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node.h
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node.h
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/*******************************************************************************
PRODIGAL (PROkaryotic DynamIc Programming Genefinding ALgorithm)
Copyright (C) 2007-2016 University of Tennessee / UT-Battelle
Code Author: Doug Hyatt
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*******************************************************************************/
#ifndef _NODE_H
#define _NODE_H
#include <stdio.h>
#include <math.h>
#include "sequence.h"
#include "training.h"
#define STT_NOD 100000
#define MIN_GENE 90
#define MIN_EDGE_GENE 60
#define MAX_SAM_OVLP 60
#define ST_WINDOW 60
#define OPER_DIST 60
#define EDGE_BONUS 0.74
#define EDGE_UPS -1.00
#define META_PEN 7.5
struct _motif {
int ndx; /* Index of the best motif for this node */
int len; /* Length of the motif */
int spacer; /* Spacer between coding start and the motif */
int spacendx; /* Index for this spacer length */
double score; /* Score for the motif */
};
struct _node {
int type; /* 0=ATG, 1=GTG, 2=TTG/Other, 3=Stop */
int edge; /* Runs off the edge; 0 = normal, 1 = edge node */
int ndx; /* position in the sequence of the node */
int strand; /* 1 = forward, -1 = reverse */
int stop_val; /* For a stop, record previous stop; for start, record
its stop */
int star_ptr[3]; /* Array of starts w/in MAX_SAM_OVLP bases of a stop in 3
frames */
int gc_bias; /* Frame of highest GC content within this node */
double gc_score[3]; /* % GC content in different codon positions */
double cscore; /* Coding score for this node (based on 6-mer usage) */
double gc_cont; /* GC Content for the node */
int rbs[2]; /* SD RBS score for this node (based on binding energy)
rbs[0] = best motif with exact match, rbs[1] = with
mismatches */
struct _motif mot; /* Upstream motif information for this node */
double uscore; /* Score for the upstream -1/-2, -15to-45 region */
double tscore; /* Score for the ATG/GTG/TTG value */
double rscore; /* Score for the RBS motif */
double sscore; /* Score for the strength of the start codon */
int traceb; /* Traceback to connecting node */
int tracef; /* Forward trace */
int ov_mark; /* Marker to help untangle overlapping genes */
double score; /* Score of total solution to this point */
int elim; /* If set to 1, eliminate this gene from the model */
};
int add_nodes(unsigned char *, unsigned char *, int, struct _node *, int,
mask *, int, struct _training *);
void reset_node_scores(struct _node *, int);
int compare_nodes(const void *, const void *);
int stopcmp_nodes(const void *, const void *);
void record_overlapping_starts(struct _node *, int, struct _training *, int);
void record_gc_bias(int *, struct _node *, int, struct _training *);
void calc_dicodon_gene(struct _training *, unsigned char *, unsigned char *,
int, struct _node *, int);
void calc_amino_bg(struct _training *, unsigned char *, unsigned char *, int,
struct _node *, int);
void score_nodes(unsigned char *, unsigned char *, int, struct _node *, int,
struct _training *, int, int);
void raw_coding_score(unsigned char *, unsigned char *, int, struct _node *,
int, struct _training *);
void calc_orf_gc(unsigned char *, unsigned char *, int, struct _node *, int,
struct _training *);
void rbs_score(unsigned char *, unsigned char *, int, struct _node *, int,
struct _training *);
void score_upstream_composition(unsigned char *, int, struct _node *,
struct _training *);
void determine_sd_usage(struct _training *);
double intergenic_mod(struct _node *, struct _node *, struct _training *);
void train_starts_sd(unsigned char *, unsigned char *, int, struct _node *,
int, struct _training *);
void train_starts_nonsd(unsigned char *, unsigned char *, int, struct _node *,
int, struct _training *);
void count_upstream_composition(unsigned char *, int, int, int,
struct _training *);
void build_coverage_map(double [4][4][4096], int [4][4][4096], double, int);
void find_best_upstream_motif(struct _training *, unsigned char *, unsigned
char *, int, struct _node *, int);
void update_motif_counts(double [4][4][4096], double *, unsigned char *,
unsigned char *, int, struct _node *, int);
void write_start_file(FILE *, struct _node *, int, struct _training *, int,
int, int, char *, char *, char *);
int cross_mask(int, int, mask *, int);
double dmax(double, double);
double dmin(double, double);
#endif