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/* (C) Copyright 1993-9, Fred Hutchinson Cancer Research Center */
/* Use, modification or distribution of these programs is subject to */
/* the terms of the non-commercial licensing agreement in license.h. */
/* scoring.h: functions for different methods of scoring a sequence against */
/* a matrix */
/* Written by: Bill Alford */
/* Change log information is at the end of the file. */
#ifndef SCORING_H_
#define SCORING_H_
/*
* Exported variables and data structures
*/
#define MIN_SAVE_SCORE 945 /* If SV option used, never save lower score*/
#define MAX_HIST_SCORE 6000 /* the top of the histogram */
/* MAX_HIST_SCORE is 6000 = 60 x 100 = max block width x max weight */
#define HIST_BOX_SIZE 20 /* must evenly divide MAX_HIST_SCORE */
#define NUM_HIST_COLS ( MAX_HIST_SCORE / HIST_BOX_SIZE )
extern double Alignments_Done;
extern double Scores_Done;
extern int histogram[];
extern Boolean DoHistogram;
/*
* Exported functions
*/
/*
* default_scoring_method
* The default scoring method. Basically a score is the sum of the scores
* in the matrix at each position-amino acid pair for one alignment.
* Parameters:
* Sequence *seq: the sequence to score
* Matrix *matrix: the matrix used for scoring
* int frame: the frame we are looking at (0 = aa seq.,
* 1, 2, 3, -1, -2, -3 = na seqs.)
* Boolean repeats: enter repeats into the score_list?
* int search_type: the type of search we are doing. If it is a
* SEARCH_TYPE_MATRIX search (block vs sequences),
* do NOT divide by the block percentile. If it is a
* SEARCH_TYPE_BLOCK search (sequence vs blocks), DO
* divide by the block percentile.
* Error codes: none
*/
extern void default_scoring_method();
/*
* print_histogram
* ouputs the histogram array from scoring.[ch] to the output stream ofp.
* Parameters:
* FILE *ofp: the output file pointer
* Return codes: none
* Error codes: none
*/
extern void print_histogram();
#endif /* SCORING_H_ */
/* Change log information follows. */
/*
Changes since version 3.2.5:
5/25/99 Renamed scores_done to Scores_Done & alignemnts_done
to Alignments_Done & changed them from unsigned long to double
2/ 3/99 Added MIN_SAVE_SCORE
10/19/94 Increased MAX_HIST_SCORE from 2000 to 6000 = 60 x 100 =
max block width x max weight
*/
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