--- /dev/null
+/*
+ Distances of Secondary Structure Ensembles
+ Peter F Stadler, Ivo L Hofacker, Sebastian Bonhoeffer
+ Vienna RNA Package
+*/
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <ctype.h>
+#include <errno.h>
+#include <string.h>
+#include <unistd.h>
+#include "part_func.h"
+#include "fold_vars.h"
+#include "dist_vars.h"
+#include "utils.h"
+#include "PS_dot.h"
+#include "read_epars.h"
+#include "profiledist.h"
+#include "RNApdist_cmdl.h"
+
+
+#define MAXLENGTH 10000
+#define MAXSEQ 1000
+/*@unused@*/
+static char rcsid[] = "$Id: RNApdist.c,v 1.8 2002/11/07 12:19:41 ivo Exp $";
+
+PRIVATE void command_line(int argc, char *argv[]);
+PRIVATE void usage(void);
+PRIVATE void print_aligned_lines(FILE *somewhere);
+
+PRIVATE char task;
+PRIVATE char outfile[FILENAME_MAX_LENGTH];
+PRIVATE char ruler[] ="....,....1....,....2....,....3....,....4"
+ "....,....5....,....6....,....7....,....8";
+static int noconv = 0;
+
+int main(int argc, char *argv[])
+
+{
+ float *T[MAXSEQ];
+ int i,j, istty, n=0;
+ int type, length, taxa_list=0;
+ float dist;
+ FILE *somewhere=NULL;
+ char *structure;
+ char *line=NULL, fname[FILENAME_MAX_LENGTH], *list_title=NULL;
+ plist *pr_pl, *mfe_pl;
+
+ pr_pl = mfe_pl = NULL;
+
+ command_line(argc, argv);
+
+ if((outfile[0]=='\0')&&(task=='m')&&(edit_backtrack))
+ strcpy(outfile,"backtrack.file");
+ if (outfile[0]!='\0') somewhere = fopen(outfile,"w");
+ if (somewhere==NULL) somewhere = stdout;
+ istty = (isatty(fileno(stdout))&&isatty(fileno(stdin)));
+
+ while (1) {
+ if ((istty)&&(n==0)) {
+ printf("\nInput sequence; @ to quit\n");
+ printf("%s\n", ruler);
+ }
+
+ type = 0;
+ do { /* get sequence to fold */
+ if (line!=NULL) free(line);
+ *fname='\0';
+ if ((line=get_line(stdin))==NULL) {type = 999; break;}
+ if (line[0]=='@') type = 999;
+ if (line[0]=='*') {
+ if (taxa_list==0) {
+ if (task=='m') taxa_list=1;
+ printf("%s\n", line);
+ type = 0;
+ } else {
+ list_title = strdup(line);
+ type = 888;
+ }
+ }
+ if (line[0]=='>') {
+ if (sscanf(line,">%" XSTR(FILENAME_ID_LENGTH) "s", fname)!=0)
+ strcat(fname, "_dp.ps");
+ if (taxa_list)
+ printf("%d : %s\n", n+1, line+1);
+ else printf("%s\n",line);
+ type = 0;
+ }
+ if (isalpha(line[0])) {
+ char *cp;
+ cp =strchr(line,' ');
+ if (cp) *cp='\0';
+ type = 1;
+ }
+ } while(type==0);
+
+ if( (task == 'm')&&(type>800) ) {
+ if (taxa_list)
+ printf("* END of taxa list\n");
+ printf("> p %d (pdist)\n",n);
+ for (i=1; i<n; i++) {
+ for (j=0; j<i; j++) {
+ printf("%g ",profile_edit_distance(T[i], T[j]));
+ if(edit_backtrack) fprintf(somewhere,"> %d %d\n",i+1,j+1);
+ print_aligned_lines(somewhere);
+ }
+ printf("\n");
+ }
+ if (type==888) { /* do another distance matrix */
+ n = 0;
+ printf("%s\n", list_title);
+ free(list_title);
+ }
+ }
+
+ if(type>800) {
+ for (i=0; i<n; i++)
+ free_profile(T[i]);
+ if (type == 888) continue;
+ if (outfile[0]!='\0') (void) fclose(somewhere);
+ if (line!= NULL) free(line);
+ return 0; /* finito */
+ }
+
+ length = (int) strlen(line);
+ for (i=0; i<length; i++) {
+ line[i]=toupper(line[i]);
+ if (!noconv && line[i] == 'T') line[i] = 'U';
+ }
+
+ /* init_pf_fold(length); <- obsolete */
+ structure = (char *) space((length+1)*sizeof(char));
+ (void) pf_fold(line,structure);
+
+ if (*fname=='\0')
+ sprintf(fname, "%d_dp.ps", n+1);
+
+ /* PS_dot_plot(line, fname); <- NOT THREADSAFE and obsolete function! */
+
+ /* get pairlist of probability matrix */
+ assign_plist_from_pr(&pr_pl, pr, length, 1e-5);
+ /* no previous mfe call thus no mfe structure information known */
+ mfe_pl = (plist *)space(sizeof(plist));
+ mfe_pl[0].i = mfe_pl[0].j = 0;
+
+ /* call threadsafe dot plot printing function */
+ PS_dot_plot_list(line, fname, pr_pl, mfe_pl, "");
+
+ T[n] = Make_bp_profile_bppm(pr, length);
+ if((istty)&&(task=='m')) printf("%s\n",structure);
+ free(structure);
+ free(mfe_pl);
+ free(pr_pl);
+ free_pf_arrays();
+
+ n++;
+ switch (task) {
+ case 'p' :
+ if (n==2) {
+ dist = profile_edit_distance(T[0],T[1]);
+ printf("%g\n",dist);
+ print_aligned_lines(somewhere);
+ free_profile(T[0]);
+ free_profile(T[1]);
+ n=0;
+ }
+ break;
+ case 'f' :
+ if (n>1) {
+ dist = profile_edit_distance(T[1], T[0]);
+ printf("%g\n",dist);
+ print_aligned_lines(somewhere);
+ free_profile(T[1]);
+ n=1;
+ }
+ break;
+ case 'c' :
+ if (n>1) {
+ dist = profile_edit_distance(T[1], T[0]);
+ printf("%g\n",dist);
+ print_aligned_lines(somewhere);
+ free_profile(T[0]);
+ T[0] = T[1];
+ n=1;
+ }
+ break;
+
+ case 'm' :
+ break;
+
+ default :
+ nrerror("This can't happen.");
+ } /* END switch task */
+ (void) fflush(stdout);
+ } /* END while */
+ if (line !=NULL) free(line);
+ return 0;
+}
+
+/* ----------------------------------------------------------------- */
+
+PRIVATE void command_line(int argc, char *argv[])
+{
+
+ int i, sym;
+ char *ns_bases=NULL, *c;
+ char *ParamFile=NULL;
+ struct RNApdist_args_info args_info;
+
+ task = 'p';
+
+ /*
+ #############################################
+ # check the command line parameters
+ #############################################
+ */
+ if(RNApdist_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
+
+ /* temperature */
+ if(args_info.temp_given)
+ temperature = args_info.temp_arg;
+
+ /* do not take special tetra loop energies into account */
+ if(args_info.noTetra_given)
+ tetra_loop=0;
+
+ /* set dangle model */
+ if(args_info.dangles_given){
+ dangles = args_info.dangles_arg;
+ if(dangles) dangles = 2;
+ }
+
+ /* set energy model */
+ if(args_info.energyModel_given)
+ energy_set = args_info.energyModel_arg;
+
+ /* do not allow weak pairs */
+ if(args_info.noLP_given)
+ noLonelyPairs = 1;
+
+ /* do not allow wobble pairs (GU) */
+ if(args_info.noGU_given)
+ noGU = 1;
+
+ /* do not allow weak closing pairs (AU,GU) */
+ if(args_info.noClosingGU_given)
+ no_closingGU = 1;
+
+ /* do not convert DNA nucleotide "T" to appropriate RNA "U" */
+ if(args_info.noconv_given)
+ noconv = 1;
+
+ /* Allow other pairs in addition to the usual AU,GC,and GU pairs */
+ if(args_info.nsp_given)
+ ns_bases = strdup(args_info.nsp_arg);
+
+ /* take another energy parameter set */
+ if(args_info.paramFile_given)
+ ParamFile = strdup(args_info.paramFile_arg);
+
+ if(args_info.compare_given){
+ switch(args_info.compare_arg[0]){
+ case 'p':
+ case 'm':
+ case 'f':
+ case 'c': task=args_info.compare_arg[0];
+ break;
+ default: RNApdist_cmdline_parser_print_help();
+ exit(EXIT_FAILURE);
+ }
+ }
+
+ if(args_info.backtrack_given){
+ if(strcmp(args_info.backtrack_arg, "none")){
+ strncpy(outfile, args_info.backtrack_arg, FILENAME_MAX_LENGTH-1);
+ }
+ edit_backtrack = 1;
+ }
+
+ /* free allocated memory of command line data structure */
+ RNApdist_cmdline_parser_free (&args_info);
+
+ /* do some preparations */
+ if (ParamFile!=NULL)
+ read_parameter_file(ParamFile);
+
+ if (ns_bases!=NULL) {
+ nonstandards = space(33);
+ c=ns_bases;
+ i=sym=0;
+ if (*c=='-') {
+ sym=1; c++;
+ }
+ while (*c!='\0') {
+ if (*c!=',') {
+ nonstandards[i++]=*c++;
+ nonstandards[i++]=*c;
+ if ((sym)&&(*c!=*(c-1))) {
+ nonstandards[i++]=*c;
+ nonstandards[i++]=*(c-1);
+ }
+ }
+ c++;
+ }
+ }
+
+}
+
+/* ------------------------------------------------------------------------- */
+
+PRIVATE void usage(void)
+{
+ nrerror("usage: RNApdist [-Xpmfc] [-B [file]] [-T temp] [-4] [-d] [-noGU]\n"
+ " [-noCloseGU] [-noLP] [-e e_set] [-P paramfile] [-nsp pairs]");
+}
+
+/*--------------------------------------------------------------------------*/
+
+PRIVATE void print_aligned_lines(FILE *somewhere)
+{
+ if (edit_backtrack)
+ fprintf(somewhere, "%s\n%s\n", aligned_line[0], aligned_line[1]);
+}
+
+/*--------------------------------------------------------------------------*/
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