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);
}
int main()
{
struct main_data data;
struct point *tail = 0;
struct point *start = 0;
pthread_t t_cockpit = 0, t_fisica = 0, t_graph = 0;
data.option = -1;
data.pdev = -1;
data.vdev = -1;
data.font_size = 16;
data.label_value_dist = 10; /*Define Some variables from main_data*/
data.window_h = 600;
data.window_w = 800;
data.tempo = 0;
data.radius = 5;
data.force_t = 0;
data.force_r = 0;
data.terminate_cp = 0;
while(1) /* Main Loop */
{
printf("\033[2J");
printf("\n");
printf(" 1. Especificação dos dados do módulo e das condições iniciais do voo (Unidades S.I.).\n");
printf(" 2. Simulação do voo em modo de \"cockpit\".\n");
printf(" 3. Apresentação em modo gráfico da trajectória do módulo.\n");
printf(" 4. Definição do perfil da superfície lunar.\n");
printf(" 5. Simulação do voo em modo gráfico.\n");
printf(" 0. Terminar Programa\n");
printf("\n");
printf(" Escolha uma opção: ");
if((scanf("%d", &data.option)) < 1){
printf("Opção Invalida\n");
__fpurge(stdin);
}
switch(data.option)
{
case 1 :
spec_input(&data);
data.option = -1;
break;
case 2 :
if(data.vdev == -1 || data.pdev == -1)
{
data.pdev = g2_open_X11(data.window_w, data.window_h);
data.vdev = g2_open_vd();
g2_attach(data.vdev, data.pdev);
strcpy(data.landing_status,"Ready");
}
pthread_join(t_cockpit, NULL);
pthread_join(t_fisica, NULL);
pthread_join(t_graph, NULL);
pthread_create(&t_cockpit, NULL, &cockpit_display, &data);
pthread_create(&t_fisica, NULL, &fisica, &data);
data.option = -1;
break;
case 3 :
data.terminate_cp = 1;
pthread_join(t_cockpit, NULL);
pthread_join(t_fisica, NULL);
pthread_join(t_graph, NULL);
data.terminate_cp = 0;
pthread_create(&t_graph, NULL, &pos_graph, &data);
data.option = -1;
break;
case 4 :
pthread_join(t_cockpit, NULL);
pthread_join(t_fisica, NULL);
pthread_join(t_graph, NULL);
surface_setup(start, tail);
break;
case 5 :
printf("\nList Points\n");
break;
case 0 :
g2_detach(data.vdev, data.pdev);
g2_close(data.pdev);
exit(0);
default :
if(data.vdev != -1 || data.pdev != -1)
data.pdev = -1; data.vdev = -1;
break;
}
usleep(100000);
}
return 0;
}
int main()
{
int i, j;
int d, dev[maxdev]={-1, -1, -1, -1, -1,-1, -1, -1, -1, -1};
int ndev=0;
char str[256];
double y;
printf("\nG2_VERSION %s\n", G2_VERSION);
d=g2_open_vd(); /* open virtual device */
printf("Adding..");
#ifdef DO_PS
printf("..PS");
dev[ndev]=g2_open_PS("g2_arc.ps", g2_A4, g2_PS_land);
g2_attach(d, dev[ndev]);
ndev++;
printf("..EPSF");
dev[ndev]=g2_open_EPSF("g2_arc.eps");
g2_attach(d, dev[ndev]);
ndev++;
printf("..EPSF_CLIP");
dev[ndev]=g2_open_EPSF_CLIP("g2_arc_clip.eps",400,400);
g2_attach(d, dev[ndev]);
ndev++;
#endif
#ifdef DO_FIG
printf("..FIG");
dev[ndev]=g2_open_FIG("g2_arc.fig");
g2_attach(d, dev[ndev]);
ndev++;
#endif
#ifdef DO_X11
printf("..X11");
dev[ndev]=g2_open_X11(400,400);
g2_attach(d, dev[ndev]);
ndev++;
#endif
#ifdef DO_GD
printf("..GD(png)");
dev[ndev]=g2_open_gd("g2_arc.png", 400, 400,g2_gd_png);
g2_attach(d, dev[ndev]);
ndev++;
printf("..GD(jpeg)");
dev[ndev]=g2_open_gd("g2_arc.jpg", 400, 400,g2_gd_jpeg);
g2_attach(d, dev[ndev]);
ndev++;
#endif
#ifdef DO_WIN32
printf("..WIN32");
dev[ndev]=g2_open_win32(400, 400,"g2_arc",0);
g2_attach(d, dev[ndev]);
ndev++;
#endif
#ifdef DO_WMF32
printf("..WMF32");
dev[ndev]=g2_open_win32(775, 575,"g2_arc.emf",1);
g2_attach(d, dev[ndev]);
ndev++;
#endif
g2_set_auto_flush(d,0);
printf("\n");
g2_string(d,10, 50,"90,90");
g2_string(d,10,100,"90,360");
g2_string(d,10,150,"90,0");
g2_string(d,10,200,"360,90");
g2_string(d,10,250,"-45,45");
g2_string(d,10,300,"-45,-315");
g2_string(d,10,350,"-495,-405");
g2_arc(d, 100, 50, 45, 25, 90, 90);
g2_arc(d, 100, 100, 45, 25, 90, 360);
g2_arc(d, 100, 150, 45, 25, 90, 0);
g2_arc(d, 100, 200, 45, 25, 360, 90);
g2_arc(d, 100, 250, 45, 25, -45, 45);
g2_arc(d, 100, 300, 45, 25, -45, -315);
g2_arc(d, 100, 350, 45, 25, -495, -405);
g2_filled_arc(d, 100, 50, 40, 20, 90, 90);
g2_filled_arc(d, 100, 100, 40, 20, 90, 360);
g2_filled_arc(d, 100, 150, 40, 20, 90, 0);
g2_filled_arc(d, 100, 200, 40, 20, 360, 90);
g2_filled_arc(d, 100, 250, 40, 20, -45, 45);
g2_filled_arc(d, 100, 300, 40, 20, -45, -315);
g2_filled_arc(d, 100, 350, 40, 20, -495, -405);
g2_string(d,320, 50,"0,0");
g2_string(d,320,100,"360,90");
g2_string(d,320,150,"0,90");
g2_string(d,320,200,"90,360");
g2_string(d,320,250,"45,-45");
g2_string(d,320,300,"-315,-45");
g2_string(d,320,350,"-405,-495");
g2_arc(d, 250, 50, 45, 25, 0, 0);
g2_arc(d, 250, 100, 45, 25, 360, 90);
g2_arc(d, 250, 150, 45, 25, 0, 90);
g2_arc(d, 250, 200, 45, 25, 90, 360);
g2_arc(d, 250, 250, 45, 25, 45, -45);
g2_arc(d, 250, 300, 45, 25, -315, -45);
g2_arc(d, 250, 350, 45, 25, -405, -495);
g2_filled_arc(d, 250, 50, 40, 20, 90, 90);
g2_filled_arc(d, 250, 100, 40, 20, 360, 90);
g2_filled_arc(d, 250, 150, 40, 20, 0, 90);
g2_filled_arc(d, 250, 200, 40, 20, 90, 360);
g2_filled_arc(d, 250, 250, 40, 20, 45, -45);
g2_filled_arc(d, 250, 300, 40, 20, -315, -45);
g2_filled_arc(d, 250, 350, 40, 20, -405, -495);
g2_flush(d);
printf("\nDone.\n[Enter]\n");
getchar();
g2_close(d);
return 0;
}
void FIF(g2_attach)(F_REAL *vd_dev, F_REAL *dev)
{
g2_attach(dtoi(*vd_dev), dtoi(*dev));
}
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);
}
