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training.h
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training.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 _TRAIN_H
#define _TRAIN_H
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
struct _training {
double gc; /* GC Content */
int trans_table; /* 11 = Standard Microbial, NCBI Trans Table to
use */
double st_wt; /* Start weight */
double bias[3]; /* GC frame bias for each of the 3 positions */
double type_wt[3]; /* Weights for ATG vs GTG vs TTG */
int uses_sd; /* 0 if doesn't use SD motif, 1 if it does */
double rbs_wt[28]; /* Set of weights for RBS scores */
double ups_comp[32][4]; /* Base composition weights for non-RBS-distance
motifs. 0-1 are the -1/-2 position, 2-31 are
the -15 to -44 positions. Second array is
the base A,C,T,G,etc. */
double mot_wt[4][4][4096]; /* Weights for upstream motifs. First index is
the motif length (3-6), the second is the
spacer distance (0 = 5-10bp, 1 = 3-4bp, 2 =
11-12bp, 3 = 13-15bp), and the last is the
numerical value of the motif (ranging from 0
to 4095 for 6-mers, less for shorter
motifs) */
double no_mot; /* Weight for the case of no motif */
double gene_dc[4096]; /* Coding statistics for the genome */
};
int write_training_file(char *, struct _training *);
int read_training_file(char *, struct _training *);
void initialize_metagenome_0(struct _training *);
void initialize_metagenome_1(struct _training *);
void initialize_metagenome_2(struct _training *);
void initialize_metagenome_3(struct _training *);
void initialize_metagenome_4(struct _training *);
void initialize_metagenome_5(struct _training *);
void initialize_metagenome_6(struct _training *);
void initialize_metagenome_7(struct _training *);
void initialize_metagenome_8(struct _training *);
void initialize_metagenome_9(struct _training *);
void initialize_metagenome_10(struct _training *);
void initialize_metagenome_11(struct _training *);
void initialize_metagenome_12(struct _training *);
void initialize_metagenome_13(struct _training *);
void initialize_metagenome_14(struct _training *);
void initialize_metagenome_15(struct _training *);
void initialize_metagenome_16(struct _training *);
void initialize_metagenome_17(struct _training *);
void initialize_metagenome_18(struct _training *);
void initialize_metagenome_19(struct _training *);
void initialize_metagenome_20(struct _training *);
void initialize_metagenome_21(struct _training *);
void initialize_metagenome_22(struct _training *);
void initialize_metagenome_23(struct _training *);
void initialize_metagenome_24(struct _training *);
void initialize_metagenome_25(struct _training *);
void initialize_metagenome_26(struct _training *);
void initialize_metagenome_27(struct _training *);
void initialize_metagenome_28(struct _training *);
void initialize_metagenome_29(struct _training *);
void initialize_metagenome_30(struct _training *);
void initialize_metagenome_31(struct _training *);
void initialize_metagenome_32(struct _training *);
void initialize_metagenome_33(struct _training *);
void initialize_metagenome_34(struct _training *);
void initialize_metagenome_35(struct _training *);
void initialize_metagenome_36(struct _training *);
void initialize_metagenome_37(struct _training *);
void initialize_metagenome_38(struct _training *);
void initialize_metagenome_39(struct _training *);
void initialize_metagenome_40(struct _training *);
void initialize_metagenome_41(struct _training *);
void initialize_metagenome_42(struct _training *);
void initialize_metagenome_43(struct _training *);
void initialize_metagenome_44(struct _training *);
void initialize_metagenome_45(struct _training *);
void initialize_metagenome_46(struct _training *);
void initialize_metagenome_47(struct _training *);
void initialize_metagenome_48(struct _training *);
void initialize_metagenome_49(struct _training *);
#endif