--- /dev/null
+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
+
+
+