Pair_aln::Pair_aln(const char *blastfile) throw (std::exception):
score(0.0f),
len_x(0),
aln_len_x(0),
len_y(0),
aln_len_y(0),
len_aln(0),
len_equ(0),
idents(0),
pos_matches(0),
neg_zero_matches(0),
gaps(0),
gaps_x(0),
gaps_y(0),
x_aln_start(0),
x_aln_end(0),
y_aln_start(0),
y_aln_end(0){
#ifndef CM_NO_BOOST
std::ifstream in(blastfile);
if(!in) throw MyException("Cannot open '%s'!", blastfile);
boost::regex blanc("^\\s*$");
boost::regex query_expr("^Query:\\s+(\\d+)\\s+(\\S+)\\s+.*");
boost::regex subjt_expr("^Sbjct:\\s+(\\d+)\\s+(\\S+)\\s+.*");
const size_t L = 4*1024*1024;
char buffer[L];
size_t consecutive_blanc_lines=0;
std::string x_seq="", y_seq="";
std::vector<int> xvec, yvec;
int xs=-1, ys=-1;
bool found_data = false;
while( in.good() ){
in.getline(buffer, L);
//std::cout << buffer << std::endl;
if( boost::regex_match(buffer, blanc) ){
if( ys!=-1 && xs!=-1 ){
//std::cout << x_seq << std::endl;
//std::cout << y_seq << std::endl <<std::endl;
_eval_seqs(xvec, yvec, xs, ys, x_seq, y_seq);
}
++consecutive_blanc_lines;
if( consecutive_blanc_lines>2 && found_data ) break;
xs=-1;
ys=-1;
}else{
consecutive_blanc_lines=0;
}
boost::cmatch matches;
if( boost::regex_match(buffer, matches, query_expr) ){
xs = atoi( matches.str(1).c_str() );
x_seq = matches.str(2);
found_data = true;
}else
if( boost::regex_match(buffer, matches, subjt_expr) ){
ys = atoi( matches.str(1).c_str() );
y_seq = matches.str(2);
found_data = true;
}
}
len_aln = xvec.size();
x = new int[len_aln];
y = new int[len_aln];
for( size_t i=0; i<len_aln; ++i ){
x[i] = xvec[i]-1;
y[i] = yvec[i]-1;
}
#else
throw MyException("Constructor not available - compile with libboost.");
#endif
}
// main program
int main(int argc, char *argv[]) {
Spectrum blanc(1.0);
FresnelOne myFresnel;
IsotropicBeckmann myD(1.0);
//Blinn myD(0.5);
MSHAC myMSHAC(&myD);
Microfacetpp myBRDF(blanc, &myFresnel, &myD, &myMSHAC);
Spectrum integral(0.0);
float theta_o = M_PI / 2.2f;
float phi_o = 0.f;
Vector w_o(cosf(phi_o) * sinf(theta_o), sinf(phi_o) * sinf(theta_o), cosf(theta_o));
Vector w_i(0.0,0.0,1.0);
Vector w_g(0.0, 0.0, 1.0);
//float myG = myMSHAC.G(w_o,w_i,Normalize(w_o + w_i));
//float lambda(myD.Lambda(w_o));
float deltaPhi = 0.01, deltaTheta = 0.01;
/*RNG myRNG;
const int n(300);
const int nSamplers(n*n);
float samples[nSamplers*2];*/
/*for (int i(0); i < n; i++) {
float u1 = (float)i / (float)n;
for (int j(0); j < n; j++) {
float u2 = (float)j / (float)n;
samples[i * n + j * 2] = u1;
samples[i * n + j * 2 + 1] = u2;
}
}*/
/*for (int i(0); i < nSamplers * 2; i++) {
samples[i] = myRNG.RandomFloat();
}*/
for (float phi = 0.0; phi <= 2 * M_PI; phi += deltaPhi) {
for (float theta = 0.0; theta <= M_PI / 2.0; theta += deltaTheta) {
w_i.x = cos(phi) * sin(theta);
w_i.y = sin(phi) * sin(theta);
w_i.z = cos(theta);
integral += myBRDF.f(w_o, w_i) * AbsDot(w_g,w_i) * deltaPhi * deltaTheta * sin(theta);
//integral += myD.D(w_i) * AbsDot(w_g, w_i) * deltaPhi * deltaTheta * sin(theta);
}
}
integral = Spectrum(1.0) - integral;
//Spectrum retour = myBRDF.rho(w_o,nSamplers, samples);
/*Options options;
vector<string> filenames;
// Process command-line arguments
for (int i = 1; i < argc; ++i) {
if (!strcmp(argv[i], "--ncores")) options.nCores = atoi(argv[++i]);
else if (!strcmp(argv[i], "--outfile")) options.imageFile = argv[++i];
else if (!strcmp(argv[i], "--quick")) options.quickRender = true;
else if (!strcmp(argv[i], "--quiet")) options.quiet = true;
else if (!strcmp(argv[i], "--verbose")) options.verbose = true;
else if (!strcmp(argv[i], "--help") || !strcmp(argv[i], "-h")) {
printf("usage: pbrt [--ncores n] [--outfile filename] [--quick] [--quiet] "
"[--verbose] [--help] <filename.pbrt> ...\n");
return 0;
}
else filenames.push_back(argv[i]);
}
// Print welcome banner
if (!options.quiet) {
printf("pbrt version %s of %s at %s [Detected %d core(s)]\n",
PBRT_VERSION, __DATE__, __TIME__, NumSystemCores());
printf("Copyright (c)1998-2014 Matt Pharr and Greg Humphreys.\n");
printf("The source code to pbrt (but *not* the book contents) is covered by the BSD License.\n");
printf("See the file LICENSE.txt for the conditions of the license.\n");
fflush(stdout);
}
pbrtInit(options);
// Process scene description
PBRT_STARTED_PARSING();
if (filenames.size() == 0) {
// Parse scene from standard input
ParseFile("-");
} else {
// Parse scene from input files
for (u_int i = 0; i < filenames.size(); i++)
if (!ParseFile(filenames[i]))
Error("Couldn't open scene file \"%s\"", filenames[i].c_str());
}
pbrtCleanup();*/
return 0;
}
