Function init_parameters

dialign/parameters.c:33–73

* PROTEIN DEFAULT VALUES! * ****************************/

* PROTEIN DEFAULT VALUES!   *
****************************/
void init_parameters()
{
	if((para =(struct parameters *) malloc(sizeof(struct parameters)) ) == NULL) 
	{
		error("init_parameters(): Out of memory when allocating data !");
	}
	para->VERSION = "1.0.2";
	para->DEBUG = 0;
	para->MAX_SEQ_AMOUNT = 5000;
	para->MAX_FASTA_LINE_LENGTH = 100;
	para->PRINT_SEQ_LINE_LENGTH = 80;
	para->SCR_MATRIX_FILE_NAME="BLOSUM.scr";
	para->DIAG_CALC_WEIGHT_THRESHOLD = 0.000000065;
	para->DIAG_PROB_FILE_NAME="BLOSUM.diag_prob_t10";
	para->SCR_MATRIX_ADD = 0; 
	para->PROT_SIM_SCORE_THRESHOLD = 4.0;
	//para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = 4;
	//para->PROT_DIAG_MIN_LENGTH_THRESHOLD = 10.0;
	para->PROT_DIAG_MAX_UNDER_THRESHOLD_POS = 4;
	para->PROT_DIAG_MIN_LENGTH_THRESHOLD = 40.0;
	para->PROT_DIAG_AVG_SCORE_THRESHOLD = 4.0;
	para->DO_ANCHOR = 0;
	para->ANCHOR_FILE_NAME = NULL;
	para->DO_OVERLAP = 0;
	para->DIAG_MIN_LENGTH = 1;
	para->FAST_MODE = 0;
	para->SENS_MODE = 0;
	para->DIAG_THRESHOLD_WEIGHT = -log(0.5);
	para->FAST_PAIRWISE_ALIGNMENT = 0;
	para->conf_dir = NULL;
	para->in_file = NULL;
	para->out_file = NULL;
 	para->COMPUTE_PROB=0;
	para->STATE_ORPHANE=1;
	para->STATE_INHERITED=2;
	para->DNA_PARAMETERS = 0;
	para->DNA_TRANSLATION = 0;
	para->FIND_ORF = 0;
	para->ORF_FRAME = 0;
	para->OUTPUT = 0;
}

/****************************
*     DNA DEFAULT VALUES!   *