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/******************************************************************************
* MELTING v4.3 *
* This program computes for a nucleotide probe, the enthalpy, the entropy *
* and the melting temperature of the binding to its complementary template. *
* Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. *
* Copyright (C) Nicolas Le Novère and Marine Dumousseau 1997-2009 *
* *
* File: decode.h *
* Date: 01/APR/2009 *
* Aim : Variable definitions for decode.c *
******************************************************************************/
/* 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Nicolas Le Novère and Marine Dumousseau
Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus
Hinxton CB10 1SD United-Kingdom. e-mail: lenov@ebi.ac.uk
*/
#ifndef DECODE_H
#define DECODE_H
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>MACRO DEFINITIONS<<<<<<<<<<<<<<<<<<<<<<<<<<*/
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>VARIABLE DEFINITIONS<<<<<<<<<<<<<<<<<<<<<<<<<*/
int i_alt_nn = FALSE; /* an alternative set of nn parameters is required */
int i_alt_mm = FALSE; /* an alternative set of mismatches parameters is required */
int i_alt_inosine = FALSE; /* an alternative set of inosine mismatches parameters is required */
int i_alt_de = FALSE; /* an alternative set of dangling ends parameters is required */
int i_approx = FALSE; /* approximative tm computation? */
int i_complement = FALSE; /* correct complementary sequence? */
int i_dnadna = FALSE; /* those flags specify the type of hybridisation */
int i_dnarna = FALSE; /* (useful fo the approximative computations) */
int i_rnarna = FALSE;
int i_hybridtype = FALSE; /* correct hybridisation type? */
int i_infile = FALSE; /* infile furnished? */
int i_mismatchesneed = FALSE; /* We need mismaches parameters */
int i_inosineneed = FALSE; /* We need inosine mismaches parameters */
int i_dangendsneed = FALSE; /* We need dangling ends parameters */
int i_outfile = FALSE; /* outfile requested? */
int i_probe = FALSE; /* correct nucleic acid concentration? */
int i_quiet = FALSE; /* stay quiet, i.e. no interactive correction of parameters */
int i_salt = FALSE; /* correct sodium concentration? */
int i_magnesium = FALSE; /* can we use magnesium correction algorithm? */
int i_seq = FALSE; /* correct sequence? */
int i_verbose = FALSE; /* is verbose mode on? */
int i_threshold = MAX_SIZE_NN; /* threshold before approximative calculus */
/*>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>FUNCTION PROTOTYPES<<<<<<<<<<<<<<<<<<<<<<<<<*/
extern void usage(void); /*precises the command line parameters*/
struct param *decode_input(struct param *pst_in_param, char *ps_input, char *ps_path);
struct nnset *read_nn(char *ps_nn_set, char *ps_path); /* read a file containing a nn set */
struct mmset *read_mismatches(char *ps_mm_set, char *ps_path); /* read a file containing a mismatch set */
struct inosineset *read_inosine(char *ps_inosine_set, char *ps_path); /* read a file containing a inosine mismatch set */
struct deset *read_dangends(char *ps_de_set, char *ps_path); /* read a file containing a dangling ends set */
char *read_string(FILE *stream); /* read a line of input of unknown size */
void legal(void); /* precises the copyright under which melting is released*/
#endif /* DECODE_H */
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