is partitioned between D & N or E & Q.
* the matrix scores for B and Z are computed from the matrix scores of
* D & N and E & Q.
* Parameters:
* Block *block: the block to be converted
* Matrix *matrix: where the resulting matrix will be put
* Error codes: none
*/
extern void pre_weighted_conversion_method();
extern void pb_weights();
extern void altschul_data_dependent_conversion_method();
extern void gribskov_conversion_method();
/* Pauline's routines (renamed) */
extern void SIFT_conversion_method();
extern void SIFT_pssm(); /* SIFT_alts() */
extern struct diri *load_diri(); /* load_diri_file() */
extern void counts_nogaps(); /* counts_no_gaps */
extern double similarity_dependent_scale(); /* ..._0() */
extern void pseudo_diri(); /* pseudo_diric() */
extern int find_max_aa_col(); /* ..._in_col() */
extern int find_max_aa_pssm(); /* ..._in_pssm() */
extern double add_logs(); /* add_logs() */
#endif /* CONVERT_H_ */
/* Change log information follows.
Changes since version 3.4:
Made normalize() external
12/29/00 Added Pauline's SIFT stuff.
Changes for version 3.0.1:
5/23/96 Added gribskov_conversion_method()
Changes for version 3.0.0:
9/16/95 Added pb_weights() routine. JGH
* 9/9/95 Added LOCAL_QIJ_FILE & LOCAL_QIJ_RTOT JGH
*/
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