X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=sources%2Fmulticoil%2Flikelihood.h;fp=sources%2Fmulticoil%2Flikelihood.h;h=28f78ab32b4921d4a60f37d3aae0a073eded3be6;hb=81362e35a140cd040e948b921053e74267f8a6e3;hp=0000000000000000000000000000000000000000;hpb=2cf032f4b987ba747c04159965aed78e3820d942;p=jpred.git

diff --git a/sources/multicoil/likelihood.h b/sources/multicoil/likelihood.h
new file mode 100644
index 0000000..28f78ab
--- /dev/null
+++ b/sources/multicoil/likelihood.h
@@ -0,0 +1,48 @@
+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
+
+
+