--- /dev/null
+/*
+ Last changed Time-stamp: <2010-06-24 17:15:16 ivo>
+ c Christoph Flamm and Ivo L Hofacker
+ {xtof,ivo}@tbi.univie.ac.at
+ Kinfold: $Name: $
+ $Id: globals.c,v 1.8 2008/10/07 09:03:14 ivo Exp $
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <errno.h>
+#include <getopt.h>
+#include "utils.h"
+#include "fold_vars.h"
+#include "globals.h"
+#include "cmdline.h"
+
+/* forward declarations privat functions */
+static void ini_globs(void);
+static void ini_gtoggles (void);
+static void ini_gvars(void);
+static void ini_garrays (void);
+static void usage(int status);
+static void display_settings(void);
+static void display_fileformat(void);
+static char *verbose(int optval, const char *which);
+static int process_options (int argc, char *argv[]);
+static void process_options_gg (int argc, char *argv[]);
+
+static const char *costring(const char *str);
+
+static char UNUSED rcsid[] ="$Id: globals.c,v 1.8 2008/10/07 09:03:14 ivo Exp $";
+#define MAXMSG 8
+static char msg[MAXMSG][60] =
+{{"off"},
+ {"on"},
+ {"current time"},
+ {"take from input file"},
+ {"open chain"},
+ {"mfe structure of sequence"},
+ {"ViennaRNA-Package-1.4 defaults"},
+ {""}
+};
+
+static struct option const long_options[] =
+{ {"dangle", required_argument, 0, 0},
+ {"Temp", required_argument, 0, 0},
+ {"Par", required_argument, 0, 0},
+ {"phi", required_argument, 0, 0},
+ {"pbounds", required_argument, 0, 0},
+ {"logML", no_argument, >V.logML, 0},
+ {"noShift", no_argument, >V.noShift, 1},
+ {"noLP", no_argument, >V.noLP, 1},
+ {"seed", required_argument, 0, 0},
+ {"time", required_argument, 0, 0},
+ {"num", required_argument, 0, 0},
+ {"start", no_argument, >V.start, 1},
+ {"stop", no_argument, >V.stop, 1},
+ {"fpt", no_argument, >V.fpt, 0},
+ {"met", no_argument, >V.mc, 1},
+ {"grow", required_argument, 0, 0},
+ {"glen", required_argument, 0, 0},
+ {"log", required_argument, 0, 0},
+ {"silent", no_argument, 0, 0},
+ {"lmin", no_argument, >V.lmin, 1},
+ {"cut", required_argument, 0, 0},
+ {"help", no_argument, 0, 'h'},
+ {"verbose", no_argument, 0, 0},
+ {NULL, 0, NULL, 0}
+};
+
+/**/
+void decode_switches(int argc, char *argv[]) {
+ ini_globs();
+ strcpy(GAV.ProgramName, argv[0]);
+ process_options_gg(argc, argv);
+}
+
+/**/
+void clean_up_globals(void) {
+ int i;
+ free(GAV.ProgramName);
+ free(GAV.BaseName);
+ free(GAV.farbe);
+ free(GAV.farbe_full);
+ free(GAV.startform);
+ free(GAV.currform);
+ free(GAV.prevform);
+ for (i = 0; i < GSV.maxS; i++) free(GAV.stopform[i]);
+ free(GAV.stopform);
+ free(GAV.sE);
+}
+
+/**/
+static void usage(int status) {
+ fprintf(stderr, "\n%s - Kinetic Folding Program for Nucleic Acids -\n",
+ GAV.ProgramName);
+ fprintf(stderr, "Usage: %s [OPTION] < FILE\n", GAV.ProgramName);
+ fprintf(stderr,
+ "Options:\n"
+ " EnergyModel\n"
+ " --dangle <0|1|2> set dangling end model to (non|normal|double)\n"
+ " --Temp <float> set simulation temperature to <float>\n"
+ " --Par <string> use energy-parameter-file <string>\n"
+ " --logML use linear multiloop-function not logarithmic\n"
+ " MoveSet\n"
+ " --noShift turn off shift-moves\n"
+ " --noLP forbit structures with isolated base-pairs\n"
+ " Simulation\n"
+ " --seed <int=int=int> set random seed to <int=int=int>\n"
+ " --time <float> set maxtime of simulation to <float>\n"
+ " --num <int> set number of simulations to <int>\n"
+ " --start set start structure\n"
+ " --stop set stop structure(s)\n"
+ " --met use Metropolis rule not Kawasaki rule\n"
+ " --fpt stop stop structure(s) is reached\n"
+ " --grow <float> grow chain every <float> time steps\n"
+ " --phi <double> set phi value to <double>\n"
+ " --pbounds <d1=d2=d3> set phi_min to d1\n"
+ " phi_inc to d2\n"
+ " phi_max to d2\n"
+ " (d? is a double value)\n"
+ " Output\n"
+ " --log <string> set basename of log-file to <string>\n"
+ " --err <string> set basename of error-log-file to <string>\n"
+ " --silent no output to stdout\n"
+ " --verbose more information to stdout\n"
+ " --lmin output only local minima to stdout\n"
+ " --cut <float> output structures with E <= <float> to stdout\n");
+ display_settings();
+ display_fileformat();
+ exit (status);
+}
+
+/**/
+static void display_fileformat(void) {
+ fprintf(stderr,
+ "Input File Format:\n"
+ "1st line sequence\n"
+ "2nd line start structure (if option --start is used)\n"
+ "following lines stop structures\n\n");
+}
+
+/**/
+void log_prog_params(FILE *FP) {
+ fprintf( FP,
+ "#<\n#Date: %s"
+ "#EnergyModel: dangle=%d Temp=%.1f logML=%s Par=%s\n"
+ "#MoveSet: noShift=%s noLP=%s\n"
+ "#Simulation: num=%d time=%.2f seed=%s fpt=%s mc=%s\n"
+ "#Simulation: phi=%g pbounds=%s\n"
+ "#Output: log=%s silent=%s lmin=%s cut=%.2f\n",
+ time_stamp(),
+ GTV.dangle,
+ GSV.Temp,
+ verbose(GTV.logML, "logML"),
+ GAV.ParamFile,
+ verbose(GTV.noShift, NULL),
+ verbose(GTV.noLP, NULL),
+ GSV.num,
+ GSV.time,
+ verbose(GTV.seed, "seed"),
+ verbose(GTV.fpt, NULL),
+ verbose(GTV.mc, "met"),
+ GSV.phi,
+ verbose(GTV.phi, "pbounds"),
+ GAV.BaseName,
+ verbose(GTV.silent, NULL),
+ verbose(GTV.lmin, NULL),
+ GSV.cut);
+ fflush(FP);
+}
+
+/**/
+void log_start_stop(FILE *FP) {
+ int i;
+ fprintf(FP, "#%s\n#%s (%6.2f)\n", costring(GAV.farbe),
+ costring(GAV.startform), GSV.startE);
+ for (i = 0; i < GSV.maxS; i++) {
+ fprintf(FP, "#%s (%6.2f) X%02d\n", costring(GAV.stopform[i]), GAV.sE[i], i+1);
+ }
+ fprintf(FP, "(%-5hu %5hu %5hu)", GAV.subi[0], GAV.subi[1], GAV.subi[2]);
+ costring(NULL);
+ fflush(FP);
+}
+
+/**/
+static void display_settings(void) {
+ fprintf(stderr,
+ "Default Settings:\n"
+ " EnergyModel\n"
+ " --dangle = %d\n"
+ " --Temp = %.2f\n"
+ " --Par = %s\n"
+ " --logML = %s\n"
+ " MoveSet\n"
+ " --noShift = %s\n"
+ " --noLP = %s\n"
+ " Simulation\n"
+ " --seed = %s\n"
+ " --time = %.1f\n"
+ " --phi = %g\n"
+ " --pbounds = %s\n"
+ " --num = %d\n"
+ " --start = %s\n"
+ " --stop = %s\n"
+ " --met = %s\n"
+ " --fpt = %s\n"
+ " Output\n"
+ " --log = %s\n"
+ " --silent = %s\n"
+ " --verbose = %s\n"
+ " --lmin = %s\n"
+ " --cut = %.2f\n",
+ GTV.dangle,
+ GSV.Temp,
+ GAV.ParamFile,
+ verbose(GTV.logML, "logML"),
+ verbose(GTV.noShift, NULL),
+ verbose(GTV.noLP, NULL),
+ verbose(GTV.seed, "seed"),
+ GSV.time,
+ GSV.phi,
+ verbose(GTV.phi, "pbounds"),
+ GSV.num,
+ verbose(GTV.start, "start"),
+ verbose(GTV.stop, "stop"),
+ verbose(GTV.mc, "met"),
+ verbose(GTV.fpt, NULL),
+ GAV.BaseName,
+ verbose(GTV.silent, NULL),
+ verbose(GTV.verbose, NULL),
+ verbose(GTV.lmin, NULL),
+ GSV.cut);
+}
+
+/**/
+static char *verbose (int optval, const char *which) {
+ if (which == NULL) return msg[optval];
+ else {
+ if ( strcmp(which, "seed") == 0 ) {
+ if (optval == 0 ) return "clock";
+ else {
+ sprintf(msg[MAXMSG - 1],
+ "%hu %hu %hu", GAV.subi[0], GAV.subi[1],GAV.subi[2]);
+ return msg[MAXMSG - 1];
+ }
+ }
+
+ if (strcmp(which, "pbounds") == 0) {
+ sprintf(msg[MAXMSG - 1],
+ "%g %g %g",
+ GAV.phi_bounds[0], GAV.phi_bounds[1], GAV.phi_bounds[2]);
+ return msg[MAXMSG - 1];
+ }
+
+ if ( strcmp(which, "met") == 0 ) {
+ if ( optval == 0 ) return "Kawasaki";
+ else return "Metropolis";
+ }
+
+ if ( strcmp(which, "logML") == 0 ) {
+ if ( optval == 0 ) return "linear";
+ else return "logarithmic";
+ }
+
+ if ( strcmp(which, "start") == 0 ) {
+ if ( optval == 0 ) return "OpenChain";
+ else return "input file";
+ }
+
+ if ( strcmp(which, "stop") == 0 ) {
+ if ( optval == 0 ) return "Mfe";
+ else return "input file";
+ }
+ }
+ return "hae?";
+}
+
+/**/
+static void ini_globs (void) {
+ ini_gtoggles();
+ ini_gvars();
+ ini_garrays();
+}
+
+static void process_options_gg (int argc, char *argv[]) {
+ struct gengetopt_args_info args_info;
+ if (cmdline_parser (argc, argv, &args_info) != 0)
+ exit(1) ;
+ if (args_info.help_given) cmdline_parser_print_help();
+ if (args_info.full_help_given) cmdline_parser_print_full_help();
+
+ GTV.dangle = args_info.dangle_arg;
+ GSV.Temp = args_info.Temp_arg;
+ strncpy(GAV.ParamFile,255,args_info.Par_arg);
+ GTV.Par = args_info.Par_given;
+ GTV.logML = args_info.logML_flag;
+
+ GTV.noShift = args_info.noShift_flag;
+ GTV.noLP = args_info.noLP_flag;
+
+ GTV.start= args_info.start_flag;
+ GTV.stop = args_info.stop_flag;
+ GTV.mc = args_info.met_flag;
+ GTV.lmin = args_info.lmin_flag;
+
+ GTV.verbose = args_info.verbose_flag;
+ GTV.silent = (GTV.verbose==0)?
+ args_info.silent_flag : 0;
+ if (args_info.seed_given)
+ if (sscanf(args_info.seed_arg, "%hu=%hu=%hu",
+ &GAV.subi[0], &GAV.subi[1], &GAV.subi[2]) != 3)
+ usage(EXIT_FAILURE);
+ else GTV.seed = 1;
+
+ /* laplace stuff */
+ if (args_info.phi_given) {
+ if (args_info.phi_arg>0) {
+ GTV.phi = 1;
+ GSV.phi = args_info.phi_arg;
+ }
+ else {
+ fprintf(stderr, "Value of --phi must be > 0 >%lf<\n", args_info.phi_arg);
+ exit(EXIT_FAILURE);
+ }
+ }
+ if (args_info.pbounds_given) {
+ if (sscanf(args_info.pbounds_arg, "%g=%g=%g",
+ &GAV.phi_bounds[0],
+ &GAV.phi_bounds[1],
+ &GAV.phi_bounds[2]) == 0)
+ usage(EXIT_FAILURE);
+ else
+ GTV.phi = 1;
+ /* check if values are proper */
+ if (GAV.phi_bounds[0] > GAV.phi_bounds[2]
+ || GAV.phi_bounds[1] > GAV.phi_bounds[2]) {
+ fprintf(stderr,
+ "Unmet requirements for pbounds:\n"
+ "phi_min < phi_max && phi_inc < phi_max\n"
+ "phi_min: %g phi_inc: %g phi_max: %g\n",
+ GAV.phi_bounds[0], GAV.phi_bounds[1], GAV.phi_bounds[2]);
+ exit(EXIT_FAILURE);
+ }
+ }
+ GSV.time = args_info.time_arg;
+ GSV.num = args_info.num_arg;
+ strncpy(GAV.BaseName, args_info.log_arg, 255);
+ GSV.cut = args_info.cut_arg;
+ GSV.grow = args_info.grow_arg;
+ GSV.glen = args_info.glen_arg;
+ GTV.lmin = args_info.lmin_flag;
+ GTV.fpt = args_info.fpt_flag;
+ cmdline_parser_free(&args_info);
+}
+/**/
+static int process_options (int argc, char *argv[]) {
+ int c, itmp;
+ float ftmp;
+ double dtmp;
+ int option_index = 0;
+ while ((c = getopt_long (argc, argv, "h",
+ long_options, &option_index)) != EOF) {
+ switch (c) {
+ case 0:
+ if (strcmp(long_options[option_index].name,"dangle")==0) {
+ itmp = -1;
+ if (sscanf(optarg, "%d", &itmp) == 0)
+ usage(EXIT_FAILURE);
+ else if (itmp == 0 || itmp == 1 || itmp == 2 || itmp == 3)
+ GTV.dangle = itmp;
+ else {
+ fprintf(stderr, "Value of --dangle must be 0|1|2 >%d<\n", itmp);
+ usage (EXIT_FAILURE);
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"Temp")==0) {
+ ftmp = -1.0;
+ if (sscanf(optarg, "%f", &ftmp) == 0)
+ usage(EXIT_FAILURE);
+ else if ( ftmp >= 0 )
+ GSV.Temp = ftmp;
+ else {
+ fprintf(stderr, "Value of --Temp must be >= 0 >%.2f<\n", ftmp);
+ usage (EXIT_FAILURE);
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"Par")==0) {
+ if (sscanf(optarg, "%s", GAV.ParamFile) == 0)
+ usage(EXIT_FAILURE);
+ else {
+ GTV.Par = 1;
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"silent")==0) {
+ GTV.silent = 1;
+ GTV.verbose = 0;
+ }
+
+ if (strcmp(long_options[option_index].name,"verbose")==0) {
+ if (GTV.silent == 0)
+ GTV.verbose = 1;
+ }
+
+ if (strcmp(long_options[option_index].name,"seed")==0) {
+ if (sscanf(optarg, "%hu=%hu=%hu",
+ &GAV.subi[0], &GAV.subi[1], &GAV.subi[2]) == 0)
+ usage(EXIT_FAILURE);
+ else GTV.seed = 1;
+ }
+
+ /* laplace stuff */
+ if (strcmp(long_options[option_index].name,"pbounds")==0) {
+ if (sscanf(optarg, "%g=%g=%g",
+ &GAV.phi_bounds[0],
+ &GAV.phi_bounds[1],
+ &GAV.phi_bounds[2]) == 0)
+ usage(EXIT_FAILURE);
+ else
+ GTV.phi = 1;
+ /* check if values are proper */
+ if (GAV.phi_bounds[0] > GAV.phi_bounds[2]
+ || GAV.phi_bounds[1] > GAV.phi_bounds[2]) {
+ fprintf(stderr,
+ "Unmet requirements for pbounds:\n"
+ "phi_min < phi_max && phi_inc < phi_max\n"
+ "phi_min: %g phi_inc: %g phi_max: %g\n",
+ GAV.phi_bounds[0], GAV.phi_bounds[1], GAV.phi_bounds[2]);
+ exit(EXIT_FAILURE);
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"time")==0) {
+ dtmp = -1.0;
+ if (sscanf(optarg, "%lf", &dtmp) == 0)
+ usage(EXIT_FAILURE);
+ else if ( dtmp > 0 )
+ GSV.time = dtmp;
+ else {
+ fprintf(stderr, "Value of --time must be > 0 >%lf<\n", dtmp);
+ usage(EXIT_FAILURE);
+ }
+ }
+
+ /* laplace stuff */
+ if (strcmp(long_options[option_index].name, "phi")==0) {
+ dtmp = -1.0;
+ if (sscanf(optarg, "%lf", &dtmp) == 0)
+ usage(EXIT_FAILURE);
+ else if ( dtmp > 0 ) {
+ GSV.phi = dtmp;
+ GTV.phi = 1;
+ }
+ else {
+ fprintf(stderr, "Value of --phi must be > 0 >%lf<\n", dtmp);
+ exit(EXIT_FAILURE);
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"num")==0) {
+ itmp = -1;
+ if (sscanf(optarg, "%d", &itmp) == 0)
+ usage(EXIT_FAILURE);
+ else if ( itmp > 0 )
+ GSV.num = itmp;
+ else {
+ fprintf(stderr, "Value of --num must be > 0 >%d<\n", itmp);
+ usage(EXIT_FAILURE);
+ }
+ }
+
+ if (strcmp(long_options[option_index].name,"log")==0)
+ if (sscanf(optarg, "%s", GAV.BaseName) == 0)
+ usage(EXIT_FAILURE);
+
+ if (strcmp(long_options[option_index].name,"cut")==0)
+ if (sscanf(optarg, "%f", &GSV.cut) == 0)
+ usage(EXIT_FAILURE);
+
+ if (strcmp(long_options[option_index].name,"grow")==0)
+ if (sscanf(optarg, "%lf", &GSV.grow) == 0)
+ usage(EXIT_FAILURE);
+
+ if (strcmp(long_options[option_index].name,"glen")==0)
+ if (sscanf(optarg, "%d", &GSV.glen) == 0)
+ usage(EXIT_FAILURE);
+
+ break;
+
+ case 'h':
+ usage (0);
+ default:
+ usage (EXIT_FAILURE);
+ }
+ }
+ return optind;
+}
+
+/**/
+static void ini_gtoggles(void) {
+ GTV.Par = 0;
+ GTV.seed = 0;
+ GTV.dangle = 2;
+ GTV.logML = 1;
+ GTV.noLP = 0;
+ GTV.noShift = 0;
+ GTV.start = 0;
+ GTV.stop = 0;
+ GTV.silent = 0;
+ GTV.phi = 0;
+ GTV.verbose = 0;
+ GTV.lmin = 0;
+ GTV.fpt = 1;
+ GTV.mc = 0;
+}
+
+/**/
+static void ini_gvars(void) {
+ GSV.len = 0;
+ GSV.num = 1;
+ GSV.maxS = 99;
+ GSV.cut = 20;
+ GSV.Temp = 37.0;
+ GSV.startE = 0.0;
+ GSV.stopE = 0.0;
+ GSV.currE = 0.0;
+ GSV.time = 500.0;
+ GSV.phi = 1.0;
+ GSV.simTime = 0.0;
+ GSV.glen = 15;
+}
+
+/**/
+static void ini_garrays(void) {
+ GAV.ProgramName = (char *)calloc((size_t)256, sizeof(char));
+ assert(GAV.ProgramName != NULL);
+ GAV.ParamFile = (char *)calloc((size_t)256, sizeof(char));
+ assert(GAV.ParamFile != NULL);
+ strcpy(GAV.ParamFile,"VRNA-1.4");
+ GAV.BaseName = (char *)calloc((size_t)256, sizeof(char));
+ assert(GAV.BaseName != NULL);
+ strcpy(GAV.BaseName, "kinout");
+ GAV.stopform = (char **)calloc(GSV.maxS + 1, sizeof(char *));
+ assert(GAV.stopform != NULL);
+ GAV.farbe = NULL;
+ GAV.startform = NULL;
+ GAV.currform = NULL;
+ GAV.prevform = NULL;
+ GAV.phi_bounds[0] = 0.1;
+ GAV.phi_bounds[1] = 0.1;
+ GAV.phi_bounds[2] = 2.0;
+}
+
+static const char *costring(const char *str) {
+ static char* buffer=NULL;
+ static int size=0;
+ int n;
+ if ((str==NULL) && (buffer)) {
+ /* make it possible to free buffer */
+ free(buffer);
+ return NULL;
+ }
+ n=strlen(str);
+ if (n>size) {
+ size = n+2;
+ buffer = realloc(buffer, size);
+ }
+ if ((cut_point>0)&&(cut_point<=n)) {
+ strncpy(buffer, str, cut_point-1);
+ buffer[cut_point-1] = '&';
+ strncpy(buffer+cut_point, str+cut_point-1, n-cut_point+1);
+ buffer[n+1] = '\0';
+ } else {
+ strncpy(buffer, str, n+1);
+ }
+ return buffer;
+}
+/* End of file */
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