Function wrong_input

dialign/parameters.c:279–320

}

void wrong_input()
{
	printf("Usage: dialign-t [OPTIONS] <conf-directory> <fasta-file> [<fasta-out-file>]\n");
	printf("\n  -d\tDebug-Mode  [DEFAULT 0]\n");
	printf("   \t\t 0 no debug statements\n");
	printf("   \t\t 1 debugs the current phase of the processing\n");
	printf("   \t\t 2 very loquacious debugging\n");
	printf("   \t\t 5 hardcore debugging\n");
	printf("  -s\tmaximum amount of input sequences [DEFAULT 5000]\n");
	printf("  -a\tmaximum number of characters per line in a FASTA file [DEFAULT 100]\n");
	printf("  -c\tmaximum amount of characters per line when printing a sequence\n     \t[DEFAULT 80]\n");
	printf("  -l\tsensitivity mode, the higher the level the less likely\n");
	printf("    \tspurious random fragments are aligned in local alignments \n     \t[DEFAULT 0]\n");
	printf("   \t\t 0 switched off \n");
	printf("   \t\t 1 level-1, reduced sensitivity\n");
	printf("   \t\t 2 level-2, strongly reduced sensitivity\n");
	printf("  -m\tscore matrix file name (in the configuration directory)\n     \t\t[DEFAULT PROTEIN: BLOSUM.scr]\n \t\t[DEFAULT DNA: dna_matrix.scr]\n");
	printf("  -w\tdefines the minimum weight when the weight formula is changed\n     \tto 1-pow(1-prob, factor) [DEFAULT 0.000000065]\n");
	printf("  -p\tprobability distribution file name (in the configuration\n     \tdirectory) \n \t\t[DEFAULT PROTEIN: BLOSUM.diag_prob_t10]\n\t\t[DEFAULT DNA: dna_diag_prob_100_exp_550000]\n");
	printf("  -v\tadd to each score (to prevent negative values) [DEFAULT 0]\n");
	printf("  -t\t\"even\" threshold for low score for sequences alignment \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 0]\n");
	printf("  -n\tmaximum number of consecutive positions for window containing\n     \tlow scoring positions \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 4]\n");
	printf("  -g\tglobal minimum fragment length for stop criterion \n \t\t[DEFAULT PROTEIN: 40] \n\t\t[DEFAULT DNA: 40]\n");
	printf("  -m\tminimal allowed average score in frag window containing low \n     \tscoring positions \n \t\t[DEFAULT PROTEIN: 4.0]\n\t\t[DEFAULT DNA: 0.25]\n");
	printf("  -o\twhether overlap weights are calculated or not [DEFAULT 0]\n");
	printf("  -f\tminimum fragment length [DEFAULT 1]\n");
	printf("  -r\tthreshold weight to consider the fragment at all [DEFAULT 0.0]\n");
	printf("  -u\t[DEFAULT 0]\n");
	printf("    \t\t1: only use a sqrt(amount_of_seqs) stripe of neighbour\n     \t\t   sequences to calculate pairwise alignments (increase performance)\n");
	printf("    \t\t0: all pairwise alignments will be calculated\n");
	printf("  -A\toptional anchor file [DEFAULT none]\n");

	printf("  -D\tinput is DNA-sequence\n");
	printf("  -T\ttranslate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0)\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n");
 	printf("  -L\tcompare only longest Open Reading Frame\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n");
 	printf("  -O\ttranslate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF\n\tWARNING: Do not use -D with this option \n\t(Default values for PROTEIN input will be loaded)\n");
	printf("  -P\toutput in aminoacids, no retranslation of DNA sequences\n\t[DEFAULT: input = output]\n");
 	printf("  -F\tfast mode (implies -l0, since it already significantly reduces sensitivity)\n");
 	printf("  -C\tgenerate probability table saved in <config_dir>/prob_table and exit\n");
	printf("  -H -h\tprint this message\n\n");
	exit(1);
}

void parameters(int argc, char** argv)
{