WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / Kinfold / main.c

diff --git a/binaries/src/ViennaRNA/Kinfold/main.c b/binaries/src/ViennaRNA/Kinfold/main.c
new file mode 100644 (file)
index 0000000..a71853e
--- /dev/null
+++ b/binaries/src/ViennaRNA/Kinfold/main.c
@@ -0,0 +1,224 @@
+/*
+  Last changed Time-stamp: <2010-06-24 14:50:01 ivo>
+  c  Christoph Flamm and Ivo L Hofacker
+  {xtof,ivo}@tbi.univie.ac.at
+  Kinfold: $Name:  $
+  $Id: main.c,v 1.5 2008/08/28 09:40:55 ivo Exp $
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include <unistd.h>
+#include "fold_vars.h"
+#include "fold.h"
+#include "baum.h"
+#include "nachbar.h"
+#include "cache_util.h"
+#include "utils.h"
+#include "globals.h"
+
+static char UNUSED rcsid[] ="$Id: main.c,v 1.5 2008/08/28 09:40:55 ivo Exp $";
+extern void  read_parameter_file(const char fname[]);
+extern void get_from_cache(cache_entry *c);
+
+/* PRIVAT FUNCTIONS */
+static void ini_energy_model(void);
+static void read_data(void);
+static void clean_up(void);
+
+/**/
+int main(int argc, char *argv[]) {
+  int i;
+  char * start;
+  
+  /*
+    process command-line optiones
+  */
+  decode_switches(argc, argv);
+
+  /*
+    initialize energy parameters
+  */
+  ini_energy_model();
+  
+  /*
+    read input file
+  */
+  read_data();
+
+  /*
+    perform GSV.num simulations
+  */
+    
+  start = strdup(GAV.startform); /* remember startform for next run */
+  for (i = 0; i < GSV.num; i++) {
+
+    /*
+      initialize or reset ringlist to start conditions
+    */
+    ini_or_reset_rl();
+    if (GSV.grow>0) {
+      if (strlen(GAV.farbe)>GSV.glen) {
+       start[GSV.glen] = '\0';
+       GAV.farbe[GSV.glen] = '\0';
+       strcpy(GAV.startform,start);
+       strcpy(GAV.currform,start);
+       GSV.len=GSV.glen;
+      }
+      clean_up_rl();
+      ini_or_reset_rl();
+    }
+
+    /*
+      perform simulation
+    */
+    for (GSV.steps = 1;; GSV.steps++) {
+      cache_entry *c;
+
+      /*
+       take neighbourhood of current structure from cache if there
+       else generate it from scratch
+      */
+      if ( (c = lookup_cache(GAV.currform)) ) get_from_cache(c);
+      else move_it();
+       
+      /*
+       select a structure from neighbourhood of current structure
+       and make it to the new current structure.
+       stop simulation if stop condition is met.
+      */
+      if ( sel_nb() > 0 ) break;
+
+      /* if (GSV.grow>0) grow_chain(); */
+    }
+  }
+  
+  /*
+    clean up memory
+  */
+  free(start);
+  clean_up();
+  return(0);
+}
+
+/**/
+static void ini_energy_model(void) {
+  if ( !GTV.seed ) {
+    init_rand();
+    GAV.subi[0] = xsubi[0];
+    GAV.subi[1] = xsubi[1];
+    GAV.subi[2] = xsubi[2];
+  }
+  else {
+    xsubi[0] = GAV.subi[0];
+    xsubi[1] = GAV.subi[1];
+    xsubi[2] = GAV.subi[2];
+  }
+  logML = GTV.logML;
+  dangles = GTV.dangle;
+  temperature = GSV.Temp;
+  if( GTV.Par ) read_parameter_file(GAV.ParamFile);
+  update_fold_params();
+}
+
+/**/
+static void read_data(void) {
+  char *ctmp, *c, **s;
+  int i, len;
+
+  /*
+    read sequence
+  */
+  ctmp = get_line(stdin);
+  len = strlen(ctmp);
+  if (c=strchr(ctmp, '&')) {
+    cut_point = (int)(c-ctmp)+1;
+    for (; *c; c++) *c = *(c+1); /* splice out the & */
+  }
+  GAV.farbe = (char *)calloc(len+1, sizeof(char));
+  assert(GAV.farbe != NULL);
+  sscanf(ctmp, "%s", GAV.farbe);
+  GSV.len = strlen(GAV.farbe);
+  for (i = 0; i < len; i++) GAV.farbe[i] = toupper(GAV.farbe[i]);
+  free (ctmp);
+  /* allocate some global arrays */
+  GAV.currform = (char *)calloc(GSV.len +1, sizeof(char));
+  assert(GAV.currform != NULL);
+  GAV.prevform = (char *)calloc(GSV.len +1, sizeof(char));
+  assert(GAV.prevform != NULL);
+  GAV.startform = (char *)calloc(GSV.len +1, sizeof(char));
+  assert(GAV.startform != NULL);
+
+  /*
+    read start structure
+  */
+  if (GTV.start) {
+    ctmp = get_line(stdin);
+    len = strlen(ctmp);
+    sscanf(ctmp, "%s", GAV.startform);
+    if (c=strchr(GAV.startform, '&')) {
+      for (; *c; c++) *c = *(c+1); /* splice out the & */
+    }
+
+    if (strlen(GAV.startform) != GSV.len) {
+      fprintf(stderr,
+             "read_data():\n%s\n%s\n unequal length!\n",
+             GAV.farbe, GAV.startform);
+      exit(1);
+    }
+    free (ctmp);
+  }
+  else { /* start structure is open chain */
+    for (i = 0; i< GSV.len; i++) GAV.startform[i] = '.';
+  }
+
+  /*
+    read stop structure(s)
+  */
+  if (GTV.stop) {
+    s = GAV.stopform;
+    while (( ctmp = get_line(stdin))) {
+      *s = (char *)calloc(GSV.len+1, sizeof(char));
+      sscanf(ctmp, "%s", *s);
+      if (c=strchr(ctmp, '&')) {
+       for (; *c; c++) *c = *(c+1); /* splice out the & */
+      }
+ 
+      if ( (s-GAV.stopform) >= GSV.maxS ) {
+       fprintf(stderr,
+               "WARNING: Can handle a maximum of %d stop structures\n",
+               GSV.maxS );
+        break;
+      }
+      
+      if (strlen(*s) != GSV.len) {
+       fprintf(stderr, "read_data():\n%s\n%s\n unequal length!\n",
+               GAV.farbe, *s);
+       exit(1);
+      }
+
+      s++;
+      free (ctmp);
+    }
+    GSV.maxS = (s-GAV.stopform);
+  }
+  else {
+    GSV.maxS = 1;
+    GAV.stopform[0] = (char *)calloc(GSV.len+1, sizeof(char));
+  }
+
+  GAV.farbe_full = strdup(GAV.farbe);
+
+  GAV.sE = (float *)calloc(GSV.maxS, sizeof(float)); 
+}
+
+/**/
+void clean_up(void) {
+  clean_up_globals();
+  clean_up_rl();
+  clean_up_nbList();
+  kill_cache();
+}