int main()
{
int d;
int x[N];
int y[N];
int c[N];
int i,t;
d=g2_open_win32(W, H, "simple_animation", 0);
g2_set_auto_flush(d,0);
for (i=0;i<N;i++)
{
x[i] = rand()%(W/4)+H/2;
y[i] = rand()%(H/4)+W/2;
c[i] = rand()%16;
}
for (t=0; t<1000; t++)
{
g2_clear(d);
for (i=0; i<N; i++)
{
g2_filled_circle(d,(double)x[i],(double)y[i],(double)5);
g2_pen(d,c[i]);
x[i] += (rand()%2) * 2 - 1;
y[i] += (rand()%2) * 2 - 1;
}
g2_flush(d);
}
getchar();
return 0;
}
/**
*
* Set pen color for all following operations, see also g2_ink().
*
* \param dev device
* \param color pen (either one of default pens 0-26, or a pen returned by g2_ink() )
*
* \ingroup color
*/
void g2_pen(int dev, int color)
{
g2_device *devp;
int i;
if((devp=g2_get_device_pointer(dev))==NULL) {
fprintf(stderr, "g2_pen: No such device: %d\n", dev);
return;
}
switch(devp->t) {
case g2_PD:
g2_pen_pd(devp->d.pd, color);
break;
case g2_VD:
for(i=0;i<devp->d.vd->N;i++)
g2_pen(devp->d.vd->dix[i], color);
break;
case g2_ILLEGAL:
break;
case g2_NDEV:
break;
}
__g2_last_device=dev;
}
/*
*
* Attach PS device
*
*/
int g2_open_PS(const char *file_name,
enum g2_PS_paper paper,
enum g2_PS_orientation orientation)
{
g2_PS_device *psout=NULL;
int pid=-1, i;
int vid;
FILE *fp;
if((fp=fopen(file_name, "w"))==NULL) {
fprintf(stderr, "g2_attach_PS: Error! Can not open file '%s'\n",
file_name);
return -1;
}
if(g2_PS_dev==NULL) {
g2_PS_dev=g2_malloc(sizeof(g2_PS_device));
N_PS=1; /* first PS device */
psout=&g2_PS_dev[N_PS-1];
pid=0;
} else {
for(i=0; i<N_PS; i++) /* find free place */
if(g2_PS_dev[i].fp==NULL) {
psout=&g2_PS_dev[i];
pid=i;
break;
}
if(i==N_PS) { /* free place not avail. */
N_PS++;
g2_PS_dev=g2_realloc(g2_PS_dev,
sizeof(g2_PS_device)*N_PS);
psout=&g2_PS_dev[N_PS-1];
pid=N_PS-1;
}
}
vid = g2_register_physical_device(pid, NULL,
g2_DoubleCoor, g2_PS_funix,
1.0, 1.0,
0.0, 0.0);
psout->fp=fp; /* init PostScript structures */
psout->paper=paper;
psout->orient=orientation;
psout->inks=NULL;
psout->N_ink=0;
psout->pen=0;
psout->page_counter=0;
g2_PS_write_file_header(psout);
g2_PS_set_line_width(pid, NULL, 0.0);
g2_PS_set_font_size(pid, NULL, 12.0);
/* g2 settings */
g2_allocate_basic_colors(vid);
g2_pen(vid, 1);
return vid;
}
void RNAProfileAlignment::drawBaseCircles(int device_id,const BaseProbs &bp,double center_x,double center_y) const
{
const double box_size=6.0;
const double max_radius=3.0;
double xpos,ypos;
int color;
// double dashes=0.5;
// draw the base probabilities as circles on the edges of the square and the gap probability
// as the center square
// upper left corner = a
xpos=center_x-box_size/2.0;
ypos=center_y+box_size/2.0;
color=g2_ink(device_id,1,0,0);
g2_pen(device_id,color);
g2_filled_circle(device_id,xpos,ypos,max_radius*bp.a);
// upper right corner = c
xpos=center_x+box_size/2.0;
ypos=center_y+box_size/2.0;
color=g2_ink(device_id,0,1,0);
g2_pen(device_id,color);
g2_filled_circle(device_id,xpos,ypos,max_radius*bp.c);
// lower right corner = g
xpos=center_x+box_size/2.0;
ypos=center_y-box_size/2.0;
color=g2_ink(device_id,0,0,1);
g2_pen(device_id,color);
g2_filled_circle(device_id,xpos,ypos,max_radius*bp.g);
// lower right corner = u
xpos=center_x-box_size/2.0;
ypos=center_y-box_size/2.0;
color=g2_ink(device_id,1,0,1);
g2_pen(device_id,color);
g2_filled_circle(device_id,xpos,ypos,max_radius*bp.u);
// gap in the center
color=g2_ink(device_id,0,0,0);
g2_pen(device_id,color);
g2_filled_circle(device_id,center_x,center_y,max_radius*bp.gap);
// draw rectangle for orientation
//g2_set_dash(device_id,1,&dashes);
color=g2_ink(device_id,0.75,0.75,0.75);
g2_pen(device_id,color);
g2_rectangle(device_id,center_x-box_size/2,center_y-box_size/2,center_x+box_size/2,center_y+box_size/2);
}
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);
}
void FIF(g2_pen)(F_REAL *dev, F_REAL *color)
{
g2_pen(dtoi(*dev), dtoi(*color));
}
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);
}
