/*---------------------------------------------------------------------------*/
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 */
}
void RNAFuncs::generateRNAAlignmentXML(const string &structure, const string &altStructure, const string &seq1, const string &seq2, const string &strname1, const string &strname2, ostream &s)
{
string base;
Uint i;
float *X, *Y;
short *pair_table,*alt_pair_table;
Uint basenr_x=1, basenr_y=1;
string filename;
X = new float[structure.size()];
Y = new float[structure.size()];
assert(seq1.size() == seq2.size());
assert(seq1.size() == structure.size());
assert(seq1.size() == altStructure.size());
// calculate coordinates
pair_table = make_pair_table(structure.c_str());
alt_pair_table = make_pair_table(altStructure.c_str());
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=structure.size())
cerr << "strange things happening in squigglePlot ..." << endl;
// generate XML
s << "<alignment xname=\"" << strname1 << "\" yname=\"" << strname2 << "\">" << endl;
// seqalignment
s << " <seqalignment>" << endl;
for(i=0;i<seq1.length();i++)
{
s << " <base id=\"" << i+1 << "\" xbasenr=\"" << basenr_x << "\" ybasenr=\"" << basenr_y << "\" xbase=\"" << seq1[i] <<"\" ybase=\"" << seq2[i] << "\" />" << endl;
if(seq1[i]!='-')
basenr_x++;
if(seq2[i]!='-')
basenr_y++;
}
s << " </seqalignment>" << endl;
// pairs
s << " <pairs>" << endl;
for(i=0;i<structure.size();i++)
{
// both
if((unsigned short)pair_table[i+1]>i+1 && (unsigned short)alt_pair_table[i+1]>i+1)
{
s << " <pair drawbaseid1=\"" << i+1 << "\" drawbaseid2=\"" << pair_table[i+1] << "\"/>" << endl;
}
else
{
if((unsigned short)pair_table[i+1]>i+1)
{
s << " <pair drawbaseid1=\"" << i+1 << "\" drawbaseid2=\"" << pair_table[i+1] << "\" structid=\"1\"/>" << endl;
}
else
{
if((unsigned short)alt_pair_table[i+1]>i+1)
s << " <pair drawbaseid1=\"" << i+1 << "\" drawbaseid2=\"" << alt_pair_table[i+1] << "\" structid=\"2\"/>" << endl;
}
}
}
s << " </pairs>" << endl;
// coordinates
// x structure
s << " <structure id=\"1\">" << endl;
s << " <drawbases>" << endl;
for(i=0;i<seq1.length();i++)
{
s << " <drawbase id=\"" << i+1 << "\" xcoor=\"" << X[i] << "\" ycoor=\"" << -Y[i] << "\"/>" << endl;
}
s << " </drawbases>" << endl;
s << " </structure>" << endl;
DELETE(X);
DELETE(Y);
X = new float[altStructure.size()];
Y = new float[altStructure.size()];
// y structure
i = naview_xy_coordinates(alt_pair_table, X, Y);
if(i!=structure.size())
cerr << "strange things happening in squigglePlot ..." << endl;
s << " <structure id=\"2\">" << endl;
s << " <drawbases>" << endl;
for(i=0;i<seq1.length();i++)
{
s << " <drawbase id=\"" << i+1 << "\" xcoor=\"" << X[i] << "\" ycoor=\"" << -Y[i] << "\"/>" << endl;
}
s << " </drawbases>" << endl;
s << " </structure>" << endl;
s << "</alignment>" << endl;
free(pair_table);
free(alt_pair_table);
DELETE(X);
DELETE(Y);
}
void RNAFuncs::drawRNAAlignment(const string &structure, const string &altStructure, const string &seq1, const string &seq2, const string &strname1, const string &strname2, const string &filename_prefix, const bool atX, const SquigglePlotOptions &options)
{
const double base_fontsize=12;
string base,structname;
float *X, *Y,min_X=0,max_X=0,min_Y=0,max_Y=0;
Uint i;
short *pair_table,*alt_pair_table;
int id_PS,id;
int ps_color_black,ps_color_red,ps_color_blue,ps_color_green;
Uint basenr_x=0, basenr_y=0;
double xpos,ypos;
char buf[10];
bool isDel,isIns;
string filename;
#ifdef HAVE_LIBGD
int id_PNG=0,id_JPG=0;
int png_color_black,png_color_red,png_color_blue,png_color_green;
int jpg_color_black,jpg_color_red,jpg_color_blue,jpg_color_green;
#endif
X = new float[structure.size()];
Y = new float[structure.size()];
assert(seq1.size() == seq2.size());
assert(seq1.size() == structure.size());
assert(seq1.size() == altStructure.size());
pair_table = make_pair_table(structure.c_str());
alt_pair_table = make_pair_table(altStructure.c_str());
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=structure.size())
cerr << "strange things happening in squigglePlot ..." << endl;
// scale image
for(i=0;i<structure.size();i++)
{
X[i]*=static_cast<float>(options.scale);
Y[i]*=static_cast<float>(options.scale);
}
// calculate image dimensions
for(i=0;i<structure.size();i++)
{
min_X=min(min_X,X[i]);
max_X=max(max_X,X[i]);
min_Y=min(min_Y,Y[i]);
max_Y=max(max_Y,Y[i]);
}
// add a border to image size
min_X-=10;
max_X+=10;
min_Y-=10;
max_Y+=10;
//id_PS = g2_open_PS("ali.ps", g2_A4, g2_PS_port);
filename=filename_prefix + ".ps";
id_PS = g2_open_EPSF((char*)filename.c_str());
g2_set_coordinate_system(id_PS,-min_X,-min_Y,1,1);
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
filename=filename_prefix + ".png";
id_PNG=g2_open_gd((char*)filename.c_str(),(int)(max_X-min_X),(int)(max_Y-min_Y),g2_gd_png);
g2_set_coordinate_system(id_PNG,-min_X,-min_Y,1,1);
}
if(options.generateJPG)
{
filename=filename_prefix + ".jpg";
id_JPG=g2_open_gd((char*)filename.c_str(),(int)(max_X-min_X),(int)(max_Y-min_Y),g2_gd_jpeg);
g2_set_coordinate_system(id_PS,-min_X,-min_Y,1,1);
}
#endif
id = g2_open_vd();
g2_attach(id,id_PS);
#ifdef HAVE_LIBGD
if(options.generatePNG)
g2_attach(id,id_PNG);
if(options.generateJPG)
g2_attach(id,id_JPG);
#endif
// cout << "min_X: " << min_X <<",max_X: " << max_X << ",min_Y: " << min_Y << "max_Y: " << max_Y << endl;
// g2_set_coordinate_system(id_PS,595/2.0,842/2.0,0.5,0.5);
g2_set_line_width(id,0.2);
// mark 5' end
g2_string(id,X[0]-20,Y[0],"5'");
// define colors
if(options.greyColors)
{
ps_color_black=g2_ink(id_PS,0,0,0);
ps_color_red=g2_ink(id_PS,0,0,0);
ps_color_blue=g2_ink(id_PS,0.7,0.7,0.7);
ps_color_green=g2_ink(id_PS,0.4,0.4,0.4);
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
png_color_black=g2_ink(id_PNG,0,0,0);
png_color_red=g2_ink(id_PNG,0,0,0);
png_color_blue=g2_ink(id_PNG,0.7,0.7,0.7);
png_color_green=g2_ink(id_PNG,0.4,0.4,0.4);
}
if(options.generateJPG)
{
jpg_color_black=g2_ink(id_JPG,0,0,0);
jpg_color_red=g2_ink(id_JPG,0,0,0);
jpg_color_blue=g2_ink(id_JPG,0.7,0.7,0.7);
jpg_color_green=g2_ink(id_JPG,0.4,0.4,0.4);
}
#endif
}
else
{
ps_color_black=g2_ink(id_PS,0,0,0);
ps_color_red=g2_ink(id_PS,1,0,0);
ps_color_blue=g2_ink(id_PS,0,0,0.5);
ps_color_green=g2_ink(id_PS,0,0.5,0);
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
png_color_black=g2_ink(id_PNG,0,0,0);
png_color_red=g2_ink(id_PNG,1,0,0);
png_color_blue=g2_ink(id_PNG,0,0,0.5);
png_color_green=g2_ink(id_PNG,0,0.5,0);
}
if(options.generateJPG)
{
jpg_color_black=g2_ink(id_JPG,0,0,0);
jpg_color_red=g2_ink(id_JPG,1,0,0);
jpg_color_blue=g2_ink(id_JPG,0,0,0.5);
jpg_color_green=g2_ink(id_JPG,0,0.5,0);
}
#endif
}
// draw sequence
g2_set_font_size(id,base_fontsize*options.scale);
for(i=0;i<structure.size();i++)
{
isDel = false;
isIns = false;
//base
g2_pen(id,ps_color_black); // match
base = "";
if(seq1[i]!='-')
{
base += seq1[i];
basenr_x++;
}
else
{
g2_pen(id,ps_color_green); // insertion
isIns=true;
}
if(seq2[i]!='-')
{
base += seq2[i];
basenr_y++;
}
else
{
g2_pen(id,ps_color_blue); // deletion
isDel=true;
}
if(base.size()==2 && base[0]!=base[1])
g2_pen(id,ps_color_red); // mismatch
else
base = base[0]; // show duplicate base only once
xpos=X[i]-base.length()*(base_fontsize*options.scale)/2;
ypos=Y[i]-4;
g2_string(id,xpos,ypos,(char*)base.c_str());
if(!options.hideBaseNumbers)
{
// draw base number
if(!isIns && basenr_x % options.baseNumInterval == 0)
{
g2_pen(id,ps_color_blue);
sprintf(buf,"%d",basenr_x);
g2_string(id,xpos-20,ypos,buf);
}
if(!isDel && basenr_y % options.baseNumInterval == 0)
{
g2_pen(id,ps_color_green);
sprintf(buf,"%d",basenr_y);
g2_string(id,xpos+20,ypos,buf);
}
}
// connection to next base
if(i<structure.size()-1)
{
// if the connected bases are only in one of the structures
// use the appropriate color
if(seq1[i]=='-' && seq1[i+1]=='-')
g2_pen(id,ps_color_green);
else
if(seq2[i]=='-' && seq2[i+1]=='-')
g2_pen(id,ps_color_blue);
else
g2_pen(id,ps_color_black);
g2_line(id,X[i],Y[i],X[i+1],Y[i+1]);
// draw circles at line endpoints
if(seq1[i]=='-')
g2_pen(id,ps_color_green);
else
if(seq2[i]=='-')
g2_pen(id,ps_color_blue);
else
g2_pen(id,ps_color_black);
g2_filled_circle(id,X[i],Y[i],0.7*options.scale); // circles are drawn twice, but thats ok ...
if(seq1[i+1]=='-')
g2_pen(id,ps_color_green);
else
if(seq2[i+1]=='-')
g2_pen(id,ps_color_blue);
else
g2_pen(id,ps_color_black);
g2_filled_circle(id,X[i+1],Y[i+1],0.7*options.scale);
}
}
// draw pairings
// !!! pair_table indexing begins at 1 !!!
for(i=0;i<structure.size();i++)
{
if((unsigned short)pair_table[i+1]>i+1 && (unsigned short)alt_pair_table[i+1]>i+1)
{
// pairs in both structures
g2_pen(id,ps_color_black);
g2_line(id,X[i],Y[i],X[pair_table[i+1]-1],Y[pair_table[i+1]-1]);
}
else
{
if((unsigned short)pair_table[i+1]>i+1 && (unsigned short)alt_pair_table[i+1]<=i+1)
{
// pairs only in first structure
if(atX)
g2_pen(id,ps_color_blue);
else
g2_pen(id,ps_color_green);
g2_line(id,X[i],Y[i],X[pair_table[i+1]-1],Y[pair_table[i+1]-1]);
}
else
{
if((unsigned short)pair_table[i+1]<=i+1 && (unsigned short)alt_pair_table[i+1]>i+1)
{
// pairs only in second structure
if(atX)
g2_pen(id,ps_color_green);
else
g2_pen(id,ps_color_blue);
double dashes=2.0;
g2_set_dash(id,1,&dashes);
g2_line(id,X[i],Y[i],X[alt_pair_table[i+1]-1],Y[alt_pair_table[i+1]-1]);
dashes=0;
g2_set_dash(id,1,&dashes);
}
}
}
}
// draw structure names
// x-at-y or y-at-x
if(atX)
{
g2_pen(id,ps_color_green);
g2_string(id,min_X,max_Y-10,(char*)strname2.c_str());
g2_pen(id,ps_color_black);
g2_string(id,min_X,max_Y-20,"at");
g2_pen(id,ps_color_blue);
g2_string(id,min_X,max_Y-30,(char*)strname1.c_str());
}
else
{
g2_pen(id,ps_color_blue);
g2_string(id,min_X,max_Y-10,(char*)strname1.c_str());
g2_pen(id,ps_color_black);
g2_string(id,min_X,max_Y-20,"at");
g2_pen(id,ps_color_green);
g2_string(id,min_X,max_Y-30,(char*)strname2.c_str());
}
g2_flush(id);
g2_close(id);
free(pair_table);
free(alt_pair_table);
DELETE(X);
DELETE(Y);
}
void RNAFuncs::drawRNAStructure(const string &seq, const string &structure, const string &filename_prefix, const string &structname, const list<pair<Uint,Uint> > ®ions, const SquigglePlotOptions &options)
{
const double base_fontsize=12;
float *X, *Y,min_X=0,max_X=0,min_Y=0,max_Y=0;
Uint i;
short *pair_table;
int id_PS,id_FIG=0,id;
int color_black, *colors;
double xpos,ypos;
char buf[10];
string filename;
double *points;
int numPoints;
#ifdef HAVE_LIBGD
int id_PNG=0,id_JPG=0;
#endif
X = new float[structure.size()];
Y = new float[structure.size()];
points=new double[2*structure.size()];
colors=new int[NUM_COLORS];
assert(seq.size() == structure.size());
pair_table = make_pair_table(structure.c_str());
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=structure.size())
cerr << "strange things happening in squigglePlot ..." << endl;
// scale image
for(i=0;i<structure.size();i++)
{
X[i]*=static_cast<float>(options.scale);
Y[i]*=static_cast<float>(options.scale);
}
// calculate image dimensions
for(i=0;i<structure.size();i++)
{
min_X=min(min_X,X[i]);
max_X=max(max_X,X[i]);
min_Y=min(min_Y,Y[i]);
max_Y=max(max_Y,Y[i]);
}
// add a border to image size
min_X-=10;
max_X+=10;
min_Y-=10;
max_Y+=10;
//id_PS = g2_open_PS("ali.ps", g2_A4, g2_PS_port);
filename=filename_prefix + ".ps";
id_PS = g2_open_EPSF((char*)filename.c_str());
g2_set_coordinate_system(id_PS,-min_X,-min_Y,1,1);
if(options.generateFIG)
{
filename=filename_prefix + ".fig";
id_FIG=g2_open_FIG((char*)filename.c_str());
g2_set_coordinate_system(id_FIG,-min_X,-min_Y,1,1);
}
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
filename=filename_prefix + ".png";
id_PNG=g2_open_gd((char*)filename.c_str(),(int)(max_X-min_X),(int)(max_Y-min_Y),g2_gd_png);
g2_set_coordinate_system(id_PNG,-min_X,-min_Y,1,1);
}
if(options.generateJPG)
{
filename=filename_prefix + ".jpg";
id_JPG=g2_open_gd((char*)filename.c_str(),(int)(max_X-min_X),(int)(max_Y-min_Y),g2_gd_jpeg);
g2_set_coordinate_system(id_PS,-min_X,-min_Y,1,1);
}
#endif
id = g2_open_vd();
g2_attach(id,id_PS);
if(options.generateFIG)
{
g2_attach(id,id_FIG);
}
#ifdef HAVE_LIBGD
if(options.generatePNG)
g2_attach(id,id_PNG);
if(options.generateJPG)
g2_attach(id,id_JPG);
#endif
// cout << "min_X: " << min_X <<",max_X: " << max_X << ",min_Y: " << min_Y << "max_Y: " << max_Y << endl;
// g2_set_coordinate_system(id_PS,595/2.0,842/2.0,0.5,0.5);
// define colors
if(options.greyColors)
{
color_black=g2_ink(id_PS,0,0,0);
for(i=0;i<NUM_COLORS;i++)
colors[i]=g2_ink(id_PS,0,0,0);
if(options.generateFIG)
{
color_black=g2_ink(id_FIG,0,0,0);
for(i=0;i<NUM_COLORS;i++)
colors[i]=g2_ink(id_FIG,0,0,0);
}
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
color_black=g2_ink(id_PNG,0,0,0);
for(i=0;i<NUM_COLORS;i++)
colors[i]=g2_ink(id_PNG,0,0,0);
}
if(options.generateJPG)
{
color_black=g2_ink(id_JPG,0,0,0);
for(i=0;i<NUM_COLORS;i++)
colors[i]=g2_ink(id_JPG,0,0,0);
}
#endif
}
else
{
color_black=g2_ink(id,0,0,0);
colors[COLOR_RED]=g2_ink(id_PS,COLOR_DEF_RED);
colors[COLOR_GREEN]=g2_ink(id_PS,COLOR_DEF_GREEN);
colors[COLOR_BLUE]=g2_ink(id_PS,COLOR_DEF_BLUE);
colors[COLOR_YELLOW]=g2_ink(id_PS,COLOR_DEF_YELLOW);
colors[COLOR_MAGENTA]=g2_ink(id_PS,COLOR_DEF_MAGENTA);
colors[COLOR_TURKIS]=g2_ink(id_PS,COLOR_DEF_TURKIS);
if(options.generateFIG)
{
color_black=g2_ink(id_FIG,0,0,0);
colors[COLOR_RED]=g2_ink(id_FIG,COLOR_DEF_RED);
colors[COLOR_GREEN]=g2_ink(id_FIG,COLOR_DEF_GREEN);
colors[COLOR_BLUE]=g2_ink(id_FIG,COLOR_DEF_BLUE);
colors[COLOR_YELLOW]=g2_ink(id_FIG,COLOR_DEF_YELLOW);
colors[COLOR_MAGENTA]=g2_ink(id_FIG,COLOR_DEF_MAGENTA);
colors[COLOR_TURKIS]=g2_ink(id_FIG,COLOR_DEF_TURKIS);
}
#ifdef HAVE_LIBGD
if(options.generatePNG)
{
color_black=g2_ink(id_PNG,0,0,0);
colors[COLOR_RED]=g2_ink(id_PNG,COLOR_DEF_RED);
colors[COLOR_GREEN]=g2_ink(id_PNG,COLOR_DEF_GREEN);
colors[COLOR_BLUE]=g2_ink(id_PNG,COLOR_DEF_BLUE);
colors[COLOR_YELLOW]=g2_ink(id_PNG,COLOR_DEF_YELLOW);
colors[COLOR_MAGENTA]=g2_ink(id_PNG,COLOR_DEF_MAGENTA);
colors[COLOR_TURKIS]=g2_ink(id_PNG,COLOR_DEF_TURKIS);
}
if(options.generateJPG)
{
color_black=g2_ink(id_JPG,0,0,0);
colors[COLOR_RED]=g2_ink(id_JPG,COLOR_DEF_RED);
colors[COLOR_GREEN]=g2_ink(id_JPG,COLOR_DEF_GREEN);
colors[COLOR_BLUE]=g2_ink(id_JPG,COLOR_DEF_BLUE);
colors[COLOR_YELLOW]=g2_ink(id_JPG,COLOR_DEF_YELLOW);
colors[COLOR_MAGENTA]=g2_ink(id_JPG,COLOR_DEF_MAGENTA);
colors[COLOR_TURKIS]=g2_ink(id_JPG,COLOR_DEF_TURKIS);
}
#endif
}
for(i=0;i<structure.size();i++)
{
// connection to next base
if(i<structure.size()-1)
{
// if the connected bases are only in one of the structures
// use the appropriate color
g2_line(id,X[i],Y[i],X[i+1],Y[i+1]);
// draw circles at line endpoints
g2_filled_circle(id,X[i],Y[i],0.7*options.scale); // circles are drawn twice, but thats ok ...
}
}
// draw pairings
// !!! pair_table indexing begins at 1 !!!
for(i=0;i<structure.size();i++)
{
if((unsigned short)pair_table[i+1]>i+1)
{
// pairs in both structures
g2_line(id,X[i],Y[i],X[pair_table[i+1]-1],Y[pair_table[i+1]-1]);
}
}
// draw regions
g2_set_line_width(id,0.4);
list<pair<Uint,Uint> >::const_iterator it;
Uint regionNr=0;
for(it=regions.begin();it!=regions.end();it++)
{
double center_x=0,center_y=0;
// fill coordinate list
for(i=0;i < it->second;i++)
{
points[2*i]=X[it->first+i];
points[2*i+1]=Y[it->first+i];
center_x+=X[it->first+i];
center_y+=Y[it->first+i];
}
numPoints=it->second-1;
center_x/=numPoints; // center of gravity
center_y/=numPoints;
g2_pen(id,colors[regionNr % NUM_COLORS]);
g2_poly_line(id,numPoints,points);
sprintf(buf,"%d",regionNr+1);
g2_string(id,center_x,center_y,buf); // draw region number
regionNr++;
}
// mark 5' end
g2_pen(id,color_black);
g2_string(id,X[0]-20,Y[0],"5'");
g2_set_font_size(id,base_fontsize*options.scale);
g2_set_line_width(id,0.2);
// draw sequence
for(i=0;i<structure.size();i++)
{
g2_pen(id,color_black); // match
xpos=X[i]-(base_fontsize*options.scale)/2;
ypos=Y[i]-4;
sprintf(buf,"%c",seq[i]);
g2_string(id,xpos,ypos,buf);
/*
if(!options.hideBaseNumbers)
{
// draw base number
if(basenr % options.baseNumInterval == 0)
{
sprintf(buf,"%d",basenr);
g2_string(id,xpos-20,ypos,buf);
}
}*/
}
// draw structure name
g2_string(id,min_X,max_Y-10,(char*)structname.c_str());
g2_flush(id);
g2_close(id);
free(pair_table);
DELETE(X);
DELETE(Y);
DELETE(points);
DELETE(colors);
}
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);
}
void RNAProfileAlignment::squigglePlot(const string &filename, SquigglePlotOptions &options) const
{
const double base_fontsize=8;
const Uint num_grey_colors=100;
const double min_grey_color=1.0;
string seq,structure;
string base,structname;
float *X,*Y,min_X=0,max_X=0,min_Y=0,max_Y=0;
Uint i;
short *pair_table;
int id_PS,id;
int ps_grey_colors[num_grey_colors];
int ps_color_red;
int ps_color_black;
double xpos,ypos;
deque<double> pairprob;
deque<BaseProbs> baseprobs;
getStructureAlignment(options.minPairProb,structure,pairprob);
getSequenceAlignment(baseprobs);
// filterConsensus(structure,pairprob,baseprobs,0.5);
//assert(baseprobs.size() == structure.size());
if(baseprobs.size() != structure.size())
cerr << "Error in resolving consensus structure!" << endl;
X = new float[structure.size()];
Y = new float[structure.size()];
pair_table = make_pair_table(structure.c_str());
i = naview_xy_coordinates(pair_table, X, Y);
if(i!=structure.size())
cerr << "strange things happening in squigglePlot ..." << endl;
// calculate image dimesions
for(i=0;i<structure.size();i++)
{
min_X=min(min_X,X[i]);
max_X=max(max_X,X[i]);
min_Y=min(min_Y,Y[i]);
max_Y=max(max_Y,Y[i]);
}
// id_PS = g2_open_PS("ali.ps", g2_A4, g2_PS_port);
id_PS = g2_open_EPSF((char*)filename.c_str());
id = g2_open_vd();
g2_attach(id,id_PS);
// cout << "min_X: " << min_X <<",max_X: " << max_X << ",min_Y: " << min_Y << "max_Y: " << max_Y << endl;
g2_set_coordinate_system(id_PS,595/2.0,842/2.0,0.5,0.5);
g2_set_line_width(id,0.2);
// set colors
double intv=min_grey_color/(double)num_grey_colors;
for(i=0;i<num_grey_colors;i++)
{
double grey_color=min_grey_color-i*intv;
ps_grey_colors[i]=g2_ink(id_PS,grey_color,grey_color,grey_color);
}
ps_color_black=g2_ink(id_PS,0,0,0);
if(options.greyColors)
ps_color_red=g2_ink(id_PS,0,0,0);
else
ps_color_red=g2_ink(id_PS,1,0,0);
// draw sequence
g2_set_font_size(id,base_fontsize);
for(i=0;i<structure.size();i++)
{
if(options.mostLikelySequence)
{
double p=getMlBaseFreq(baseprobs[i]);
//base color
if(p==1)
g2_pen(id,ps_color_red);
else
g2_pen(id,ps_grey_colors[(int)floor(p*num_grey_colors-1)]);
base=getMlBase(baseprobs[i]);
xpos=X[i]-base.length()*base_fontsize/2.0;
ypos=Y[i]-4;
g2_string(id,xpos,ypos,(char*)base.c_str());
}
else
{
drawBaseCircles(id_PS,baseprobs[i],X[i],Y[i]);
}
// connection to next base
if(i<structure.size()-1)
{
if((1-baseprobs[i].gap)*(1-baseprobs[i+1].gap)==1)
g2_pen(id,ps_color_red);
else
g2_pen(id,ps_grey_colors[(int)floor((1-baseprobs[i].gap)*(1-baseprobs[i+1].gap)*num_grey_colors-1)]);
g2_line(id,X[i],Y[i],X[i+1],Y[i+1]);
}
}
// draw pairings
// !!! pair_table indexing begins at 1 !!!
for(i=0;i<structure.size();i++)
{
if((unsigned short)pair_table[i+1]>i+1)
{
// pairs in both structures
if(pairprob[i]==1)
g2_pen(id,ps_color_red);
else
g2_pen(id,ps_grey_colors[(int)floor(pairprob[i]*num_grey_colors-1)]);
g2_line(id,X[i],Y[i],X[pair_table[i+1]-1],Y[pair_table[i+1]-1]);
}
}
g2_flush(id);
g2_close(id);
free(pair_table);
DELETE(X);
DELETE(Y);
}
