void usage();



#define PERCENT_COILED .02    /** DEFAULT VALUE ASSUMES 5% of residues are */
	                      /** in coiled coils.  */

#define ALGORITHM_SWITCH "-a"  /** with parameter "method" which says which
			 method to use to compute the likelihood **/
#define MEAN_SWITCH "-m"     /** Consider the histogram boxes to be centered   
			     at the mean of the scores in that box.        **/
#define PERCENT_COIL_SWITCH "-p" /** Given -p %, find the mean by finding  **/
                                 /** the score such that                   **/
                                 /** n_halfgauss/n[histogram] = %          **/
#define SCATTER_SWITCH "-s"  /** Type "-s scatter_outfile.ps score.log"    **/
                             /** where score.log is output from scboth -v  **/
#define NO_HEADER_SWITCH "-no_head" 
                             /** In ps file just output list of points **/
                             /** but no postscript header, trailer.        **/

#define RATIO_BOX_SWITCH "BoxRatio"
#define RATIO_TRAP_SWITCH "TrapRatio"
#define STOCK_SWITCH "stock"
#define RATIO_BOXES_GT_SWITCH "BoxesGTRatio"
#define FRACTION_POS_SWITCH "FracPos"
#define LEAST_SQ_PARAM_SWITCH "-lsq"

#define RATIO_BOX_METHOD 1   
#define RATIO_TRAP_METHOD 2
#define STOCK_METHOD 4
#define RATIO_BOXES_GT_METHOD 8
#define FRACTION_POS_METHOD 16
#define MEAN_MODE 32
#define PERCENT_COIL_MODE 64
#define SCATTER_MODE 128
#define NO_HEADER_MODE 256

#define DEFAULT_SWITCH RATIO_TRAP_SWITCH
#define DEFAULT_METHOD RATIO_TRAP_METHOD

#define DEFAULT_LOW .2
#define DEFAULT_HIGH .8
#define DEFAULT_ERROR .03

#define MINSCORE -2000