/*---------------------------------------------------------------------------*/
PUBLIC int xrna_plot(char *string, char *structure, char *ssfile)
{ /* produce input for XRNA RNA drawing program */
FILE *ss_file;
int i;
int length;
short *pair_table;
float *X, *Y;
ss_file = fopen(ssfile, "w");
if (ss_file == NULL) {
fprintf(stderr, "can't open file %s - not doing xy_plot\n", ssfile);
return 0;
}
length = strlen(string);
pair_table = make_pair_table(structure);
/* make coordinates */
X = (float *) space((length+1)*sizeof(float));
Y = (float *) space((length+1)*sizeof(float));
if (rna_plot_type == 0)
i = simple_xy_coordinates(pair_table, X, Y);
else
i = naview_xy_coordinates(pair_table, X, Y);
if (i!=length)
fprintf(stderr,"strange things happening in xrna_plot...\n");
fprintf(ss_file,
"# Vienna RNA Package %s, XRNA output\n"
"# CreationDate: %s\n"
"# Options: %s\n", VERSION, time_stamp(), option_string());
for (i=1; i<=length; i++)
/* XRNA likes to have coordinate mirrored, so we use (-X, Y) */
fprintf(ss_file, "%d %c %6.2f %6.2f %d %d\n", i, string[i-1],
-X[i-1], Y[i-1], (pair_table[i]?1:0), pair_table[i]);
fclose(ss_file);
free(pair_table);
free(X); free(Y);
return 1; /* success */
}
PUBLIC int gmlRNA(char *string, char *structure, char *ssfile, char option)
{
FILE *gmlfile;
int i;
int length;
int labels=0;
short *pair_table;
float *X, *Y;
if (isupper(option)) labels = 1;
gmlfile = fopen(ssfile, "w");
if (gmlfile == NULL) {
fprintf(stderr, "can't open file %s - not doing xy_plot\n", ssfile);
return 0;
}
length = strlen(string);
pair_table = make_pair_table(structure);
switch(option){
case 'X' :
case 'x' :
/* Simple XY Plot */
X = (float *) space((length+1)*sizeof(float));
Y = (float *) space((length+1)*sizeof(float));
if (rna_plot_type == 0)
i = simple_xy_coordinates(pair_table, X, Y);
else
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=length) fprintf(stderr,"strange things happening in gmlRNA ...\n");
break;
default:
/* No Graphics Information */
X = NULL;
Y = NULL;
}
fprintf(gmlfile,
"# Vienna RNA Package %s\n"
"# GML Output\n"
"# CreationDate: %s\n"
"# Name: %s\n"
"# Options: %s\n", VERSION, time_stamp(), ssfile, option_string());
fprintf(gmlfile,
"graph [\n"
" directed 0\n");
for (i=1; i<=length; i++){
fprintf(gmlfile,
" node [ id %d ", i);
if (option) fprintf(gmlfile,
"label \"%c\"",string[i-1]);
if ((option == 'X')||(option=='x'))
fprintf(gmlfile,
"\n graphics [ x %9.4f y %9.4f ]\n", X[i-1], Y[i-1]);
fprintf(gmlfile," ]\n");
}
for (i=1; i<length; i++)
fprintf(gmlfile,
"edge [ source %d target %d ]\n", i, i+1);
for (i=1; i<=length; i++) {
if (pair_table[i]>i)
fprintf(gmlfile,
"edge [ source %d target %d ]\n", i, pair_table[i]);
}
fprintf(gmlfile, "]\n");
fclose(gmlfile);
free(pair_table);
free(X); free(Y);
return 1; /* success */
}
PUBLIC int ssv_rna_plot(char *string, char *structure, char *ssfile)
{ /* produce input for the SStructView java applet */
FILE *ssvfile;
int i, bp;
int length;
short *pair_table;
float *X, *Y;
float xmin, xmax, ymin, ymax;
ssvfile = fopen(ssfile, "w");
if (ssvfile == NULL) {
fprintf(stderr, "can't open file %s - not doing xy_plot\n", ssfile);
return 0;
}
length = strlen(string);
pair_table = make_pair_table(structure);
/* make coordinates */
X = (float *) space((length+1)*sizeof(float));
Y = (float *) space((length+1)*sizeof(float));
if (rna_plot_type == 0)
i = simple_xy_coordinates(pair_table, X, Y);
else
i = naview_xy_coordinates(pair_table, X, Y);
if (i!=length)
fprintf(stderr,"strange things happening in ssv_rna_plot...\n");
/* make coords nonegative */
xmin = xmax = X[0];
ymin = ymax = Y[0];
for (i = 1; i < length; i++) {
xmin = X[i] < xmin ? X[i] : xmin;
xmax = X[i] > xmax ? X[i] : xmax;
ymin = Y[i] < ymin ? Y[i] : ymin;
ymax = Y[i] > ymax ? Y[i] : ymax;
}
if (xmin<1) {
for (i = 0; i <= length; i++)
X[i] -= xmin-1;
xmin = 1;
}
if (ymin<1) {
for (i = 0; i <= length; i++)
Y[i] -= ymin-1;
ymin = 1;
}
#if 0
{
float size, xoff, yoff;
float JSIZE = 500; /* size of the java applet window */
/* rescale coordinates, center on square of size HSIZE */
size = MAX((xmax-xmin),(ymax-ymin));
xoff = (size - xmax + xmin)/2;
yoff = (size - ymax + ymin)/2;
for (i = 0; i <= length; i++) {
X[i] = (X[i]-xmin+xoff)*(JSIZE-10)/size + 5;
Y[i] = (Y[i]-ymin+yoff)*(JSIZE-10)/size + 5;
}
}
#endif
/* */
fprintf(ssvfile,
"# Vienna RNA Package %s\n"
"# SStructView Output\n"
"# CreationDate: %s\n"
"# Name: %s\n"
"# Options: %s\n", VERSION, time_stamp(), ssfile, option_string());
for (i=1; i<=length; i++)
fprintf(ssvfile, "BASE\t%d\t%c\t%d\t%d\n",
i, string[i-1], (int) (X[i-1]+0.5), (int) (Y[i-1]+0.5));
for (bp=1, i=1; i<=length; i++)
if (pair_table[i]>i)
fprintf(ssvfile, "BASE-PAIR\tbp%d\t%d\t%d\n", bp++, i, pair_table[i]);
fclose(ssvfile);
free(pair_table);
free(X); free(Y);
return 1; /* success */
}
int svg_rna_plot(char *string, char *structure, char *ssfile)
{
float xmin, xmax, ymin, ymax, size;
int i, length;
float *X, *Y;
FILE *xyplot;
short *pair_table;
length = strlen(string);
xyplot = fopen(ssfile, "w");
if (xyplot == NULL) {
fprintf(stderr, "can't open file %s - not doing xy_plot\n", ssfile);
return 0;
}
pair_table = make_pair_table(structure);
X = (float *) space((length+1)*sizeof(float));
Y = (float *) space((length+1)*sizeof(float));
if (rna_plot_type == 0)
i = simple_xy_coordinates(pair_table, X, Y);
else
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=length) fprintf(stderr,"strange things happening in PS_rna_plot...\n");
xmin = xmax = X[0];
ymin = ymax = Y[0];
for (i = 1; i < length; i++) {
xmin = X[i] < xmin ? X[i] : xmin;
xmax = X[i] > xmax ? X[i] : xmax;
ymin = Y[i] < ymin ? Y[i] : ymin;
ymax = Y[i] > ymax ? Y[i] : ymax;
}
for (i = 0; i < length; i++)
Y[i] = ymin+ymax - Y[i]; /* mirror coordinates so they look as in PS */
size = MAX((xmax-xmin),(ymax-ymin));
size += 10; /* add some so the bounding box isn't too tight */
fprintf(xyplot,
"<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n"
"<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"452\" width=\"452\">\n");
fprintf(xyplot,
"<script type=\"text/ecmascript\">\n"
" <![CDATA[\n"
" var shown = 1;\n"
" function click() {\n"
" var seq = document.getElementById(\"seq\");\n"
" if (shown==1) {\n"
" seq.setAttribute(\"style\", \"visibility: hidden\");\n"
" shown = 0;\n"
" } else {\n"
" seq.setAttribute(\"style\", \"visibility: visible\");\n"
" shown = 1;\n"
" }\n"
" }\n"
" ]]>\n"
"</script>\n");
fprintf(xyplot,
" <rect style=\"stroke: white; fill: white\" height=\"452\" x=\"0\" y=\"0\" width=\"452\" onclick=\"click(evt)\" />\n"
" <g transform=\"scale(%7f,%7f) translate(%7f,%7f)\">\n",
SIZE/size, SIZE/size, (size-xmin-xmax)/2, (size-ymin-ymax)/2);
fprintf(xyplot,
" <polyline style=\"stroke: black; fill: none; stroke-width: 1.5\" id=\"outline\" points=\"\n");
for (i = 0; i < length; i++)
fprintf(xyplot, " %3.3f,%3.3f\n", X[i], Y[i]);
fprintf(xyplot," \" />\n");
fprintf(xyplot," <g style=\"stroke: black; stroke-width: 1\" id=\"pairs\">\n");
for (i = 1; i <= length; i++) {
int j;
if ((j=pair_table[i])>i)
fprintf(xyplot,
" <line id=\"%d,%d\" x1=\"%6.3f\" y1=\"%6.3f\" x2=\"%6.3f\" y2=\"%6.3f\" />\n",
i,j, X[i-1], Y[i-1], X[j-1], Y[j-1]);
}
fprintf(xyplot, " </g>\n");
fprintf(xyplot, " <g style=\"font-family: SansSerif\" transform=\"translate(-4.6, 4)\" id=\"seq\">\n");
for (i = 0; i < length; i++)
fprintf(xyplot, " <text x=\"%.3f\" y=\"%.3f\">%c</text>\n", X[i], Y[i], string[i]);
fprintf(xyplot, " </g>\n");
fprintf(xyplot, " </g>\n");
fprintf(xyplot, "</svg>\n");
fclose(xyplot);
free(pair_table);
free(X); free(Y);
return 1; /* success */
}
int PS_rna_plot_a(char *string, char *structure, char *ssfile, char *pre, char *post)
{
float xmin, xmax, ymin, ymax, size;
int i, length;
float *X, *Y;
FILE *xyplot;
short *pair_table;
char *c;
length = strlen(string);
xyplot = fopen(ssfile, "w");
if (xyplot == NULL) {
fprintf(stderr, "can't open file %s - not doing xy_plot\n", ssfile);
return 0;
}
pair_table = make_pair_table(structure);
X = (float *) space((length+1)*sizeof(float));
Y = (float *) space((length+1)*sizeof(float));
if (rna_plot_type == 0)
i = simple_xy_coordinates(pair_table, X, Y);
else
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=length) fprintf(stderr,"strange things happening in PS_rna_plot...\n");
xmin = xmax = X[0];
ymin = ymax = Y[0];
for (i = 1; i < length; i++) {
xmin = X[i] < xmin ? X[i] : xmin;
xmax = X[i] > xmax ? X[i] : xmax;
ymin = Y[i] < ymin ? Y[i] : ymin;
ymax = Y[i] > ymax ? Y[i] : ymax;
}
size = MAX((xmax-xmin),(ymax-ymin));
fprintf(xyplot,
"%%!PS-Adobe-3.0 EPSF-3.0\n"
"%%%%Creator: %s, ViennaRNA-%s\n"
"%%%%CreationDate: %s"
"%%%%Title: RNA Secondary Structure Plot\n"
"%%%%BoundingBox: 66 210 518 662\n"
"%%%%DocumentFonts: Helvetica\n"
"%%%%Pages: 1\n"
"%%%%EndComments\n\n"
"%%Options: %s\n", rcsid+5, VERSION, time_stamp(), option_string());
fprintf(xyplot, "%% to switch off outline pairs of sequence comment or\n"
"%% delete the appropriate line near the end of the file\n\n");
fprintf(xyplot, "%s", RNAss_head);
if (pre || post) {
fprintf(xyplot, "%s", anote_macros);
}
fprintf(xyplot, "%%%%EndProlog\n");
fprintf(xyplot, "RNAplot begin\n"
"%% data start here\n");
if ((c = strchr(structure, '&'))) {
int cutpoint;
cutpoint = c - structure;
string[cutpoint] = ' '; /* replace & with space */
fprintf(xyplot, "/cutpoint %d def\n", cutpoint);
}
/* sequence */
fprintf(xyplot,"/sequence (\\\n");
i=0;
while (i<length) {
fprintf(xyplot, "%.255s\\\n", string+i); /* no lines longer than 255 */
i+=255;
}
fprintf(xyplot,") def\n");
/* coordinates */
fprintf(xyplot, "/coor [\n");
for (i = 0; i < length; i++)
fprintf(xyplot, "[%3.3f %3.3f]\n", X[i], Y[i]);
fprintf(xyplot, "] def\n");
/* base pairs */
fprintf(xyplot, "/pairs [\n");
for (i = 1; i <= length; i++)
if (pair_table[i]>i)
fprintf(xyplot, "[%d %d]\n", i, pair_table[i]);
fprintf(xyplot, "] def\n\n");
fprintf(xyplot, "init\n\n");
/* draw the data */
if (pre) {
fprintf(xyplot, "%% Start Annotations\n");
fprintf(xyplot, "%s\n", pre);
fprintf(xyplot, "%% End Annotations\n");
}
fprintf(xyplot,
"%% switch off outline pairs or bases by removing these lines\n"
"drawoutline\n"
"drawpairs\n"
"drawbases\n");
if (post) {
fprintf(xyplot, "%% Start Annotations\n");
fprintf(xyplot, "%s\n", post);
fprintf(xyplot, "%% End Annotations\n");
}
fprintf(xyplot, "%% show it\nshowpage\n");
fprintf(xyplot, "end\n");
fprintf(xyplot, "%%%%EOF\n");
fclose(xyplot);
free(pair_table);
free(X); free(Y);
return 1; /* success */
}
int main(int argc, char *argv[])
{
struct RRNAfold_args_info args_info;
/* let's call our cmdline parser */
if (RRNAfold_parser (argc, argv, &args_info) != 0)
exit(1) ;
// for ( unsigned i = 0 ; i < args_info.inputs_num ; ++i )
// printf("%s\n",args_info.inputs[i]) ;
int type = args_info.fold_type_arg;
char *iname = args_info.input_file_arg;
char *oname = args_info.output_file_arg;
double temp = args_info.temperature_arg;
printf("Using temp: %f",temp);
int length,n,i,j;
/* Reads in a file containing(-I) one sequence per line and outputs (-O) a file containing the corresponiding structures
*/
char *let,*seq1, *struct1,* struct2,* xstruc,*ffname;
float *x,*y,e1, e2, tree_dist, string_dist, profile_dist, kT,**pf1, **pf2;
FILE *fi,*fo;
short *pair_table;
/* open the file */
fi = fopen(iname, "r");
fo = fopen(oname, "a");
if (fi == NULL) {printf("I couldn't open results.dat for reading.\n");}
i=0;//Index used to keep track of line in the file
/* Scanning each line in the file and folding the given sequence */
seq1 = (char* ) space(sizeof(char)*(1000+1));
while (fscanf(fi, "%s\n",seq1) == 1){
printf("%s\n",seq1);
length=strlen(seq1);
/* fold at 30C instead of the default 37C */
temperature = temp; /* must be set *before* initializing */
update_fold_params();
/* allocate memory for fold(), could be skipped */
//initialize_fold(strlen(seq1));
/* allocate memory for structure and fold */
struct1 = (char* ) space(sizeof(char)*(length+1));
let = (char* ) space(sizeof(char)*(length+1));
x = (float* ) space(sizeof(float)*(length+1));
y = (float* ) space(sizeof(float)*(length+1));
/* Folding the sequence */
e1 = fold(seq1, struct1);
// fprintf(fo,"%s\n",struct1);
pair_table=make_pair_table(struct1);
if(type==2){
j=simple_xy_coordinates(pair_table,x,y);
}else{
j=naview_xy_coordinates(pair_table,x,y);
}
j=0;
let = seq1;
while(j < (length)){
fprintf(fo,"%d,%f,%f,%c,%d,%d\n",i,x[j],y[j],*let,j,(pair_table[(j+1)]-1));
let++;
j++;
}
/* Makes .ps file of RNA fold */
///////////////////////////////////////////
/*
ffname=(char*) space(sizeof(char)*10);
n=sprintf(ffname, "rna%d.ps",i);
printf("%s\n",ffname);
(void) PS_rna_plot(seq1, struct1, ffname);
*/
///////////////////////////////////////////
free_arrays(); /* free arrays used in fold() */
i++;
} /* close the file */
fclose(fi);
fclose(fo);
}
