JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / multicoil / switches.h

diff --git a/sources/multicoil/switches.h b/sources/multicoil/switches.h
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+/* switches.h defines all the switches that the user can type in at the  */
+/* command line to do various options with the program.                  */
+/* SC2SEQ and SCSTOCK keep track of what algorithm the program is running.*/
+
+#ifndef __switches_h__
+#define __switches_h__ 1
+
+
+#define SC2SEQ   1
+#define SCSTOCK  2
+
+
+
+/* Switches Definitions */
+#define FUNCTNUM_SWITCH "-f"
+#define POS_SWITCH "-pos" 
+#define VER_SWITCH "-v"
+#define PRN_SWITCH "-p"
+#define TST_SWITCH0 "-1"
+#define TST_SWITCH1 "-2"
+#define VIEW_SWITCH "-g"
+#define NOT_PROLINE_FREE_SWITCH "-P"
+#define DEBUG_SWITCH "-d"  /* Used to print out coils in log file.  */
+                           /* If the option is written a "-d + <int>"     */
+                           /* then that means to only print out coils     */
+                           /* from the .pos file, and to print residues   */
+                           /* in the range [bound, bound+int] in capitals */
+                           /* where bound comes from -p option            */
+#define PLUS_SWITCH "+" /*  This switch is currently used to indicate that */
+                        /*  only coils in .pos file should be printed out  */
+                        /*  by -d.  It could be a multipurpose switch to   */
+                        /*  augment other modes.                           */
+#define MINUS_SWITCH "-"    /* Switch to indicate not to print correct coils */
+#define PLUS_MINUS_SWITCH "+-" 
+#define CONFIG_SWITCH "-config"
+
+
+#define VER_MODE   1
+#define PRN_MODE   2
+#define TST_MODE0  4
+#define TST_MODE1  512
+#define POS_MODE   8
+#define VIEW_MODE  16
+#define DEBUG_MODE 32
+#define PLUS_MODE 64
+#define MINUS_MODE 128
+#define PROLINE_FREE_MODE 256
+#define MAX_WINDOW_BEFORE_COMBINE_MODE 1024
+#define ABOVE_BOUND_MODE 2048   /* Only print txt file stuff above bound. */
+#define NO_GUI 4096
+#define WEIGHTED_PROBS 8192    /*  Uses statistical signif in computing */
+                               /*  residue prob. from tables.           */
+#define RAW_OUT 16384          /*  Outputs raw scores instead of likes for */
+                               /*  multicoil. **/
+#define USE_LIKE_LINE   32768  /* For PairCoil, if use like line or do the */
+                               /* actual probability formula.              */
+#define POS_STYLE_LOG 65536 /* If 0 will use singles in trimer scorer */
+#define ONLY_COILED_CLASSES 131072 /* If in this mode then multicoil      */
+                      /*  like will be like[class]/total_pos[like] (i.e.  */
+                      /*  for class dimer it will be the prob a coil is   */
+                      /*  dimer vs.  trimer. */
+#define PAIRCOIL_PAIRS 262144     /* Determines if do PairCoil or SingleCoil */
+                                  /* Should fix to 1 if not in TEST_VERSION */
+#define LIB_AT_COMMAND_LINE 524288
+#define WEB_OUT_MODE 1048576
+
+#endif   /* __switches_h__ */
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