void MciPlayer::playInSeperateThread(const string& fileName)
{
std::thread bgm( &MciPlayer::play, this, fileName );
bgm.detach();
}
int main(int argc, const char* argv[])
{
size_t tex_side =(argc>1)? std::atoi(argv[1]) : 512;
const char* font_desc_str = (argc>2)? argv[2] : "Sans 18";
unsigned plane = (argc>3)? std::atoi(argv[3]) : 0;
cairo_surface_t *surface = cairo_image_surface_create(
CAIRO_FORMAT_A8,
tex_side,
tex_side
);
cairo_t *cr = cairo_create(surface);
PangoFontDescription *font_desc = pango_font_description_from_string(
font_desc_str
);
PangoFontMap* font_map = pango_cairo_font_map_get_default();
PangoContext* context = pango_font_map_create_context(font_map);
PangoFont* font = pango_font_map_load_font(
font_map,
context,
font_desc
);
PangoFontMetrics* font_metrics = pango_font_get_metrics(font, nullptr);
// The Bitmap Glyph Metrics file
std::ofstream bgm((argc>5) ? argv[5] : "out.bgm");
unsigned step = tex_side / 16;
for(unsigned y=0; y!=16; ++y)
{
for(unsigned x=0; x!=16; ++x)
{
render_glyph(
cr,
font_desc,
font,
256*plane + y*16 + x,
x, y,
step,
tex_side,
pango_font_metrics_get_ascent(font_metrics),
pango_font_metrics_get_descent(font_metrics),
bgm
);
}
}
bgm.close();
pango_font_metrics_unref(font_metrics);
pango_font_description_free(font_desc);
g_object_unref(context);
cairo_destroy(cr);
cairo_status_t status = cairo_surface_write_to_png(
surface,
(argc>4) ? argv[4] : "out.png"
);
cairo_surface_destroy(surface);
return 0;
}
int main(int argc, const char* argv[]) {
if(argc != 6) {
cerr << "Usage:\n";
cerr << "scanmot <ace_file> <motif_number> <sequence_file> <output_file> <max_sites>\n";
exit(0);
}
string ace_file(argv[1]);
string motnum(argv[2]);
string seq_file(argv[3]);
string out_file(argv[4]);
unsigned int ms = atoi(argv[5]);
// Read sequences and create background model
vector<string> seqs, nameset;
get_fasta_fast(seq_file.c_str(), seqs, nameset, 12);
Seqset scan_sseq(seqs);
BGModel bgm(scan_sseq, 0.5);
// Read motif from ACE file
vector<string> hits;
string line;
ifstream acein(ace_file.c_str());
bool found = false;
while(acein.good()) {
getline(acein, line);
istringstream iss(line);
vector<string> fields;
copy(istream_iterator<string>(iss),
istream_iterator<string>(),
back_inserter<vector<string> >(fields));
if(found) {
if(line[0] != '*') {
hits.push_back(fields[0]);
} else {
break;
}
} else {
if(fields.size() > 0
&& (fields[0].compare("Motif") == 0)
&& (fields[1].compare(motnum) == 0)) {
found = true;
}
}
}
if(! found) {
cerr << "Motif number " << motnum << " not found in ACE file '" << ace_file << "'\n";
exit(1);
}
Seqset ace_sseq(hits);
Motif mot(ace_sseq, 12, bgm.gcgenome());
mot.clear_cols();
for(unsigned int i = 0; i < line.length(); i++) {
if(line[i] == '*') mot.add_col(i);
}
for(unsigned int i = 0; i < hits.size(); i++) {
mot.add_site(i, 0, 1);
}
acein.close();
// Scan sequences
SiteHeap sh(ms);
double* sm = new double[mot.ncols() * 4];
double* am = new double[mot.ncols()];
mot.calc_score_matrix(sm, am);
int width = mot.get_width();
int n = 0;
double msc, bsc, scw, scc;
for(int c = 0; c < scan_sseq.num_seqs(); c++) {
for(int p = 0; p < scan_sseq.len_seq(c) - width; p++) {
msc = mot.score_site(scan_sseq, sm, am, c, p, 1);
bsc = bgm.score_site(mot, c, p, 1);
scw = msc - bsc;
// cerr << c << '\t' << p << '\t' << seqs[c].substr(p, width) << '\t' << 1 << '\t' << setprecision(4) << msc << '\t' << bsc << '\t' << scw << '\n';
ScoredSite ssw(scw, c, p, 1);
sh.add(ssw);
msc = mot.score_site(scan_sseq, sm, am, c, p, 0);
bsc = bgm.score_site(mot, c, p, 0);
scc = msc - bsc;
// cerr << c << '\t' << p << '\t' << seqs[c].substr(p, width) << '\t' << 0 << '\t' << setprecision(4) << msc << '\t' << bsc << '\t' << scc << '\n';
ScoredSite ssc(scc, c, p, 0);
sh.add(ssc);
n += 2;
}
}
delete [] sm;
// Print out the sites
ofstream scout(out_file.c_str());
for(int i = 0; i < sh.sitecount(); i++) {
ScoredSite bestss = sh.get_site(i);
scout << nameset[bestss.site.chrom()] << '\t';
scout << bestss.site.posit() << '\t';
scout << bestss.site.posit() + width - 1 << '\t';
scout << bestss.site.strand() << "\t";
if(bestss.site.strand())
scout << seqs[bestss.site.chrom()].substr(bestss.site.posit(), width) << '\t';
else
scout << reverse_comp(seqs[bestss.site.chrom()].substr(bestss.site.posit(), width)) << '\t';
scout << bestss.score << '\n';
}
scout.close();
}
