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all.h
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all.h
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/* miranda.h */
/*--------------------------------------------------------------------------------*/
/* miRanda- An miRNA target scanner, aims to predict mRNA targets for microRNAs, */
/* using dynamic-programming alignment and thermodynamics */
/* */
/* Copyright (C) (2003) Memorial Sloan-Kettering Cancer Center, New York */
/* */
/* Distributed under the GNU Public License (GPL) */
/* See the files 'COPYING' and 'LICENSE' for details */
/* */
/* Authors: Anton Enright, Bino John, Chris Sander and Debora Marks */
/* Email: mirnatargets@cbio.mskcc.org - reaches all authors */
/* */
/* Written By: Anton Enright (enrighta@mskcc.org) */
/* */
/* Please send bug reports to: miranda@cbio.mskcc.org */
/* */
/* If you use miRanda in your research please cite: */
/* Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS; */
/* (2003) Genome Biology; 5(1):R1. */
/* */
/* This software will be further developed under the open source model, */
/* coordinated by Anton Enright and Chris Sander: */
/* miranda@cbio.mskcc.org (reaches both). */
/*--------------------------------------------------------------------------------*/
/*
* Copyright (C) (2003) Memorial Sloan-Kettering Cancer Center
*
* 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 2 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, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/* Setup Traceback Flags */
#define DIAG 0
#define UP 1
#define LEFT -1
int CURR;
/* Setup Strands */
#define FORWARD 0
#define REVERSE 1
/* Adjustable Algorithm Parameters */
double scale;
int nomodel;
double gap_open;
double gap_extend;
double average;
double stdev;
double z_threshold;
double score_threshold;
double energy_threshold;
int do_shuffle;
int no_energy;
int shuffle_window;
int total_shuffles;
int verbosity;
unsigned int uniform;
int outfile;
int truncated;
int total_hits;
/* Output Filehandle */
FILE *fpout;
/* Generic structure to store individual hit information */
typedef struct hit_struct
{
double score;
int query_start;
int query_end;
int ref_start;
int ref_end;
char *alignment[3];
char *rest[6];
}
hit_struct;
/* Generic structure to store consecutive UTR hit information */
typedef struct final_score
{
double scan_score;
int no_hits;
double max_hit;
double max_score;
double total_score;
char positional[1000];
}
final_score;
/* Score structure for non-optimal path detection */
typedef struct score_struct
{
double score;
int path;
int i;
int j;
}
score_struct;
/* Declare Functions */
double max (double, double, double);
double score (char, char);
void traceback (double **, int **, char *, char *, int, int, int,
hit_struct *, int);
long readinseq (long, FILE *, char *, char *, char *);
void shuffle (char *, int, int);
void build_matrix (double **, int **, int **, char *, char *, int, int,
score_struct *);
double build_matrix_quick (double **, int **, char *, char *, int, int);
void revstring (char s[]);
void irand (int);
int nrand (int);
void printhit (char *, char *, hit_struct *, char *, char *, int, double, double, FILE *);
void print_license();
void print_small_license();
double get_energy (hit_struct *);
double vfold (char *);
void clear_hit (hit_struct *, int, int);
void clear_matrix (double **, int, int, int, int);
void initialize_bases ();
int cmpscores (const void *, const void *);
int find_targets (FILE *, FILE *, FILE *, char *);
double do_alignment (double **, int **, int **, char *, char *,
score_struct *, hit_struct *, int, int, int,
final_score *, int, char *, char *, FILE *);
void print_banner();
void print_usage();
void print_options();
/* scmatrix.h */
/*--------------------------------------------------------------------------------*/
/* miRanda- An miRNA target scanner, aims to predict mRNA targets for microRNAs, */
/* using dynamic-programming alignment and thermodynamics */
/* */
/* Copyright (C) (2003) Memorial Sloan-Kettering Cancer Center, New York */
/* */
/* Distributed under the GNU Public License (GPL) */
/* See the files 'COPYING' and 'LICENSE' for details */
/* */
/* Authors: Anton Enright, Bino John, Chris Sander and Debora Marks */
/* Email: mirnatargets@cbio.mskcc.org - reaches all authors */
/* */
/* Written By: Anton Enright (enrighta@mskcc.org) */
/* */
/* Please send bug reports to: miranda@cbio.mskcc.org */
/* */
/* If you use miRanda in your research please cite: */
/* Enright AJ, John B, Gaul U, Tuschl T, Sander C and Marks DS; */
/* (2003) Genome Biology; 5(1):R1. */
/* */
/* This software will be further developed under the open source model, */
/* coordinated by Anton Enright and Chris Sander: */
/* miranda@cbio.mskcc.org (reaches both). */
/*--------------------------------------------------------------------------------*/
/*
* Copyright (C) (2003) Memorial Sloan-Kettering Cancer Center
*
* 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 2 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, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/* Scoring Matrix - Only Takes Normal Nucleotides */
double match[6][6] = {
/* C G A T U X */
/* C */ {-3, +5, -3, -3, -3, -1},
/* G */ {+5, -3, -3, +2, +2, -1},
/* A */ {-3, -3, -3, +5, +5, -1},
/* T */ {-3, +2, +5, -3, -3, -1},
/* U */ {-3, +2, +5, -3, -3, -1},
/* X */ {-1, -1, -1, -1, -1, -1}
};
/* Master list of Nucleotide Bases */
unsigned char baselist[6] = { 'C', 'G', 'A', 'T', 'U', 'X' };
unsigned char bases[1000];