int main(int argc, char **argv) {
if( argc <= 1 ){
cerr << "Missing input file "<< argv[0] <<" [infile]" << endl;
return -1;
}
string fileName = argv[1];
vector<SequenceRead>* gfaReads;
string ctg_seg = "";
if (argc > 2) {
fileName = argv[2];
GfaParser* gfaParser = new GfaParser;
gfaReads = gfaParser->parseGfaFormat(fileName);
ctg_seg = gfaParser->segments[0].sequence;
fileName = argv[1];
}
InputParser* parser = InputParserFactory::instantiateParser(fileName);
vector<pair<string, string>> data = argc > 2 ? parser->parseInputWithGfa(fileName, gfaReads) : parser->parseInput(fileName);
POAGraph *poaGraph = new POAGraph(ctg_seg, "contig");
for (auto it = gfaReads->begin(); it!=gfaReads->end(); ++it) {
cout << it->readName << endl << "Num of nodes: " << poaGraph->numberOfNodes << endl;
BandwidthAlignment *alignment = new BandwidthAlignment(it->read, poaGraph, it->firstNode, it->lastNode, poaGraph->numberOfNodes);
alignment->align();
poaGraph->incorporateSequenceAlignment(alignment, it->read, it->readName);
delete alignment;
}
auto alignments = poaGraph->generateAlignmentStrings();
delete poaGraph;
// for (auto pair : alignments) {
// cout << pair.first << "\t" << pair.second << endl;
// }
return 0;
}
void InputConverterOPEquilibria::convert(std::istream& i, std::ostream& o)
{
InputParser p;
p.parse(i, pcd.mcs());
writeProgram(o, pcd.mcs());
}
bool Shell::mainLoop(std::istream &in, Environment &env) const
{
InputParser iParser;
ShellCommand::Args args;
const Shell *oldShell = env.shell();
env.shell() = this;
bool success = true;
do {
if(env.interactive()) cout << endl << "dbxml> ";
env.lineNo() += iParser.parse(in, args);
string command = args.empty() ? string("") : args.front();
try {
ShellCommand *cmd = findCommand(command);
if (cmd)
cmd->execute(args, env);
else if(!args.empty()) {
throw CommandException("Unknown command");
}
}
//catches XmlException
catch(exception &e) {
cerr << env.streamName() << ":" << env.lineNo() <<
": " << command << " failed, ";
cerr << e.what() << endl;
success = false;
if(!env.interactive() && !env.ignoreErrors())
env.quit() = true;
}
catch(...) {
cerr << env.streamName() << ":" << env.lineNo() <<
": " << command << " failed" << endl;
success = false;
if(!env.interactive() && !env.ignoreErrors())
env.quit() = true;
}
} while(!env.quit() && !in.eof() && !env.sigBlock().isInterrupted());
env.shell() = oldShell;
return success;
}
void debugLots() {
lots.clear();
debugOffset = 0.005;
vector<Polygon> debugBlocks;
Polygon p;
p.vertices.push_back(Vector3d(0.398803, 0.363752, 0));
p.vertices.push_back(Vector3d(0.407103, 0.352854, 0));
p.vertices.push_back(Vector3d(0.414602, 0.357363, 0));
p.vertices.push_back(Vector3d(0.408383, 0.371349, 0));
p.vertices.push_back(Vector3d(0.401586, 0.36584, 0));
debugBlocks.push_back(p);
lg = LotGenerator(debugBlocks,
parser.get(LOT_EDGE_MAX_WIDTH)*wMult,
0, //area
parser.get(LOT_SPLIT_DEVIANCE),
is);
lg.getLots(lots);
gotLots = true;
debug = true;
stage = CS_BUILDINGS;
}
void InputReader::parseFile(istream& fin, InputParser& parser)
{
string line;
string token;
// ... reset input file
fin.clear();
fin.seekg(0);
section = -1;
// ... read each line from input file
for (;;)
{
if ( errcount >= MAXERRS ) break;
getline(fin, line, '\n');
if (fin.fail())
{
if ( fin.eof() ) break; // end of file reached - normal termination
}
// ... remove any comment from input line
trimLine(line);
// ... read 1st token from input line
sin.clear(); // clear string stream status flags
sin.str(line); // assign input line to string stream
sin >> token; // read 1st token from string stream
// ... skip blank lines
if ( sin.fail() || token[0] == '\0' ) continue;
try
{
// ... see if at start of new input section
if ( token[0] == '[' ) findSection(token);
// ... otherwise parse input line of data
else parser.parseLine(line, section);
}
catch (InputError& e)
{
errcount++;
if ( section >= 0 )
{
parser.network->msgLog << e.msg << " at following line of " <<
sections[section] << "] section:\n";
}
else
{
parser.network->msgLog << e.msg << " at following line of file:\n";
}
parser.network->msgLog << line << "\n";
}
catch (...)
{
errcount++;
}
}
// ... throw general input file exception if errors were found
if ( errcount > 0 ) throw InputError(InputError::ERRORS_IN_INPUT_DATA, "");
}
int main(int argc, char** argv) {
string ModelConf, FileOut;
try {
// get the name of the current directory
char dir[255];
getcwd(dir,255);
// set filenames
options_description desc("Allowed (positional) options");
string inputFile(dir), outputFile(dir);
inputFile += "/tests/StandardModel.conf";
outputFile += "/tests/LEP2test.root";
desc.add_options()
("modconf", value<string>()->default_value(inputFile),
"model config filename (1st)")
("rootfile", value<string>()->default_value(outputFile),
"output root filename (2nd)")
("help", "help message")
;
positional_options_description pd;
pd.add("modconf", 1);
pd.add("rootfile", 1);
variables_map vm;
store(command_line_parser(argc, argv).options(desc).positional(pd).run(), vm);
notify(vm);
if (vm.count("help")) {
cout << desc << endl;
return EXIT_SUCCESS;
}
ModelConf = vm["modconf"].as<string > ();
FileOut = vm["rootfile"].as<string>();
cout << "# set " << ModelConf << " for the model config file" << endl;
cout << "# set " << FileOut << " for the output file" << endl;
// read parameters
InputParser myInputParser;
std::vector<ModelParameter> ModPars;
std::vector<Observable> Obs;
std::vector<Observable2D> Obs2D;
std::vector<CorrelatedGaussianObservables> CGO;
std::vector<ModelParaVsObs> ParaObs;
std::map<string, double> DP;
cout << "# Model: "
<< myInputParser.ReadParameters(ModelConf, ModPars, Obs, Obs2D, CGO, ParaObs)
<< endl;
for (std::vector<ModelParameter>::iterator it = ModPars.begin(); it < ModPars.end(); it++)
DP[it->name] = it->ave;
if (!myInputParser.getMyModel()->Init(DP)) {
cout << "parameter(s) missing in model initialization" << endl;
exit(EXIT_FAILURE);
}
//////////////////////////////////////////////////////////////////////
// TEST for inputs
//cout << "Mz = " << myInputParser.getMyModel()->getMz() << endl;
ZFitterWrapper* ZF = new ZFitterWrapper(*myInputParser.getMyModel());
ZF->FlagInfo();
// TESTs
//ZF->printIntermediateResults();
//ZF->printInputs();
//ZF->printConstants();
ZFMw* myZFMw = new ZFMw(*ZF);
cout << "Mw = " << myZFMw->computeThValue() << " " << endl << endl;
//////////////////////////////////////////////////////////////////////
// Differential cross sections
const double cos_theta[11] = {-1.0, -0.8, -0.6, -0.4, -0.2, 0.0,
0.2, 0.4, 0.6, 0.8, 1.0};
ZFDsigmaQuarksLEP2* myZFDsigmaQuarks[11];
ZFDsigmaMuLEP2* myZFDsigmaMu[11];
ZFDsigmaTauLEP2* myZFDsigmaTau[11];
cout << "sqrt{s} cos(theta) dsigma(q)/dcos_theta dsigma(mu)/dcos_theta dsigma(tau)/dcos_theta"
<< endl;
for (int i=0; i<11; i++) {
myZFDsigmaQuarks[i] = new ZFDsigmaQuarksLEP2(*ZF,200.0,cos_theta[i]);
myZFDsigmaMu[i] = new ZFDsigmaMuLEP2(*ZF,200.0,cos_theta[i]);
myZFDsigmaTau[i] = new ZFDsigmaTauLEP2(*ZF,200.0,cos_theta[i]);
cout << " 200.0 " << setw(6) << cos_theta[i]
<< setw(20) << myZFDsigmaQuarks[i]->computeThValue()
<< setw(20) << myZFDsigmaMu[i]->computeThValue()
<< setw(20) << myZFDsigmaTau[i]->computeThValue()
<< endl;
}
cout << endl;
//////////////////////////////////////////////////////////////////////
// LEP2 CM energies
const double sqrt_s[12] = {130.0, 136.0, 161.0, 172.0, 183.0, 189.0,
192.0, 196.0, 200.0, 202.0, 205.0, 207.0};
// LEP2 CM energies for heavy flavors
const double sqrt_s_HF[10] = {133.0, 167.0, 183.0, 189.0, 192.0,
196.0, 200.0, 202.0, 205.0, 207.0};
ZFsigmaQuarksLEP2* myZFsigmaQuarks[12];
ZFsigmaMuLEP2* myZFsigmaMu[12];
ZFsigmaTauLEP2* myZFsigmaTau[12];
ZFAFBmuLEP2* myZFAFBmu[12];
ZFAFBtauLEP2* myZFAFBtau[12];
cout << "sqrt{s} sigma(q) sigma(mu) sigma(tau) A_FB(mu) A_FB(tau)"
<< endl;
for (int i=0; i<12; i++) {
myZFsigmaQuarks[i] = new ZFsigmaQuarksLEP2(*ZF,sqrt_s[i]);
myZFsigmaMu[i] = new ZFsigmaMuLEP2(*ZF,sqrt_s[i]);
myZFsigmaTau[i] = new ZFsigmaTauLEP2(*ZF,sqrt_s[i]);
myZFAFBmu[i] = new ZFAFBmuLEP2(*ZF,sqrt_s[i]);
myZFAFBtau[i] = new ZFAFBtauLEP2(*ZF,sqrt_s[i]);
cout << setw(6) << sqrt_s[i]
<< setw(10) << myZFsigmaQuarks[i]->computeThValue()
<< setw(10) << myZFsigmaMu[i]->computeThValue()
<< setw(10) << myZFsigmaTau[i]->computeThValue()
<< setw(10) << myZFAFBmu[i]->computeThValue()
<< setw(10) << myZFAFBtau[i]->computeThValue()
<< endl;
//ZF->CutInfo();// TEST
}
cout << endl;
//////////////////////////////////////////////////////////////////////
const int INTF_NEW = 2;
ZF->setFlag("INTF",INTF_NEW); // with ISR/FSR interference contribution
cout << "Flag update: INTF=2" << endl << endl;
ZFRbottomLEP2* myZFRbottom[10];
ZFAFBbottomLEP2* myZFAFBbottom[10];
ZFRcharmLEP2* myZFRcharm[10];
ZFAFBcharmLEP2* myZFAFBcharm[10];
cout << "sqrt{s} R_b A_FB(b) R_c A_FB(c)" << endl;
for (int i=0; i<10; i++) {
myZFRbottom[i] = new ZFRbottomLEP2(*ZF,sqrt_s_HF[i]);
myZFAFBbottom[i] = new ZFAFBbottomLEP2(*ZF,sqrt_s_HF[i]);
myZFRcharm[i] = new ZFRcharmLEP2(*ZF,sqrt_s_HF[i]);
myZFAFBcharm[i] = new ZFAFBcharmLEP2(*ZF,sqrt_s_HF[i]);
cout << setw(6) << sqrt_s_HF[i]
<< setw(10) << myZFRbottom[i]->computeThValue()
<< setw(10) << myZFAFBbottom[i]->computeThValue()
<< setw(10) << myZFRcharm[i]->computeThValue()
<< setw(10) << myZFAFBcharm[i]->computeThValue()
<< endl;
}
cout << endl;
//////////////////////////////////////////////////////////////////////
cout << "Test finished" << endl;
return EXIT_SUCCESS;
} catch (const runtime_error& e) {
cerr << e.what() << endl;
return EXIT_FAILURE;
}
}
int main(int argc, char *argv[])
{
opt::options_description visibleOptions("Allowed options");
visibleOptions.add_options()
("help,h","Display this help message.")
("output,o",opt::value<string>(),"Write output to specified file.")
("undef,u","Generate an undefines file.")
("version,v","Show version information.");
opt::options_description options("All program options");
options.add(visibleOptions);
options.add_options()("input",opt::value<vector<string> >(),"Input...");
opt::positional_options_description pos;
pos.add("input",-1);
opt::variables_map vm;
opt::store(opt::command_line_parser(argc,argv).options(options).positional(pos).run(),vm);
opt::notify(vm);
if(vm.count("help"))
{
cout<<"Usage: "<<argv[0]<<" [OPTION]... [FILE]..."<<endl
<<"Generate Verilog include file from XML variable"<<endl
<<"definitions file."<<endl
<<endl<<visibleOptions<<endl
<<"If supplied, input is read from the listed files."<<endl
<<"By default, input is taken from stdin and output"<<endl
<<"is written to stdout."<<endl;
return 0;
}
else if(vm.count("version"))
{
cout<<PACKAGE_STRING<<endl
<<"Compiled "<<__DATE__<<" "<<__TIME__<<"."<<endl
<<endl
<<"Report bugs to "<<PACKAGE_BUGREPORT<<"."<<endl;
return 0;
}
//Parse input files.
map<string,MacroEntry*> vars;
vector<string> verilog;
int errorCount=0;
if(vm.count("input"))
{
vector<string> inputFiles=vm["input"].as<vector<string> >();
for(vector<string>::iterator i=inputFiles.begin();
i!=inputFiles.end();
i++)
{
InputParser in(*i);
errorCount+=in.Parse(vars,verilog);
}
}
else
{
InputParser in;
errorCount+=in.Parse(vars,verilog);
}
//Print output file.
if(errorCount==0)
{
ofstream outFile;
ostream *out=NULL;
if(!vm.count("output"))out=&cout;
else
{
outFile.open(vm["output"].as<string>().c_str());
if(outFile.good())out=&outFile;
else cerr<<"Error: unable to open output file '"
<<vm["output"].as<string>()<<"'."<<endl;
}
if(out!=NULL)
{
int errorCount=0;
string output;
output="//Generated by "+string(PACKAGE_STRING)+", compiled on "+string(__DATE__)+" "+string(__TIME__)+".\n";
output+="//This file has been automatically generated.\n";
output+="//Edit contents with extreme caution.\n\n";
if(!vm.count("undef") && verilog.size()>0)
{
for(vector<string>::iterator i=verilog.begin();
i!=verilog.end();
i++)
{
output+=(*i)+"\n";
}
output+="\n";
}
map<string,Expression*> expList;
for(map<string,MacroEntry*>::iterator i=vars.begin();
i!=vars.end();
i++)
{
expList[(*i).first]=(*i).second->expression;
}
boost::regex newline("\\n");
for(map<string,MacroEntry*>::iterator i=vars.begin();
i!=vars.end();
i++)
{
string variable=(*i).first;
MacroEntry *entry=(*i).second;
if(vm.count("undef"))
{
output+="`ifdef "+variable+"\n";
output+=" `undef "+variable+"\n";
output+="`endif\n";
output+="\n";
}
else
{
if(!entry->print)continue;
try
{
if(entry->comments!="")
{
output+="//";
output+=boost::regex_replace(entry->comments,newline,"\\n//");
output+="\n";
}
output+="`ifndef "+variable+"\n";
output+=" `define "+variable+" "+entry->expression->Value(expList)+"\n";
output+="`endif\n";
output+="\n";
}
catch(Expression::ExpressionError &e)
{
errorCount++;
e.SetVariable(variable);
cerr<<e.what()<<endl;
}
}
}
if(errorCount==1)cerr<<"Found 1 error."<<endl;
else if(errorCount>0)cerr<<"Found "<<errorCount<<" errors."<<endl;
else (*out)<<output;
if(vm.count("output"))outFile.close();
}
}
else
{
if(errorCount==1)cerr<<"Found 1 error."<<endl;
else if(errorCount>0)cerr<<"Found "<<errorCount<<" errors."<<endl;
}
//Cleanup expressions.
for(map<string,MacroEntry*>::iterator i=vars.begin();
i!=vars.end();
i++)
{
delete (*i).second;
}
return errorCount!=0;
}
void keyboard(unsigned char key, int x, int y) {
if(key == ' ') {
roadsystem.generate(1);
}
if(key == 'x') {
roadsystem.generate(100);
}
if(key == 'z') {
roadsystem.generate(1000);
}
if(key == 'q') {
roadsystem.printStats();
}
if(key == 'i') {
scale *= 1.1;
}
if(key == 'k') {
scale /= 1.1;
}
/*
if(key == 'u') {
wMult += 0.05;
debugLots();
}
if(key == 'j') {
wMult -= 0.05;
debugLots();
}
*/
if(key == 'd') {
if(stage >= CS_ROADS) {
printf("dumping roads to roads.mel...");
roadsystem.dumpRoads();
printf("done!\n");
}
}
if(key == 'f') {
if(stage >= CS_LOTS) {
printf("dumping blocks to blocks.obj...");
roadsystem.dumpPolygons();
printf("done!\n");
}
}
if(key == 'g') {
if(stage >= CS_BUILDINGS) {
printf("dumping lots to lots.obj...");
dumpLots();
printf("done!\n");
}
}
/*
if(key == 'f') {
printf("debugging\n");
debugLots();
}
*/
if(key == 'p') {
switch(stage) {
case(CS_ROADS):
printf("extracting blocks...");
roadsystem.getPolygons();
blocks.clear();
roadsystem.extractPolygons(blocks);
gotBlocks = true;
printf("done!\n");
stage = CS_LOTS;
printf("-------------------------------------\n");
printf("Lot Subdivision\n");
printf("(p) to generate lots\n");
printf("(f) to dump blocks to blocks.obj\n");
printf("(d) to dump roads to roads.mel\n");
printf("The code likes to blow up at this stage :(\n");
printf("If it does, just restart the program\n");
break;
case(CS_LOTS):
lg = LotGenerator(blocks,
parser.get(LOT_EDGE_MAX_WIDTH),
parser.get(LOT_MIN_AREA),
parser.get(LOT_SPLIT_DEVIANCE),
is);
lg.getLots(lots);
gotLots = true;
printf("Done subdividing blocks!\n");
stage = CS_BUILDINGS;
printf("-------------------------------------\n");
printf("Building Generation\n");
printf("(p) to generate buildings\n");
printf("(g) to dump lots to lots.obj\n");
printf("(f) to dump blocks to blocks.obj\n");
printf("(d) to dump roads to roads.mel\n");
printf("output will be written to outputFile.obj\n");
break;
case(CS_BUILDINGS):
printf("generating buildings...");
bg = BuildingGenerator(lots);
bg.getBuildings(parser.get(BUILDING_MAX_HEIGHT), is);
bg.generateObjFile();
printf("done!\n");
printf("(p) to quit\n");
printf("(g) to dump lots to lots.obj\n");
printf("(f) to dump blocks to blocks.obj\n");
printf("(d) to dump roads to roads.mel\n");
stage = CS_DONE;
break;
case(CS_DONE):
exit(0);
break;
}
}
glutPostRedisplay();
}