void ViewerCmdLine::parse()
{
const CmdLineOption options[] = {
HELP,
HELP_SHORT,
OPTIONS_FILE,
LISTEN,
HOST,
PORT,
PASSWORD,
SHOW_CONTROLS,
VIEW_ONLY,
USE_CLIPBOARD,
SCALE,
FULL_SCREEN,
WARN_FULL_SCREEN,
ENCODING,
COPY_RECT,
MOUSE_CURSOR,
MOUSE_LOCAL,
MOUSE_SWAP,
JPEG_IMAGE_QUALITY,
COMPRESSION_LEVEL
};
if (!processCmdLine(&options[0], sizeof(options) / sizeof(CmdLineOption))) {
throw CommandLineFormatException();
}
if (isHelpPresent()) {
throw CommandLineFormatHelp();
}
if (m_wpcl.getArgumentsCount() > 2) {
throw CommandLineFormatException();
}
if (m_wpcl.getArgumentsCount() > 1) {
if (isPresent(ViewerCmdLine::HOST)) {
throw CommandLineFormatException();
}
}
if (isPresent(ViewerCmdLine::OPTIONS_FILE)) {
parseOptionsFile();
} else {
if (isPresent(ViewerCmdLine::LISTEN)) {
*m_isListening = true;
} else {
if (!parseHost()) {
throw CommandLineFormatException();
}
}
}
parsePassword();
parseEncoding();
parseMouseShape();
parseMouseCursor();
parseScale();
parseFullScreen();
parseCompressionLevel();
parseWarnFullScr();
parseMouseSwap();
parseUseClipboard();
parseShowControl();
parseCopyRect();
parseViewOnly();
parseJpegImageQuality();
}
int main(int argc, char *argv[]) {
programName = "firechain";
c7c88e52_ensureUserIsRoot();
if (argc == 1) {
c7c88e52_printUsage(USAGE_MSG);
exit(EXIT_FAILURE);
} else if (f6215943_isEqual("help", argv[1])) {
printHelp(argc, argv);
exit(EXIT_SUCCESS);
}
FirewallParams firewallParams;
CmdLineParam cmdLineParm;
d7ad7024_initCmdLineParam(&cmdLineParm, argc, argv, USAGE_MSG);
processCmdLine(&cmdLineParm, &firewallParams);
if (firewallParams.action == ADD) {
processAdd(&firewallParams);
} else if (firewallParams.action == DELETE) {
processDelete(&firewallParams);
} else if (firewallParams.action == VIEW) {
for (int i=0; i < firewallParams.ruleList.length; i++) {
puts(firewallParams.ruleList.values[i]);
}
}
b196167f_destroyAllElements(&firewallParams.ruleList);
// Exit with success
exit(EXIT_SUCCESS);
}
int main(int argc, char *argv[]) {
programName = "nettuner";
TuningParams tuningParams;
CmdLineParam cmdLineParm;
d7ad7024_initCmdLineParam(&cmdLineParm, argc, argv, USAGE_MSG);
processCmdLine(&cmdLineParm, &tuningParams);
IPv4Socket ipv4Socket;
Ethernet ethDevice;
EthernetRequest ethRequest;
d3843373_initEthernetRequest(ðRequest, tuningParams.deviceName);
a34d4619_open(&ipv4Socket, IPV4_SOCKET_UDP);
d3843373_getEthernetStatus(ðDevice, ðRequest, &ipv4Socket);
d3843373_getEthernetMTU(ðDevice, ðRequest, &ipv4Socket);
a34d4619_close(&ipv4Socket);
setTuningParams(&tuningParams, ðDevice);
TuningCalcs tuningCalcs;
EthtoolSettings ethtoolSettings;
performTuningCalcs(&tuningCalcs, &tuningParams);
calcEthtoolSettings(ðtoolSettings, &tuningCalcs, &tuningParams);
if (tuningParams.generateNetworkdScript) {
generateNetworkdTuningScript(tuningParams.deviceName, ðtoolSettings);
} else if (tuningParams.generateNMScript) {
generateNetworkManagerTuningScript(tuningParams.deviceName, ðtoolSettings);
} else {
SysctlSettings sysctlSettings;
calcSysctlSettings(&sysctlSettings, ðtoolSettings, &tuningCalcs, &tuningParams);
printNetworkKernelTuningConfig(&sysctlSettings);
}
// Exit with success
exit(EXIT_SUCCESS);
}
bool init(int argc, char** argv)
{
if (!processCmdLine(argc, argv, &m_params)) {
fprintf(stderr, "process arguments failed.\n");
return false;
}
m_output.reset(DecodeOutput::create(m_params.renderMode, m_params.renderFourcc, m_params.inputFile, m_params.outputFile.c_str()));
if (!m_output) {
fprintf(stderr, "DecodeOutput::create failed.\n");
return false;
}
m_nativeDisplay = m_output->nativeDisplay();
m_vppInput = createInput(m_params, m_nativeDisplay);
if (!m_nativeDisplay || !m_vppInput) {
fprintf(stderr, "DecodeTest init failed.\n");
return false;
}
return true;
}
int main( int argc, char **argv ) {
// Process the command line
if (!processCmdLine(argc, argv)) {
exit(0);
}
// Now process the results file into the model file
try {
SchedResults sr(_resultFile, _esmolFile, _abstractFile, _debugOutput);
}
catch( SchedResultsException &ex ) {
std::cerr << "Exception: " << ex._reason << std::endl;
exit(1);
}
catch ( ... ) {
std::cerr << "Unkown exception in SchedResults!" << std::endl;
exit(1);
}
// Finish It Up
return 0;
}
int
WINAPI
WinMain(
HINSTANCE /*hInstance*/,
HINSTANCE /*hPrevInstance*/,
LPWSTR lpCmdLine,
int /*nShowCmd*/)
{
int result;
int argc;
char** argv;
// convert program name and lpCmdLine into argc/argv, and handle I/O redirection
argc = processCmdLine(lpCmdLine, &argv);
#if _WIN32_WCE < 0x500 || !defined(COREDLL_CORESIOA)
initStdHandles(); // get environment variables from ChildData
#endif
//result = main(argc, (char**)argv);
return result;
}
int main(int argc,char **argv) {
int count,j,s;
int norm;
bode::Interval *i;
std::string readsFN;
std::string inFN;
std::string outFN;
std::string inputFN;
int readsTotal,inputTotal;
double readsScale,inputScale;
int *target;
int bins,binwidth;
bode::Interval z;
bode::Flags *fset;
fset = processCmdLine(argc,argv);
norm = fset->getInt("norm");
bins = fset->getInt("bins");
binwidth = fset->getInt("binwidth");
inputFN = fset->getStr("input");
readsFN = fset->positionalArgs()[1];
inFN = fset->positionalArgs()[2];
outFN = fset->positionalArgs()[3];
// width = getBedWidth(inFN);
target = new int[bins];
bode::IntervalReader *reads = bode::IntervalReader::open(readsFN);
bode::CffReader *in = new bode::CffReader(inFN);
std::ofstream *out = new std::ofstream(outFN.c_str(),std::ofstream::out);
bode::IntervalReader *input = NULL;
if (inputFN != "") {
input = bode::IntervalReader::open(inputFN);
}
*out << "GID\tscore\tcoordinates";
s = 1;
while (s <= bins) {
*out << "\t" << s;
s++;
}
*out << std::endl;
fprintf(stderr,"loading reads...\n");
bode::IntervalSet *is = loadReads(reads,fset);
readsTotal = is->count();
fprintf(stderr,"loaded %d reads.\n",readsTotal);
readsScale = ((double) norm) / (double) readsTotal;
bode::IntervalSet *background = NULL;
if (input != NULL) {
fprintf(stderr,"loading input...\n");
background = loadReads(input,fset);
inputTotal = background->count();
fprintf(stderr,"loaded %d input reads.\n",inputTotal);
inputScale = ((double) norm) / (double) inputTotal;
}
reads->close();
count = 0;
fprintf(stderr,"processing intervals...\n");
while ((i=in->nextI())) {
bode::Bed *bi = static_cast<bode::Bed*>(i);
count++;
if (count % 1000 == 0) {
fprintf(stderr,"%9d\r",count);
}
for (j=0;j<bins;j++) {
target[j] = 0;
}
int left = bi->left() - (bins / 2) * binwidth;
int right = bi->left() + (bins / 2) * binwidth;
// is->density(i->chrom(),left,right,target);
(*out) <<bi->name() << "\t"<<bi->score()<<"\t"<<bi->chrom()<<":"<<bi->left();
s = left;
while (s < right) {
z.update(i->chrom(),s,s+binwidth);
int c = is->overlapping(&z);
int bk;
double ncbk;
if (background != NULL) {
bk = background->overlapping(&z);
ncbk = (c * readsScale) - (bk * inputScale);
} else {
ncbk = c * readsScale;
}
*out << "\t" << ncbk;
s += binwidth;
}
/* for (int j=0;j<right-left;j++) {
*out << "\t" << target[j];
}
*/
*out << std::endl;
}
in->close();
out->close();
if (input != NULL) {
input->close();
}
std::cerr << "processed " << count << " intervals." << std::endl;
return 0;
}
int main(int argc,char **argv) {
int count,j,s;
int norm;
bode::Interval *i;
bode::Bed *b;
std::string readsFN;
std::string inFN;
std::string outFN;
int readsTotal;
double readsScale;
int *target;
bode::Flags *fset;
fset = processCmdLine(argc,argv);
readsFN = fset->positionalArgs()[1];
inFN = fset->positionalArgs()[2];
outFN = fset->positionalArgs()[3];
norm = fset->getInt("norm");
target = new int[MAXINTERVAL];
bode::IntervalReader *reads = bode::IntervalReader::open(readsFN);
bode::BedReader *in = new bode::BedReader(inFN);
std::ofstream *out = new std::ofstream(outFN.c_str(),std::ofstream::out);
fprintf(stderr,"loading reads...\n");
bode::IntervalSet *is = loadReads(reads,fset);
readsTotal = is->count();
fprintf(stderr,"loaded %d reads.\n",readsTotal);
readsScale = ((double) norm) / (double) readsTotal;
reads->close();
count = 0;
fprintf(stderr,"processing intervals...\n");
while ((i=in->nextI())) {
count++;
if (count % 1000 == 0) {
fprintf(stderr,"%9d\r",count);
}
int width = i->right() - i->left();
for (j=0;j<width;j++) {
target[j] = 0;
}
is->density(i->chrom(),i->left(),i->right(),target);
if (i->strand() == '-') {
for (int k=0;k<width/2;k++) {
int x = target[k];
target[k] = target[width-k-1];
target[width-k-1] = x;
}
}
double nc = target[0] * readsScale;
b = static_cast<bode::Bed *>(i);
*out << b->name();
for (s=0;s<width;s++) {
nc = target[s] * readsScale;
*out << "\t" << nc;
}
*out << std::endl;
}
in->close();
out->close();
std::cerr << "processed " << count << " intervals." << std::endl;
return 0;
}
