// We return a copy here because the tokens_ vector may get reallocated
Token const Parser::next_next_token()
{
static const Token dummy;
if (!good())
return dummy;
// If tokenize_one() has not been called after the last get_token() we
// need to tokenize two more tokens.
if (pos_ >= tokens_.size())
tokenize_one();
if (pos_ + 1 >= tokens_.size())
tokenize_one();
return pos_ + 1 < tokens_.size() ? tokens_[pos_ + 1] : dummy;
}
// We return a copy here because the tokens_ vector may get reallocated
Token const Parser::next_token()
{
static const Token dummy;
if (!good())
return dummy;
if (pos_ >= tokens_.size())
tokenize_one();
return pos_ < tokens_.size() ? tokens_[pos_] : dummy;
}
void Parser::deparse()
{
string s;
for(size_type i = pos_ ; i < tokens_.size() ; ++i) {
s += tokens_[i].asInput();
}
is_.putback(from_utf8(s));
tokens_.erase(tokens_.begin() + pos_, tokens_.end());
// make sure that next token is read
tokenize_one();
}
// We return a copy here because the tokens_ vector may get reallocated
Token const Parser::get_token()
{
static const Token dummy;
if (!good())
return dummy;
if (pos_ >= tokens_.size()) {
tokenize_one();
if (pos_ >= tokens_.size())
return dummy;
}
// cerr << "looking at token " << tokens_[pos_]
// << " pos: " << pos_ << '\n';
return tokens_[pos_++];
}
string const Parser::getCommandLatexParam()
{
if (!good())
return string();
string res;
size_t offset = 0;
while (true) {
if (pos_ + offset >= tokens_.size())
tokenize_one();
if (pos_ + offset >= tokens_.size())
break;
Token t = tokens_[pos_ + offset];
if (t.cat() == catBegin)
break;
res += t.asInput();
++offset;
}
return res;
}
/*--------------------------------------------------------------------------*/
int main(int argc, char *argv[])
{
char *string1=NULL, *string2=NULL, *dummy=NULL, *temp=NULL, *line=NULL;
char *structure=NULL, *cstruc=NULL, *cstruc_l=NULL, *cstruc_s=NULL;
char fname[53], ffname[53], temp_name[201], first_name[53], my_contrib[10];
char up_out[250], unstrs[201], name[400], cmd_line[500];
char *ParamFile=NULL;
char *ns_bases=NULL, *c,*head;
int i, length1,length2,length, l, sym, r, *u_vals, Switch, header,output;
double energy, min_en;
double sfact=1.07;
int istty;
int noconv=0;
/* variables for output */
pu_contrib *unstr_out, *unstr_short;
interact *inter_out;
/* pu_out *longer; */
char *title;
/* commandline parameters */
int w; /* length of region of interaction */
int incr3; /* add x unpaired bases after 3'end of short RNA*/
int incr5; /* add x unpaired bases after 5'end of short RNA*/
int unstr; /* length of unpaired region for output*/
int upmode ; /* 1 compute only pf_unpaired, >1 compute interactions
2 compute intra-molecular structure only for long RNA, 3 both RNAs */
int task; /* input mode for calculation of interaction */
/* default settings for RNAup */
head = NULL;/* header text - if header wanted, see header */
header = 1; /* if header is 0 print no header in output file: option -nh */
output = 1; /* if output is 0 make no output file: option -o */
Switch = 1; /* the longer sequence is selected as the target */
task=0;
upmode = 1; /* default is one sequence, option -X[p|f] has to be set
for the calculation of an interaction, if no "&" is in
the sequence string */
unstrs[0]='\0';
default_u = 4;
unstr=default_u;
default_w = 25;
w=default_w;
u_vals=NULL;
incr3=0;
incr5=0;
do_backtrack = 1;
length1=length2=0;
title=NULL;
unstr_out=NULL;
inter_out=NULL;
my_contrib[0] = 'S';
my_contrib[1] = '\0';
first_name[0] = '\0';
/* collect the command line */
sprintf(cmd_line,"RNAup ");
length = 0;
for (i=1; i<argc; i++) {
r=sscanf(argv[i], "%100s", &temp_name);
length+=r+1;
if(length > 500) break;
strcat(cmd_line, temp_name);
strcat(cmd_line," ");
}
length = 0;
for (i=1; i<argc; i++) {
if (argv[i][0]=='-')
switch ( argv[i][1] )
{
case 'T': if (argv[i][2]!='\0') usage();
if (i==argc-1) usage();
r=sscanf(argv[++i], "%lf", &temperature);
if (!r) usage();
break;
case 'w':
/* -w maximal length of unstructured region */
if (i==argc-1) usage();
r=sscanf(argv[++i],"%d", &w);
if (!r) usage();
break;
case 't':
/* use the first sequence as the target */
if ( strcmp(argv[i], "-target")==0) {
Switch=0;
}
break;
case 'o':
/* make no output file */
output=0;
break;
case 'n':
if ( strcmp(argv[i], "-nh")==0) {
header=0;
}
if ( strcmp(argv[i], "-noGU")==0) {
noGU=1;
}
if ( strcmp(argv[i], "-noCloseGU")==0) {
no_closingGU=1;
}
if ( strcmp(argv[i], "-noLP")==0) {
noLonelyPairs=1;
}
if ( strcmp(argv[i], "-nsp") ==0) {
if (i==argc-1) usage();
ns_bases = argv[++i];
}
if ( strcmp(argv[i], "-noconv")==0) {
noconv=1;
}
break;
case '4':
tetra_loop=0;
break;
case 'e':
if (i==argc-1) usage();
r=sscanf(argv[++i],"%d", &energy_set);
if (!r) usage();
break;
case 'C':
fold_constrained=1;
break;
case 'S':
if (i==argc-1) usage();
r=sscanf(argv[++i],"%lf", &sfact);
if (!r) usage();
break;
case 'd': dangles=0;
if (argv[i][2]!='\0') {
r=sscanf(argv[i]+2, "%d", &dangles);
if (r!=1) usage();
}
break;
case 'b': upmode=3;
break;
case 'X':
/* interaction mode invoked */
if (upmode == 1) upmode=2;
switch (argv[i][2]) { /* now determine which sequences interact */
case 'p': task=1;
break; /* pairwise interaction */
case 'f': task=2;
break; /* first one interacts with all others */
}
break;
case 'u':
/* -u length of unstructured region in pr_unpaired output */
if (i==argc-1) usage();
r=sscanf(argv[++i],"%200s", unstrs);
if (!r) usage();
if (!isdigit(unstrs[0])) usage();
break;
/* incr5 and incr3 are only for the longer (target) sequence */
/* increments w (length of the unpaired region) to incr5+w+incr3*/
/* the longer sequence is given in 5'(= position 1) to */
/* 3' (=position n) direction */
/* incr5 adds incr5 residues to the 5' end of w */
case '5':
if (i==argc-1) usage();
r=sscanf(argv[++i],"%d", &incr5);
if (!r) usage();
break;
/* incr3 adds incr3 residues to the 3' end of w */
case '3':
if (i==argc-1) usage();
r=sscanf(argv[++i],"%d", &incr3);
if (!r) usage();
break;
case 'P':
if (i==argc-1) usage();
ParamFile = argv[++i];
break;
case 'c':
if (i==argc-1) usage();
r=sscanf(argv[++i], "%6s", my_contrib);
if (!r) usage();
break;
default: usage();
}
}
cmd_line[strlen(cmd_line)] = '\0';
if (dangles>0) dangles=2; /* only 0 or 2 allowed */
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++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
if ((fold_constrained)&&(istty)) {
printf("Input constraints using the following notation:\n");
printf(". : no constraint at all\n");
printf("x : base must not pair\n");
printf("matching brackets ( ): base i pairs base j\n");
printf("constraints for intramolecular folding only:\n");
printf("< : base i is intramolecularly paired with a base j<i\n");
printf("> : base i is intramolecularly paired with a base j>i\n");
printf("constraints for cofolding (intermolecular folding) only:\n");
printf("| : paired with another base intermolecularly\n");
}
RT = ((temperature+K0)*GASCONST/1000.0);
do { /* main loop: continue until end of file */
cut_point=-1;
if (istty) {
if (upmode == 1) {
printf("\nInput string (upper or lower case); @ to quit\n");
printf("%s%s\n", scale1, scale2);
}
else if (upmode > 1) {
if (task == 1 || (task == 0 && upmode == 3)) {
printf("\nUse either '&' to connect the 2 sequences or give each sequence on an extra line.\n");
printf("%s%s\n", scale1, scale2);
}
else if (task == 2) { /* option -Xf read the first two seqs */
printf("\nGive each sequence on an extra line. The first seq. is stored, every other seq. is compared to the first one.\n");
printf("%s%s\n", scale1, scale2);
}
else if (task == 3) {/* option -Xf read another sequence which
will interact with the first one */
printf("\nEnter another sequence.\n");
printf("%s%s\n", scale1, scale2);
}
}
}
fname[0]='\0';
ffname[0]='\0';
/* read the first sequence */
if ((line = get_line(stdin))==NULL) break;
/* skip comment lines and get filenames */
while ((*line=='*')||(*line=='\0')||(*line=='>')) {
if (*line=='>')
(void) sscanf(line, ">%51s", fname);
free(line);
line=NULL;
if ((line = get_line(stdin))==NULL) break;
}
if ((line == NULL) || (strcmp(line, "@") == 0)) break;
if (first_name[0] == '\0' && fname[0] !='\0' && task == 2) {
strncpy(first_name,fname,30);
first_name[30] = '\0';
}
/* if upmode == 2: check if the sequences are seperated via "&" (cut_point > -1) or given on extra lines */
if (task < 3) {
tokenize(line,&string1,&string2);
if (task == 2 && cut_point != -1) task = 3;
/* two sequences with & are given: calculate interaction */
if (task == 0 && cut_point != -1) {
task = 1;
if (upmode == 1) upmode = 2;
}
}
else if (task == 3) { /* option -Xf*/
strncpy(ffname,fname,30);
ffname[30] = '\0';
strncpy(fname,first_name,30); /* first_name: name of first seq */
fname[30] = '\0';
if (temp != NULL) { /*strings have been switched - write temp to string1*/
string1 = (char *) xrealloc (string1,sizeof(char)*strlen(temp)+1);
(void) sscanf(temp,"%s",string1);
free(temp);temp=NULL;
}
tokenize(line,&string2,&dummy); /*compare every seq to first one given */
free(dummy);dummy=NULL;
if (cut_point != -1) {
nrerror(
"After the first sequence pair: Input a single sequence (no &)!\n"
"Each input seq. is compared to the first seq. given.\n");
}
}
/* interaction mode -> get the second seq. if seq are on seperate lines*/
if (upmode > 1){ /* interaction mode */
if (cut_point == -1 && task < 3) { /* seqs are given on seperate lines */
/* read the second sequence */
if (task == 2) task = 3;
if ((line = get_line(stdin))==NULL) {
nrerror("only one sequence - can not cofold one sequence!");
}
/* skip comment lines and get filenames */
while ((*line=='*')||(*line=='\0')||(*line=='>')) {
if (*line=='>')
(void) sscanf(line, ">%51s", ffname); /* name of the 2nd seq */
free(line);
line=NULL;
if ((line = get_line(stdin))==NULL) break;
}
if ((line ==NULL) || (strcmp(line, "@") == 0)) break;
free(string2); /* string2 has been allocated in tokenize() */
string2 = (char *) space(strlen(line)+1);
(void) sscanf(line,"%s",string2); free(line);line=NULL;
}
} else { /* default mode pr_unpaired for ONE seq */
/* if a second sequence is give, cofold the sequences*/
if (cut_point != -1){
upmode = 2;
}
}
if (string1 != NULL){length1 = (int) strlen(string1);}
else {nrerror("sequence is NULL, check your input.");}
if (upmode > 1) {
if (string2 != NULL) {length2 = (int) strlen(string2);}
else{nrerror("one of the sequences is NULL, check your input.");}
/* write longer seq in string1 and and shorter one in string2 */
if (length1 < length2 && Switch) {
strncpy(temp_name,fname,30);
strncpy(fname,ffname,30);
strncpy(ffname,temp_name,30);
length=length1; length1=length2; length2=length;
temp=(char *) space(sizeof(char)*strlen(string1)+1);
(void) sscanf(string1,"%s",temp);
string1 = (char *) xrealloc (string1,sizeof(char)*length1+1);
(void) sscanf(string2,"%s",string1);
string2 = (char *) xrealloc(string2,sizeof(char)*length2+1);
(void) sscanf(temp,"%s",string2);
if (task == 1) {
free(temp);
temp = NULL;
}
}
}
/* parse cml parameters for output filename*/
/* create the name of the output file */
if (fname[0]!='\0') {
printf(">%s\n",fname);
if(strlen(fname) < 30) {
strcpy(up_out,fname);
} else {
strncpy(up_out,fname,30);
up_out[30] = '\0';
}
if (upmode > 1 && ffname[0] != '\0') {
printf(">%s\n",ffname);
if(strlen(fname) < 15) {
strcpy(up_out,fname);
} else {
strncpy(up_out,fname,15);
up_out[15] = '\0';
}
strcat(up_out, "_");
if(strlen(ffname) < 15) {
strcat(up_out,ffname);
} else {
strncat(up_out,ffname,15);
}
}
} else {
strcpy(up_out, "RNA");
}
if (upmode >1) {
sprintf(temp_name,"_w%d",w);
strncat(up_out, temp_name,10);
}
/* do this only when -X[p|f] is used or if two sequences seperated by & are given */
if (upmode > 1) {
if (task == 3) {
/* strncpy(temp_name,fname,30); */
if(strlen(fname) < 30) {
strcpy(temp_name,fname);
} else {
strncpy(temp_name,fname,30);
up_out[30] = '\0';
}
}
}
/* get values for -u */
if ( ! get_u_values(unstrs,&u_vals,length1)) {
nrerror("option -u: length value exceeds sequence length\n");
}
for (l = 0; l < length1; l++) {
string1[l] = toupper(string1[l]);
if (!noconv && string1[l] == 'T') string1[l] = 'U';
}
for (l = 0; l < length2; l++) {
string2[l] = toupper(string2[l]);
if (!noconv && string2[l] == 'T') string2[l] = 'U';
}
if (fold_constrained) {
char *temp_cstruc=NULL;
int old_cut;
temp_cstruc = get_line(stdin);
old_cut = cut_point;
cut_point=-1;
/* get contrained string without & */
cstruc = tokenize_one(temp_cstruc);
/* free(temp_cstruc); */
/* only one seq, cstruc should not have an & */
if (upmode == 1 && cut_point == -1) {
if (strlen(cstruc) == length1) {
cstruc_l=(char*)space(sizeof(char)*(length1+1));
strncpy(cstruc_l,cstruc,length1);
}else{
fprintf(stderr, "%s\n%s\n",string1,cstruc);
nrerror("RNAup -C: constrain string and structure have unequal length");
}
} else if (upmode == 1 && cut_point != -1) {
fprintf(stderr, "%s\n%s\n",string1,cstruc);
nrerror("RNAup -C: only one sequence but constrain structure for cofolding");
}
/* constrain string is for both seqs */
else if (upmode > 1 && cut_point != -1) {
if (old_cut != cut_point) {
nrerror("RNAup -C: different cut points in sequence und constrain string");
}
seperate_bp(&cstruc,length1,&cstruc_l,&cstruc_s);
if (strlen(cstruc) != (length1+length2)) {
fprintf(stderr, "%s&%s\n%s\n",string1,string2,cstruc);
nrerror("RNAup -C: constrain string and structure have unequal length");
}
if (strlen(cstruc_l) != (length1)) {
fprintf(stderr, "%s\n%s\n",string1,cstruc_l);
nrerror("RNAup -C: constrain string and structure have unequal length");
}
if (strlen(cstruc_s) != (length2)) {
fprintf(stderr, "%s\n%s\n",string2,cstruc_s);
nrerror("RNAup -C: constrain string and structure have unequal length");
}
} else {
fprintf(stderr, "%s&%s\n%s\n",string1,string2,cstruc);
nrerror("RNAup -C: no cutpoint in constrain string");
}
}
if(length1 > length2) {
structure = (char *) space(sizeof(char)*(length1+1));
} else {
structure = (char *) space(sizeof(char)*(length2+1));
}
update_fold_params();
if (cstruc_s != NULL)
strncpy(structure, cstruc_s, length2+1);
min_en = fold(string1, structure);
(void) fflush(stdout);
if (upmode != 0){
int wplus,w_sh;
if (upmode == 3) { /* calculate prob. unstruct. for shorter seq */
w_sh = w;
/* len of unstructured region has to be <= len shorter seq. */
if (w > length2) w_sh = length2;
if (cstruc_s != NULL)
strncpy(structure, cstruc_s, length2+1);
min_en = fold(string2, structure);
pf_scale = exp(-(sfact*min_en)/RT/length2);
if (length2>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
init_pf_fold(length2);
if (cstruc_s != NULL)
strncpy(structure, cstruc_s, length2+1);
energy = pf_fold(string2, structure);
unstr_short = pf_unstru(string2, w_sh);
free_pf_arrays(); /* for arrays for pf_fold(...) */
}
/* calculate prob. unstructured for longer seq */
wplus=w+incr3+incr5;
/* calculate prob. unpaired for the maximal length of -u */
if (u_vals[u_vals[0]] > wplus) wplus=u_vals[u_vals[0]];
/* length of the unstructured region has to be <= len longer seq. */
if (wplus > length1) wplus=length1;
if (cstruc_l !=NULL)
strncpy(structure, cstruc_l, length1+1);
min_en = fold(string1, structure);
pf_scale = exp(-(sfact*min_en)/RT/length1);
if (length1>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
init_pf_fold(length1);
if (cstruc_l !=NULL)
strncpy(structure, cstruc_l, length1+1);
energy = pf_fold(string1, structure);
if (upmode > 1) {
unstr_out = pf_unstru(string1, wplus);
} else {
unstr_out = pf_unstru(string1, u_vals[u_vals[0]]);
}
free_pf_arrays(); /* for arrays for pf_fold(...) */
/* now make output to stdout and to the output file */
if (upmode > 1){/* calculate interaction between two sequences */
int count;
if (upmode == 2) {
inter_out = pf_interact(string1,string2,unstr_out,NULL,w,cstruc,incr3,incr5);
print_interaction(inter_out,string1,string2,unstr_out,NULL,w,incr3,incr5);
} else if (upmode == 3){
inter_out = pf_interact(string1,string2,unstr_out,unstr_short,w,cstruc,incr3,incr5);
print_interaction(inter_out,string1,string2,unstr_out,unstr_short,w,incr3,incr5);
}
if(output) { /* make RNAup output to file */
printf("RNAup output in file: ");
/* plot for all -u values */
strcpy(name,up_out);
strcat(name, "_u");
if(u_vals[0] <= 20) {
for (count = 1; count <= u_vals[0]; count++) {
unstr = u_vals[count];
sprintf(temp_name,"%d",unstr);
if (count < u_vals[0]) {
strcat(temp_name,"_");
strncat(name, temp_name,5);
} else {
strncat(name, temp_name,5);
strcat(name, "_up.out");
printf("%s\n",name);
}
}
} else {
sprintf(temp_name,"%d",u_vals[1]);
strcat(temp_name,"_to_");
strncat(name, temp_name,5);
sprintf(temp_name,"%d",u_vals[0]);
strncat(name, temp_name,5);
strcat(name, ".out");
printf("%s\n",name);
}
if(header) {
char startl[3];
sprintf(startl,"# ");
head = (char*)space(sizeof(char)*(length1+length2+1000));
/* mach kein \n als ende von head */
sprintf(head,"%s %s\n%s %d %s\n%s %s\n%s %d %s\n%s %s",startl, cmd_line, startl,length1,fname, startl,string1, startl,length2,ffname, startl,string2);
} else {
if(head != NULL) { nrerror("error with header\n"); }
}
Up_plot(unstr_out,NULL,inter_out,name,u_vals,my_contrib,head);
if(head != NULL) {
free(head);
head = NULL;
}
if (upmode == 3 ) {/* plot opening energy for boths RNAs */
if(head != NULL) { nrerror("error with header\n"); }
Up_plot(NULL,unstr_short,NULL,name,u_vals,my_contrib,head);
}
}
} else { /* one sequence: plot only results for prob unstructured */
int count;
char collect_out[1000];
collect_out[0]='\0';
for (count = 1; count <= u_vals[0]; count++) {
unstr = u_vals[count];
print_unstru(unstr_out,unstr);
}
if(output) {/* make RNAup output to file */
printf("RNAup output in file: ");
strcpy(name,up_out);
strcat(name, "_u");
if(u_vals[0] <= 20) {
for (count = 1; count <= u_vals[0]; count++) {
unstr = u_vals[count];
sprintf(temp_name,"%d",unstr);
if (count < u_vals[0]) {
strcat(temp_name,"_");
strncat(name, temp_name,5);
} else {
strncat(name, temp_name,5);
strcat(name, ".out");
printf("%s\n",name);
}
}
} else {
sprintf(temp_name,"%d",u_vals[1]);
strcat(temp_name,"_to_");
strncat(name, temp_name,5);
sprintf(temp_name,"%d",u_vals[0]);
strncat(name, temp_name,5);
strcat(name, ".out");
printf("%s\n",name);
}
if(header) {
char startl[3];
sprintf(startl,"# ");
head = (char*)space(sizeof(char)*(length1+length2+1000));
/* mach kein \n als ende von head */
sprintf(head,"%s %s\n%s %d %s\n%s %s",startl, cmd_line, startl,length1,fname, startl,string1);
} else { if(head != NULL) { nrerror("error with header\n"); }}
Up_plot(unstr_out,NULL,NULL,name,u_vals,my_contrib,head);
if(head != NULL) { free(head); head = NULL;}
}
}
} else {
nrerror("no output format given\n");
}
if(structure != NULL) free(structure);
structure = NULL;
if (title != NULL) free(title);
title=NULL;
if (u_vals != NULL) free(u_vals);
u_vals=NULL;
if (upmode == 1) free_pu_contrib(unstr_out);
if (upmode > 1) {
free_pu_contrib(unstr_out);
free_interact(inter_out);
}
if (upmode == 3)free_pu_contrib(unstr_short);
free_arrays(); /* for arrays for fold(...) */
if (cstruc!=NULL) free(cstruc);
cstruc=NULL;
if (cstruc_l!=NULL) free(cstruc_l);
cstruc_l=NULL;
if (cstruc_s!=NULL) free(cstruc_s);
cstruc_s=NULL;
(void) fflush(stdout);
if (string1!=NULL && task != 3) {
free(string1);
string1 = NULL;
}
if (string2!=NULL) free(string2);
string2 = NULL;
} while (1);
if (line != NULL) free(line);
if (string1!=NULL) free(string1);
if (string2!=NULL) free(string2);
if (cstruc!=NULL) free(cstruc);
if (cstruc_l!=NULL) free(cstruc_l);
if (cstruc_s!=NULL) free(cstruc_s);
return 0;
}