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/**
*
* parameters.h:
*
* 2004-08-13 Dorothea Emig Volker Menrad
*
*/
/************************************************/
/* */
/* structs */
/* */
/************************************************/
struct parameters
{
char *VERSION;
// 0 no debug statements
// 1 debugs the current phase of the processing
// 2 very loquacious debugging
// 5 hardcore debugging
int DEBUG; // = 0;
// maximum amount of input sequences
int MAX_SEQ_AMOUNT; // = 5000;
// maximum number of characters per line in a FASTA file
int MAX_FASTA_LINE_LENGTH; // = 100;
// maximum amount of characters per line when printing a sequence
int PRINT_SEQ_LINE_LENGTH; // = 80;
/*******************************
*
* PROTEIN SCORING/WEIGHTING SECTION
*
*****************************/
// score matrix (e.g. BLOSUM) file name (in the configuration directory)
//#define SCR_MATRIX_FILE_NAME "BLOSUM75.scr"
char *SCR_MATRIX_FILE_NAME; // = "BLOSUM.scr";
//#define SCR_MATRIX_FILE_NAME "BLOSUM90.scr"
// defines the minimum weight when the weight is changed to
// 1-pow(1-prob, factor)
double DIAG_CALC_WEIGHT_THRESHOLD; // = 0.000000065;
//#define DIAG_CALC_WEIGHT_THRESHOLD 0.0000002
// diag prob. distribution file name (in the configuration directory)
char *DIAG_PROB_FILE_NAME; // = "BLOSUM.diag_prob_t10";
//#define DIAG_PROB_FILE_NAME "BLOSUM.diag_prob_t7" // current
//#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob_t2" //
//#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob_t1"
//#define DIAG_PROB_FILE_NAME "BLOSUM90.diag_prob"
//#define DIAG_PROB_FILE_NAME "BLOSUM75.diag_prob"
//#define DIAG_PROB_FILE_NAME "tp400_prot"
// add to each score (to prevent negative values)
int SCR_MATRIX_ADD; // = 0; // BLOSUM(62)
//#define SCR_MATRIX_ADD 5 // BLOSUM75
//#define SCR_MATRIX_ADD 6 // BLOSUM90
/*******************************
*
* PROTEIN QUALITY SECTION
*
*****************************/
// "even" sim score threshold for protein sequences alignment
//#define PROT_SIM_SCORE_THRESHOLD 6 //BLOSUM90
//#define PROT_SIM_SCORE_THRESHOLD 5 //BLOSUM75
double PROT_SIM_SCORE_THRESHOLD; // = 4; // BLOSUM62
// maximum number of consecutive positions for frag-window
int PROT_DIAG_MAX_UNDER_THRESHOLD_POS; // = 4; // old was 4
// minimum diagonal length for breaking
double PROT_DIAG_MIN_LENGTH_THRESHOLD; // = 40.0; // old was 40
// minimal allowed average csore in frag window
double PROT_DIAG_AVG_SCORE_THRESHOLD; // = 4.0; // BLOSUM62
//#define PROT_DIAG_AVG_SCORE_THRESHOLD 5.0 // BLOSUM75
/*******************************
*
* GLOBAL QUALITY/SPEED SECTION
*
*****************************/
// wether overlap weights are calculated or not
int DO_OVERLAP; // = 0;
// minimum diag length
int DIAG_MIN_LENGTH;// = 1;
// diag threshold weight
double DIAG_THRESHOLD_WEIGHT;// = -log(0.5);
// if there are anchors
char DO_ANCHOR; // = 0;
// name of optional anchor file
char *ANCHOR_FILE_NAME; // = NULL;
// sensitivity mode, does not set
// DIAG_THRESHOLD_WEIGHT to 0 four rounds >1
char SENS_MODE;// = 0;
// fast mode - behaves like dialign t 0.2.2
char FAST_MODE;// = 0;
// 1: only use a sqrt(amount_of_seqs) stripe of neighbour sequences to
// calculate pairwise alignments
// 0: all pairwise alignments will be calculated
int FAST_PAIRWISE_ALIGNMENT;// = 0;
char *conf_dir ;
char *in_file ;
char *out_file ;
char COMPUTE_PROB;
int DNA_PARAMETERS; // default Einstellungen fr DNA holen
int DNA_TRANSLATION; // Vergleich auf Proteinebene, input DNA
int FIND_ORF; // Vergleich auf Proteinebene, input DNA, mit ORF Finder
int ORF_FRAME; // Vergleich auf Proteinebene, input DNA, nur longest ORF wird aligned
int OUTPUT; // fr DNA = 1, fr Aminosuren = 0
int STATE_ORPHANE;
int STATE_INHERITED;
};
/************************************************/
/* */
/* global variable */
/* */
/************************************************/
__attribute__((__common__)) struct parameters* para;
/*********************************************/
/* */
/* functions from parameters.c */
/* */
/*********************************************/
//struct parameters*
//initialises the parameters with default values
void init_parameters();
// check, whether there are enough arguments and if options are used
void check_input(int length, char** arguments);
//error message
void wrong_input();
void parameters(int argc, char** argv);
void set_parameters_dna();
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