/*
Fade from off to given color and back.
*/
void pulse(int w) {
uint32_t c;
//uint32_t c = Wheel(map(opt, 0, 1023, 0, 255));
for(uint16_t j = 8; j <= getOpt(_pin_lev, 0, 255); j++) {
if( checkButton() ){ return; };
setBrightness(j);
c = Wheel(map(opt, 0, 1023, 0, 255));
for(uint16_t i = 0; i < numPixels(); i++) {
setPixelColor(i, c);
}
show();
delay(w);
}
delay(w*10+50);
for(uint16_t j=getOpt(_pin_lev, 0, 255); j>8; j--) {
if( checkButton() ){ return; };
setBrightness(j);
c = Wheel(map(opt, 0, 1023, 0, 255));
for(uint16_t i = 0; i < numPixels(); i++) {
setPixelColor(i, c);
}
show();
delay(w);
}
delay(w*10+50);
}
/**
* @brief Check to see if the options used by the copy number engine are valid.
*/
void CNReferenceEngine::checkOptionsImp()
{
defineStates();
setLibFileOpt("reference-file");
m_pEngine->setLibFileOpt("probeset-ids");
m_pEngine->setLibFileOpt("annotation-file");
if (m_pEngine == this)
{
if (getOpt("set-analysis-name") == "") {setOpt("set-analysis-name", "CN5");}
if (m_pEngine->getOpt("expr-summary-file") == "") {throw(Except("Must specify a expr-summary-file."));}
if (m_pEngine->getOpt("genotype-calls-file") == "") {throw(Except("Must specify a genotype-calls-file."));}
if (m_pEngine->getOpt("genotype-confidences-file") == "") {throw(Except("Must specify a genotype-confidences-file."));}
if (m_pEngine->getOpt("genotype-report-file") == "") {throw(Except("Must specify a genoptype-report-file."));}
if (m_pEngine->getOpt("reference-file") == "") {throw(Except("Must specify a reference-file."));}
}
if (m_pEngine->getOpt("annotation-file") == "") {throw(Except("Must specify a netaffx annotation-file."));}
AffxString strReferenceFileName = m_pEngine->getOpt("reference-file");
if (m_pEngine == this)
{
m_pEngine->setOpt("create-reference", "true");
m_pEngine->setOpt("reference-file", strReferenceFileName);
}
}
Actions::Action Actions::get(std::int32_t ID) {
if (auto res = getOpt(ID)) {
return res.value();
} else {
throw InvalidData{"incorrect action ID"};
}
}
//Rainbow Program
void rainbow() {
int wait = getOpt(_pin_opt, 0, 255);
uint16_t i, j;
for(j = 0; j < 256; j++) {
if( checkButton() ){ return; };
for(i = 0; i < numPixels(); i++) {
setPixelColor(i, Wheel((i + j) & 255));
}
show();
delay(wait);
}
}
/**
* compute CHP files
*/
void DmetEngine::runImp() {
setOpt("analysis-guid", affxutil::Guid::GenerateNewGuid());
string errMsg;
if(!Fs::isWriteableDir(getOpt("out-dir")))
if(Fs::mkdirPath(getOpt("out-dir"), false) != APT_OK)
Err::errAbort("Can't make or write to directory: " + getOpt("out-dir"));
if(getOptBool("run-cn-engine")) {
Verbose::out(1,"");
Verbose::out(1,"Step 1: Computing probeset summaries for copy number state calling");
if(computeCnSummaries()) {
Verbose::out(1,"");
Verbose::out(1,"Step 2: Computing copy number states");
computeCnState();
setOpt("run-cn-engine","true");
} else {
Verbose::out(1,"");
Verbose::out(1,"No CN regions to compute. Skipping step 2.");
setOpt("run-cn-engine","false");
}
} else {
Verbose::out(1,"");
Verbose::out(1,"Not computing CN state. Skipping steps 1 and 2.");
setOpt("run-cn-engine","false");
}
Verbose::out(1,"");
Verbose::out(1,"Step 3: Computing genotypes");
computeGenotypes();
if(getOptBool("cc-chp-output")) {
Verbose::out(1,"");
Verbose::out(1,"Step 4: Generating CHP files");
generateChpFiles();
}
Verbose::out(1,"");
Verbose::out(1, "Done.");
}
const char *MacroCodeReplacer::replaceField(const char *field){
if (isempty(field))
return NULL;
size_t l = strlen(field);
char *tmpfield = strdupn(field);
char MACROS = MACROS_NONE;
char MACROS1 = MACROS_NONE;
getOpt(1); //singles [xxx[a]
getOpt(2); //doubles [xxx[a]
const char *res = MacroReplacer::replaceField(tmpfield);
free(tmpfield);
const char *tmp;
switch(MACROS){
case MACROS_HTML : tmp = coder->HTMLEncode(res); break;
case MACROS_SOFT_HTML : tmp = coder->SoftHTMLEncode(res); break;
case MACROS_PHTML : tmp = coder->HTMLEncode(res, true); break;
case MACROS_SOFT_PHTML: tmp = coder->SoftHTMLEncode(res, true); break;
case MACROS_URL : tmp = coder->URLEncode(res); break;
case MACROS_NUMBER : tmp = coder->numberEncode(res); break;
case MACROS_FLOAT : tmp = coder->floatEncode(res, ctoi(MACROS1)); break;
case MACROS_SQL : tmp = coder->sqlEncode(res); break;
case MACROS_SQLNULL : tmp = coder->sqlNullEncode(res); break;
case MACROS_NO : tmp = res; break;
default : tmp = res;
printflog(LOG_NOTIFY, "Macrocode: Using macros without encoding.\n");
}
return tmp;
};
bool Parser::hasListPreamble(string const itemcmd)
{
// remember current position
unsigned int oldpos = pos_;
// jump over arguments
if (hasOpt())
getOpt();
if (hasOpt("{"))
getArg('{', '}');
// and swallow spaces and comments
skip_spaces(true);
// we have a list preamble if the next thing
// that follows is not the \item command
bool res = next_token().cs() != itemcmd;
// back to orig position
pos_ = oldpos;
return res;
}
string DmetEngine::makeVal(string name, int optionIndex) {
vector<string> vals;
vals = getOptVector(name, optionIndex);
/*
if(name.find("file") != string::npos)
for(int i=0; i<vals.size(); i++)
vals[i] = Fs::basename(vals[i]);
*/
string val;
if(vals.size() > 1) {
val = "'" + vals[0] + "'";
for(int i=1; i<vals.size(); i++) {
val += ",'" + vals[i] + "'";
}
} else if(vals.size() == 1) {
val = vals[0];
} else {
val = getOpt(name,optionIndex);
}
return val;
}
int DownloadChild::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QWidget::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
switch (_id) {
case 0: finished(); break;
case 1: download(); break;
case 2: setURL((*reinterpret_cast< QString*(*)>(_a[1]))); break;
case 3: { QString* _r = getURL();
if (_a[0]) *reinterpret_cast< QString**>(_a[0]) = _r; } break;
case 4: setSaveFile((*reinterpret_cast< QString*(*)>(_a[1]))); break;
case 5: { QString* _r = getSaveFile();
if (_a[0]) *reinterpret_cast< QString**>(_a[0]) = _r; } break;
case 6: setOpt((*reinterpret_cast< QString*(*)>(_a[1]))); break;
case 7: { QString* _r = getOpt();
if (_a[0]) *reinterpret_cast< QString**>(_a[0]) = _r; } break;
default: ;
}
_id -= 8;
}
return _id;
}
videoApp_t::videoApp_t(int &argc,argv_t &argv)
:application_t(argc, argv),
__controlPort(NULL),
__bandwidth(1000000.0)
{
strcpy(__rtpPort,"51017");
strcpy(__rtcpPort,"51019");
enum myOptions {
ctrlPort,
notify,
dport,
autoChannel,
h
};
s = static_cast<sched_t*>(this);
optionDefList_t opt;
appParamList_t *parList;
//Available options
opt << new optionDef_t("@cport", ctrlPort , "Opens a Control Socket in <port>")
<< new optionDef_t("@rtpPort", dport , "Receiver data port")
<< new optionDef_t("@notify", notify , "Notify file")
<< new optionDef_t("autoChannel", autoChannel , "autoShows playChannels")
<< new optionDef_t("h", h , "Video Help");
parList = getOpt(opt, argc, argv);
ctrlTask_t * ctrlTask = NULL;
SetAutoChannel = new bool();
*SetAutoChannel = false;
for ( ; parList->len(); parList->behead()) {
switch(parList->head()->parId) {
case ctrlPort:
char * port;
port = strdup(parList->head()->parValue);
ctrlTask = new ctrlTask_t(port);
break;
case dport:
char * strDport;
strDport = strdup(parList->head()->parValue);
strcpy(__rtpPort,strDport);
itoa(atoi(strDport) + 2,__rtcpPort,10);
break;
case notify:
char * file;
file = strdup(parList->head()->parValue);
setNotifyFile(file);
break;
case autoChannel:
*SetAutoChannel = true;
break;
case h:
default:
int i;
for(i=0; i < opt.len(); i++) {
optionDef_t * op= static_cast<optionDef_t*>(opt.nth(i));
if(op->optDesc)
fprintf(stderr, " %-10s %-5s\t-- %s\n",
op->optName,
op->optHasArg?"value":"",
op->optDesc);
else
fprintf(stderr, " %-10s %-5s\t",
op->optName,
op->optHasArg?"":"value");
}
exit(0);
break;
}
};
// RTP Object Creation
#ifdef WIN32
if (getenv("MCU_USE_ONLY_IPv4")){
rtpSession= new videoRTPSession_t(this,
"0.0.0.0",
__rtpPort,
"0.0.0.0",
__rtcpPort,
VIDEO_TIMESTAMP_UNIT
);
}
else{
rtpSession= new videoRTPSession_t(this,
NULL,
__rtpPort,
NULL,
__rtcpPort,
VIDEO_TIMESTAMP_UNIT
);
}
#else
rtpSession= new videoRTPSession_t(this,
NULL,
__rtpPort,
NULL,
__rtcpPort,
VIDEO_TIMESTAMP_UNIT
);
#endif
//init log file
struct _timeb timebuffer;
char * timeline;
_ftime( &timebuffer );
timeline = ctime( & ( timebuffer.time ) );
char auxFile[20];
char auxArgv[100];
memset(auxArgv,0,100);
for (int i = 1; i<argc; i++)
{
strcat(auxArgv,argv[i]);
strcat(auxArgv," ");
}
if (char * n = strstr(auxArgv,"File"))
{
n = strstr(n," ");
strcpy(auxFile,n);
}else{
strcpy(auxFile," Screen");
}
// Debug Session Info
NOTIFY( "\n·:======================================================:·\n\n"
" Isabel Video v0.1 Debug Session:\n\n"
" - Options: %s\n"
" - Log File:%s\n"
" - Date: %s\n"
" - Author: Vicente Sirvent Orts\n"
"\n"
"·:=======================================================:·\n\n",
auxArgv,
auxFile,
timeline);
}
int
main(int argc, char *argv[])
{
MERET ret;
int getOptSuccessed;
#if defined(_MSC_VER) && !defined(NDEBUG)
/* 厳密な演算チェックのため */
_controlfp(~_MCW_EM | _EM_INEXACT, _MCW_EM);
#endif
#if defined(__FreeBSD__)
{ /* デフォルト動作が他のOSと違う。*/
struct sigaction new_sig;
memset(&new_sig, 0, sizeof(struct sigaction));
new_sig.sa_handler = SIG_IGN;
sigaction(SIGFPE, &new_sig, NULL);
}
#endif
if(MPGE_initializeWork() == ME_NOFPU) return ERR;
getOptSuccessed = 1 < argc && getOpt(argc, argv) == NOERR;
opening();
if(!getOptSuccessed){
usage();
MPGE_endCoder();
return ERR;
}
ret = MPGE_detectConfigure();
if(ret != ME_NOERR){
if(!silent) fprintf(stderr, "%s\n", getErrMsg(ret));
return ERR;
}
putConfig();
reportInit(); /* report progress */
#if defined(USE_ITIMER) || (defined(_CONSOLE) && defined(WIN32) && defined( USE_TTIMER ))
ret = MPGE_processTrack();
if(ret != ME_NOERR){
if(!silent) fprintf(stderr, "%s\n", getErrMsg(ret));
}
#else
for(;;){
ret = MPGE_processFrame();
if(ret == ME_EMPTYSTREAM) break;
if(ret != ME_NOERR){
if(!silent) fprintf(stderr, "%s\n", getErrMsg(ret));
break;
}
reportDsp(0);
} /* main loop */
#endif
ret = MPGE_closeCoder();
if(ret != ME_NOERR) if(!silent) fprintf(stderr, "%s\n", getErrMsg(ret));
reportTerm();
MPGE_endCoder();
clkput();
return NOERR;
} /* main */
bool Config::parseArgs(int argc, ACE_TCHAR* argv[])
{
#if defined(NSRPC_HAS_PROACTOR)
ACE_Get_Opt getOpt(argc, argv, ACE_TEXT("a:c:e:k:m:n:p:s:t:hrv"));
bool isOk = true;
int c;
while ((c = getOpt()) != EOF) {
switch (c) {
case 'a':
connectHost_ = getOpt.opt_arg();
break;
case 'c':
connections_ = ACE_OS::atoi(getOpt.opt_arg());
break;
case 'e':
echoCount_ = ACE_OS::atoi(getOpt.opt_arg());
break;
case 'k':
blockSize_ = ACE_OS::atoi(getOpt.opt_arg());
break;
case 'm':
mode_ = getOpt.opt_arg();
break;
case 'n':
threads_ = ACE_OS::atoi(getOpt.opt_arg());
break;
case 'p':
port_ =
static_cast<srpc::UInt16>(ACE_OS::atoi(getOpt.opt_arg()));
break;
case 'r':
useRpc_ = true;
break;
case 's':
streamType_ = getOpt.opt_arg();
break;
case 't':
proactorType_ = getOpt.opt_arg();
break;
case 'v':
verbose_ = true;
break;
case 'h':
default:
isOk = false;
break;
}
}
if ((! isServer()) && (! isClient())) {
isOk = false;
}
if ((streamType_ != "bit") && (streamType_ != "byte")) {
isOk = false;
}
if (! isOk) {
printUsage();
}
return isOk;
#else
printUsage();
return false;
#endif // #if defined(NSRPC_HAS_PROACTOR)
}
void StabConfig::processOptions(const QCommandLineParser &parser, ErrorMessageHelper &die, QTextStream *err) {
mdConf.numThreads = getOpt(parser, die, *threadsOption, SomeInt(0), NoneInt, mdConf.numThreads,
QCoreApplication::translate("main", "Cant parse thread count."),
QCoreApplication::translate("main", "Thread count have to be possitive."));
mdConf.shakiness = getOpt(parser, die, *shakinessOption, SomeInt(1), SomeInt(10), mdConf.shakiness,
QCoreApplication::translate("main", "Cant parse shakiness."),
QCoreApplication::translate("main", "Shakiness can be in range 1-10."));
mdConf.accuracy = getOpt(parser, die, *accuracyOption, SomeInt(1), SomeInt(15), mdConf.accuracy,
QCoreApplication::translate("main", "Cant parse accuracy."),
QCoreApplication::translate("main", "Acccuracy can be in range 1-15."));
mdConf.stepSize = getOpt(parser, die, *stepSizeOption, SomeInt(1), SomeInt(1000), mdConf.stepSize,
QCoreApplication::translate("main", "Cant parse step size."),
QCoreApplication::translate("main", "Step size can be in range 1-1000."));
mdConf.contrastThreshold = getOpt(parser, die, *minContrastOption, SomeDouble(0), SomeDouble(1), mdConf.contrastThreshold,
QCoreApplication::translate("main", "Cant parse contrast threshold."),
QCoreApplication::translate("main", "Contrast threshold can be in range 0-1."));
mdConf.show = getOpt(parser, die, *showOption, SomeInt(0), SomeInt(2), mdConf.show,
QCoreApplication::translate("main", "Cant parse show option."),
QCoreApplication::translate("main", "Show option can be in range 0-2."));
tsConf.smoothing = getOpt(parser, die, *smoothingOption, SomeInt(0), NoneInt, tsConf.smoothing,
QCoreApplication::translate("main", "Cant parse smoothing option."),
QCoreApplication::translate("main", "Smoothing have to be possitive."));
if (parser.isSet(*camPathAlgoOption)) {
QString algoStr = parser.value(*camPathAlgoOption);
if (algoStr.compare("gauss", Qt::CaseInsensitive) == 0) {
tsConf.camPathAlgo = VSGaussian;
} else if (algoStr.compare("avg", Qt::CaseInsensitive) == 0) {
tsConf.camPathAlgo = VSAvg;
} else {
die << QCoreApplication::translate("main", "Invalid cam path algorithm \"%1\".").arg(algoStr);
}
}
tsConf.maxShift = getOpt(parser, die, *maxShiftOption, SomeInt(-1), NoneInt, tsConf.maxShift,
QCoreApplication::translate("main", "Cant parse max shift option."),
QCoreApplication::translate("main", "Max. shift can't be smaller than -1."));
tsConf.maxAngle = getOpt(parser, die, *maxAngleOption, SomeDouble(-1), NoneDouble, tsConf.maxAngle,
QCoreApplication::translate("main", "Cant parse max angle option."),
QCoreApplication::translate("main", "Max. angle can't be smaller than -1."));
tsConf.crop = parser.isSet(*cropBlackOption) ? VSCropBorder : VSKeepBorder;
tsConf.invert = parser.isSet(*invertOption) ? 1 : 0;
tsConf.relative = parser.isSet(*relativeOption) ? 1 : 0;
tsConf.zoom = getOpt(parser, die, *zoomOption, NoneDouble, NoneDouble, tsConf.zoom,
QCoreApplication::translate("main", "Cant parse zoom option."),
"");
tsConf.optZoom = getOpt(parser, die, *optZoomOption, SomeInt(0), SomeInt(2), tsConf.optZoom,
QCoreApplication::translate("main", "Cant parse opt-zoom option."),
QCoreApplication::translate("main", "Opt zoom can be 0, 1 or 2."));
tsConf.zoomSpeed = getOpt(parser, die, *zoomSpeedOption, SomeDouble(0), SomeDouble(5), tsConf.zoomSpeed,
QCoreApplication::translate("main", "Cant parse zoom speed option."),
QCoreApplication::translate("main", "Zoom speed can be in range 0-5."));
if (parser.isSet(*interpolOption)) {
QString interpolStr = parser.value(*interpolOption);
if (interpolStr.compare("no", Qt::CaseInsensitive) == 0) {
tsConf.interpolType = VS_Zero;
} else if (interpolStr.compare("linear", Qt::CaseInsensitive) == 0) {
tsConf.interpolType = VS_Linear;
} else if (interpolStr.compare("bilinear", Qt::CaseInsensitive) == 0) {
tsConf.interpolType = VS_BiLinear;
} else if (interpolStr.compare("bicubic", Qt::CaseInsensitive) == 0) {
tsConf.interpolType = VS_BiCubic;
} else {
die << QCoreApplication::translate("main", "Invalid interpolation algorithm \"%1\".").arg(interpolStr);
}
}
mdConf.virtualTripod = getOpt(parser, die, *tripodOption, SomeInt(0), NoneInt, mdConf.virtualTripod,
QCoreApplication::translate("main", "Cant parse tripod option."),
QCoreApplication::translate("main", "Tripod option have to be possitive."));
if (mdConf.virtualTripod > 0) {
if (tsConf.relative != 0)
*err << QCoreApplication::translate("main", "Relative transformation is disabled with tripod.") << endl;
if (tsConf.smoothing != 0)
*err << QCoreApplication::translate("main", "Smoothing is disabled with tripod.") << endl;
tsConf.relative = 0;
tsConf.smoothing = 0;
}
}
/**
* Compute genotypes
*/
void DmetEngine::computeGenotypes() {
ProbesetGenotypeEngine engine;
vector<string> celFiles = getOptVector("cels");
engine.setOpt("cels",celFiles);
vector<string> chipTypes = getOptVector("chip-type");
if(chipTypes.size() > 0)
engine.setOpt("chip-type",chipTypes);
engine.setOpt("cdf-file",getOpt("cdf-file"));
engine.setOpt("spf-file",getOpt("spf-file"));
string analysis;
if(getOpt("gt-analysis") != "") {
analysis = getOpt("gt-analysis");
} else {
///@todo If we have a reference, set analysis and qmethod-spec based on
/// what was used to build the reference
if(getOpt("reference-output") != "") {
analysis = "quant-norm.sketch=50000,pm-only,brlmm-p-multi.CM=1.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.KX=0.3.KH=0.3.KXX=0.1.KAH=-0.1.KHB=-0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.transform=MVA.AAM=2.8.BBM=-2.8.AAV=0.10.BBV=0.10.ABV=0.10.V=1.AAY=10.7.ABY=11.3.BBY=10.7.copyqc=0.00000.wobble=0.05.MS=0.1.copytype=-1.clustertype=2.CSepPen=0.5.ocean=0.0000001";
} else {
analysis = "quant-norm.sketch=50000,pm-only,brlmm-p-multi.CM=2.bins=100.mix=1.bic=2.lambda=1.0.HARD=3.SB=0.75.KX=0.3.KH=0.3.KXX=0.1.KAH=-0.1.KHB=-0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.transform=MVA.AAM=2.8.BBM=-2.8.AAV=0.10.BBV=0.10.ABV=0.10.V=1.AAY=10.7.ABY=11.3.BBY=10.7.copyqc=0.00000.wobble=0.05.MS=0.1.copytype=-1.clustertype=2.CSepPen=0.5.ocean=0.0000001";
}
analysis += ".cc-alleles=6";
analysis += ".cc-type=UCHAR";
analysis += ".cc-version=1.0";
}
if(getOpt("gt-qmethod-spec") != "")
engine.setOpt("qmethod-spec",getOpt("gt-qmethod-spec"));
else
engine.setOpt("qmethod-spec","plier.optmethod=1.FixFeatureEffect=true");
analysis = setPra(analysis,getOptInt("pra-thresh"));
engine.setOpt("analysis",analysis);
engine.setOpt("out-dir",Fs::join(getOpt("out-dir"),"apg"));
engine.setOpt("verbose",getOpt("verbose"));
engine.setOpt("force",getOpt("force"));
engine.setOpt("cc-chp-output","false");
engine.setOpt("probeset-ids-reported",getOpt("probeset-ids-reported"));
engine.setOpt("probeset-ids",getOpt("probeset-ids"));
engine.setOpt("temp-dir", getOpt("temp-dir"));
engine.setOpt("use-disk", getOpt("use-disk"));
engine.setOpt("disk-cache", getOpt("disk-cache"));
engine.setOpt("set-analysis-name", getOpt("set-analysis-name"));
engine.setOpt("call-coder-max-alleles", getOpt("call-coder-max-alleles"));
engine.setOpt("call-coder-type", getOpt("call-coder-type"));
engine.setOpt("call-coder-version", getOpt("call-coder-version"));
engine.setOpt("command-line", getOpt("command-line"));
engine.setOpt("exec-guid", getOpt("exec-guid"));
engine.setOpt("program-name", getOpt("program-name"));
engine.setOpt("program-company", getOpt("program-company"));
engine.setOpt("program-version", getOpt("program-version"));
engine.setOpt("program-cvs-id", getOpt("program-cvs-id"));
engine.setOpt("version-to-report", getOpt("version-to-report"));
engine.setOpt("prior-size", "1");
engine.setOpt("special-snps", getOpt("special-snps"));
engine.setOpt("em-gender", "false");
if(getOpt("chrX-probes") != "") {
engine.setOpt("chrX-probes", getOpt("chrX-probes"));
engine.setOpt("chrY-probes", getOpt("chrY-probes"));
engine.setOpt("set-gender-method", "cn-probe-chrXY-ratio");
engine.setOpt("no-gender-force", "false");
} else {
engine.setOpt("set-gender-method", "none");
engine.setOpt("no-gender-force", "true");
}
engine.setOpt("female-thresh", getOpt("female-thresh"));
engine.setOpt("male-thresh", getOpt("male-thresh"));
engine.setOpt("table-output", "false");
engine.setOpt("output-context", "true");
engine.setOpt("output-forced-calls", "true");
if (getOptBool("run-cn-engine") && getOpt("cn-region-gt-probeset-file") != "") {
/// @todo perhaps we should use state to track the file name
/// as it is we need to keep this in sync with the cn engine call
engine.setOpt("genotype-markers-cn-file",
Fs::join(getOpt("out-dir"),
"adc",
getOpt("set-analysis-name") + ".gt.markers.cn.call.a5"));
}
engine.setOpt("a5-global-file",getOpt("reference-output"));
engine.setOpt("a5-global-file-no-replace","true");
engine.setOpt("a5-group","ProbesetGenotypeEngine");
engine.setOpt("a5-calls","true");
engine.setOpt("a5-summaries","true");
engine.setOpt("a5-feature-effects","true");
engine.setOpt("a5-sketch","true");
engine.setOpt("a5-write-models","true");
if(getOpt("reference-output") != "") {
engine.setOpt("a5-sketch-use-global","true");
engine.setOpt("a5-feature-effects-use-global","true");
engine.setOpt("a5-write-models-use-global","true");
}
engine.setOpt("a5-global-input-file",getOpt("reference-input"));
engine.setOpt("a5-input-group","ProbesetGenotypeEngine");
if(getOpt("reference-input") != "") {
engine.setOpt("a5-sketch-input-global","true");
engine.setOpt("a5-feature-effects-input-global","true");
engine.setOpt("a5-models-input-global","true");
}
if(m_ArgvPosAPG > 0)
engine.parseArgv(m_argv, m_ArgvPosAPG);
engine.run();
}
/*
Set strip brightness based on potentiometer value
*/
void setBrightness() {
// convert analogRead's range of 0 to 1023 to brightness range 0 to 255
uint8_t brightness = (uint8_t) getOpt(_pin_lev, 0, 255);
setBrightness(brightness);
}
int main(int argc, char* argv[]) {
printf("SimpleDS\n");
printf("Build: " VERSION_STR " (" SYSTEM_NAME " " SYSTEM_PROCESSOR ")");
#ifdef SDL_HAPTIC_DISABLED
printf(" - No Haptic");
#endif
printf("\nAuthors: " VERSION_AUTHORS "\n");
args = std::vector<const char*>(argv, argv + argc);
int offset = 1;
std::string configFile = "./simpleds.conf";
if (hasOpt("-c") || hasOpt("--config")) {
configFile = getOpt("-c");
if (configFile.size() == 0) {
configFile = getOpt("--config");
}
offset += 2;
}
config = new Config(configFile);
if (config->loaded) {
printf("Config: %s\n", configFile.c_str());
if (config->has("DS.foo")) {
printf("Foo: %s\n", config->getString("DS.foo").c_str());
}
} else {
printf("Config file couldn't be loaded, won't be able to save\n");
}
uint16_t teamNum = (uint16_t)config->getInt32("DS.team");
verbose = (hasOpt("-v") || hasOpt("--verbose"));
if (hasOpt("-V") || hasOpt("--version")) {
return 0;
}
if (hasOpt("-h") || hasOpt("--help")) {
printUsage();
printf("Options:\n");
printf(" -h, --help Prints this message\n");
printf(" -v, --verbose Output debugging information\n");
printf(" -V, --version Prints version info and exits\n");
printf(" -c, --config Sets the config file to use [default: ./simpleds.conf]\n");
printf(" teamNum The team number to use, must be provided here or in configuration file\n");
return 0;
}
if (teamNum == 0 && args.begin() + offset == args.end()) { // We're out of arguments
printUsage();
return 1;
} else {
char* endptr;
uint16_t argTeamNum = (uint16_t)std::strtol(args[offset], &endptr, 10);
if (endptr == args[offset] || *endptr != '\0') { // No team number in config, and none provided
if (teamNum == 0) {
printUsage();
return 1;
}
} else {
teamNum = argTeamNum;
}
}
printf("Team Number: %d\n", teamNum);
bool quit = false;
SDL_Event e;
auto gui = new GUI();
if (!gui->isValid()) {
return 1;
}
config->setInt32("DS.team", teamNum);
config->initInt32("DS.alliance", Alliance::RED);
config->initInt32("DS.position", 1);
DS::initialize(teamNum);
auto ds = DS::getInstance();
enum GUIMode { MAIN, INFO, JOYSTICKS, CONTROL, HELP, COUNT };
GUIMode mode = GUIMode::MAIN;
auto runner = std::async(std::launch::async, &DS::run, ds);
std::map<GUIMode, Screen*> screens;
screens[MAIN] = new ScreenMain();
screens[INFO] = new ScreenInfo();
screens[JOYSTICKS] = new ScreenJoysticks();
screens[CONTROL] = new ScreenControl();
screens[HELP] = new ScreenHelp();
while (!quit) {
while (gui->pollEvent(&e) != 0) {
if (e.type == SDL_QUIT) {
quit = true;
} else if (e.type == SDL_JOYDEVICEREMOVED || e.type == SDL_JOYDEVICEADDED) {
ds->setEnable(false);
ds->loadJoysticks();
} else if (e.type == SDL_KEYDOWN && e.key.repeat == 0) {
auto key = e.key.keysym;
if (key.sym == SDLK_e) {
ds->toggleEnable();
} else if (key.sym == SDLK_SPACE) {
ds->setEnable(false);
} else if (key.sym == SDLK_0) {
ds->setEStop();
} else if (key.sym == SDLK_q) {
quit = true;
} else if (key.sym == SDLK_r) {
if (key.mod & KMOD_SHIFT) {
ds->reboot();
} else {
ds->restartCode();
}
} else if (key.sym == SDLK_BACKQUOTE) {
ds->setAlliance(ds->getAlliance() == Alliance::BLUE ? Alliance::RED : Alliance::BLUE);
} else if (key.sym >= SDLK_1 && key.sym <= SDLK_9) {
uint8_t keyNum = (uint8_t)(1 + key.sym - SDLK_1);
if (key.mod & KMOD_CTRL && keyNum >= 1 && keyNum <= 3) {
ds->setPosition(keyNum);
} else if (key.mod & KMOD_SHIFT && keyNum >= 1 && keyNum <= 3) {
ds->setEnable(false);
ds->setMode((Mode)(keyNum - 1));
} else if (keyNum >= 1 && keyNum <= GUIMode::COUNT) {
mode = (GUIMode)(keyNum - 1);
}
}
}
screens[mode]->update(e);
}
if (gui->readyToDraw()) {
gui->setOffset(10, 10);
gui->clear();
gui->drawScreen(screens[mode]);
gui->setOffset(10, gui->getHeight() - gui->getCharSize().y);
gui->drawText(0, 0, "1: Main", mode == GUIMode::MAIN ? Colors::BLACK : Colors::DISABLED);
gui->drawTextRel(9, 0, "2: Info", mode == GUIMode::INFO ? Colors::BLACK : Colors::DISABLED);
gui->drawTextRel(9, 0, "3: Joysticks", mode == GUIMode::JOYSTICKS ? Colors::BLACK : Colors::DISABLED);
gui->drawTextRel(14, 0, "4: Control", mode == GUIMode::CONTROL ? Colors::BLACK : Colors::DISABLED);
gui->drawTextRel(12, 0, "5: Help", mode == GUIMode::HELP ? Colors::BLACK : Colors::DISABLED);
gui->render();
}
std::string s = narf::util::format("Team %d", teamNum);
if (ds->isConnected()) {
auto rio = ds->getRoboRIO();
s += " - ";
if (rio->getEStop()) {
s += "E-Stopped";
} else {
s += narf::util::format("%s %s", modeNames[rio->getMode()].c_str(), rio->getEnable() ? "Enabled" : "Disabled");
}
s += narf::util::format(" - %s %d", allianceNames[ds->getAlliance()].c_str(), ds->getPosition());
if (!rio->getCode()) {
s += " - No Code";
}
} else {
s += " - No Comms";
}
gui->setTitle(s);
ds->updateJoysticks();
SDL_Delay(25);
}
ds->saveJoysticks();
ds->stop();
SDL_Quit();
return 0;
}
/**
* Compute probeset summaries values for using in computing CN state
*/
bool DmetEngine::computeCnSummaries() {
ProbesetSummarizeEngine engine;
vector<string> celFiles = getOptVector("cels");
engine.setOpt("cels",celFiles);
vector<string> chipTypes = getOptVector("chip-type");
if(chipTypes.size() > 0)
engine.setOpt("chip-type",chipTypes);
engine.setOpt("cdf-file",getOpt("cdf-file"));
engine.setOpt("spf-file",getOpt("spf-file"));
///@todo If we have a reference, set analysis based on what was used to build the reference
if(getOpt("ps-analysis") != "")
engine.setOpt("analysis",getOpt("ps-analysis"));
else
engine.setOpt("analysis",
"quant-norm.sketch=50000,pm-only,plier.optmethod=1.FixFeatureEffect=true,expr.genotype=true");
engine.setOpt("out-dir",Fs::join(getOpt("out-dir"),"aps"));
engine.setOpt("verbose",getOpt("verbose"));
engine.setOpt("force",getOpt("force"));
engine.setOpt("cc-chp-output","false");
// We only want to process intersection of probesets in consent file
// and those in regions
Fs::ensureWriteableDirPath(getOpt("out-dir", false));
FsPath probesetFile;
probesetFile.setDirName(getOpt("out-dir"));
probesetFile.setFileNameExt("probesets","txt");
if (!generateApsProbesetList(getOpt("probeset-ids-reported"),
getOpt("probeset-model"),
probesetFile.asUnixPath())) {
return false;
}
engine.setOpt("probeset-ids",probesetFile.asUnixPath());
engine.setOpt("temp-dir", getOpt("temp-dir"));
engine.setOpt("use-disk", getOpt("use-disk"));
engine.setOpt("disk-cache", getOpt("disk-cache"));
engine.setOpt("set-analysis-name", getOpt("set-analysis-name"));
engine.setOpt("command-line", getOpt("command-line"));
engine.setOpt("exec-guid", getOpt("exec-guid"));
engine.setOpt("program-name", getOpt("program-name"));
engine.setOpt("program-company", getOpt("program-company"));
engine.setOpt("program-version", getOpt("program-version"));
engine.setOpt("program-cvs-id", getOpt("program-cvs-id"));
engine.setOpt("version-to-report", getOpt("version-to-report"));
engine.setOpt("summaries","false");
engine.setOpt("a5-global-file",getOpt("reference-output"));
//engine.setOpt("a5-global-file-no-replace","true");
engine.setOpt("a5-group","ProbesetSummarizeEngine");
engine.setOpt("a5-sketch","true");
engine.setOpt("a5-summaries","true");
engine.setOpt("a5-feature-effects","true");
if(getOpt("reference-output") != "") {
engine.setOpt("a5-feature-effects-use-global","true");
engine.setOpt("a5-sketch-use-global","true");
}
engine.setOpt("a5-global-input-file",getOpt("reference-input"));
engine.setOpt("a5-input-group","ProbesetSummarizeEngine");
if(getOpt("reference-input") != "") {
engine.setOpt("a5-sketch-input-global","true");
engine.setOpt("a5-feature-effects-input-global","true");
}
if(m_ArgvPosAPS > 0)
engine.parseArgv(m_argv, m_ArgvPosAPS);
engine.run();
return true;
}
/**
* Build final CHP files
*/
void DmetEngine::generateChpFiles() {
DmetCHPWriter engine;
AnalysisInfo info;
fillInAnalysisInfo(info);
engine.setAnalysisInfo(info);
vector<string> celFiles = getOptVector("cels");
engine.setOpt("cels",celFiles);
engine.setOpt("out-dir",Fs::join(getOpt("out-dir"),"chp"));
engine.setOpt("verbose",getOpt("verbose"));
engine.setOpt("set-analysis-name", getOpt("set-analysis-name"));
engine.setOpt("exec-guid", getOpt("exec-guid"));
engine.setOpt("program-name", getOpt("program-name"));
engine.setOpt("program-company", getOpt("program-company"));
engine.setOpt("program-version", getOpt("program-version"));
engine.setOpt("batch-name", getOpt("batch-name"));
if (getOptBool("run-cn-engine")) {
engine.setOpt("a5-copynumber",
Fs::join(getOpt("out-dir"), "adc",
getOpt("set-analysis-name") + ".copynumber.a5"));
}
engine.setOpt("a5-summaries",
Fs::join(getOpt("out-dir"), "apg",
getOpt("set-analysis-name") + ".summary.a5"));
engine.setOpt("a5-calls",
Fs::join(getOpt("out-dir"), "apg",
getOpt("set-analysis-name") + ".calls.a5"));
engine.setOpt("a5-forced-calls",
Fs::join(getOpt("out-dir"), "apg", getOpt("set-analysis-name") + ".forced-calls.a5"));
engine.setOpt("a5-confidences",
Fs::join(getOpt("out-dir"), "apg",
getOpt("set-analysis-name") + ".confidences.a5"));
engine.setOpt("a5-context",
Fs::join(getOpt("out-dir"), "apg",
getOpt("set-analysis-name") + ".context.a5"));
engine.setOpt("report-file",
Fs::join(getOpt("out-dir"), "apg",
getOpt("set-analysis-name") + ".report.txt"));
engine.setOpt("spf-file",getOpt("spf-file"));
engine.setOpt("cdf-file",getOpt("cdf-file"));
engine.setOpt("region-model", getOpt("region-model"));
engine.setOpt("null-context", getOpt("null-context"));
engine.setOpt("geno-call-thresh", getOpt("geno-call-thresh"));
engine.setOpt("call-coder-max-alleles", getOpt("call-coder-max-alleles"));
engine.setOpt("call-coder-type", getOpt("call-coder-type"));
engine.setOpt("call-coder-version", getOpt("call-coder-version"));
engine.run();
}
void DmetEngine::fillInAnalysisInfo(AnalysisInfo &info) {
string prefix = "apt-";
vector<string> celFiles = getOptVector("cels");
info.m_AlgVersion = "3.0";
info.m_AlgName = getOpt("set-analysis-name");
info.m_ProgramName = getOpt("program-name");
info.m_ProgramVersion = getOpt("version-to-report");
info.m_ProgramCompany = getOpt("program-company");
info.m_ChipType = getOpt("chip-type");
info.m_ProgID = "";
info.m_ExecGuid = getOpt("exec-guid");
info.m_AnalysisGuid = getOpt("analysis-guid");
// Execution info
info.addParam("apt-engine", "DmetEngine");
info.addParam(prefix + "program-name", getOpt("program-name"));
info.addParam(prefix + "command-line", getOpt("command-line"));
info.addParam(prefix + "exec-guid", getOpt("exec-guid"));
info.addParam(prefix + "analysis-guid", getOpt("analysis-guid"));
info.addParam(prefix + "time-str", getOpt("time-start"));
info.addParam(prefix + "version", getOpt("version-to-report"));
info.addParam(prefix + "cvs-id", getOpt("program-cvs-id"));
// Engine Options
string opt = "opt-";
vector<string> initialOptionNames;
getOptionNames(initialOptionNames,1);
for(int i=0; i<initialOptionNames.size(); i++) {
string name = initialOptionNames[i];
if((name != "cels") || getOptBool("batch-info")){
info.addParam(prefix + opt + name, makeVal(name,1));
}
}
// Cel files in batch
if(getOptBool("batch-info")){
for(uint32_t i = 0; i < celFiles.size(); i++) {
std::string paramName = prefix + opt + "cel-" + ToStr(i+1);
info.addParam(paramName, Fs::basename(celFiles[i]));
affymetrix_fusion_io::FusionCELData cel;
try {
cel.SetFileName(celFiles[i].c_str());
if(!cel.ReadHeader()) {
Err::errAbort("Unable to read CEL file " + celFiles[i]);
}
affymetrix_calvin_io::GenericData *gdata = cel.GetGenericData();
if (gdata != NULL)
{
std::string paramName = prefix + opt + "cel-guid-" + ToStr(i+1);
info.addParam(paramName, gdata->Header().GetGenericDataHdr()->GetFileId());
}
cel.Close();
}
catch (...)
{
Err::errAbort("Unable to read CEL file " + celFiles[i]);
}
}
}
// Engine State
string option = "state-";
std::vector<std::string> optionNames;
getOptionNames(optionNames);
for(int i=0; i<optionNames.size(); i++) {
string name = optionNames[i];
if((name != "cels") || getOptBool("batch-info")){
info.addParam(prefix + option + name, makeVal(name));
}
}
// Sanity check
Err::check(info.m_ParamValues.size() == info.m_ParamNames.size(),
"AnalysisInfo - Names and values out of sync.");
}
/** MAIN function. -------------------------------------------------------------------------------*/
int main( int argc, char** argv )
{
Size boardSize, imageSize;
float squareSize = 1.f, aspectRatio = 1.f;
Mat cameraMatrix, distCoeffs;
//DEPRECATE proposal
const char* outputFilename = "out_camera_data.yml";
//DEPRECATE proposal
const char* inputFilename = 0;
int i, nframes = 15;
bool writeExtrinsics = false, writePoints = false;
bool undistortImage = false;
int flags = 0;
VideoCapture capture;
bool flipVertical = false;
bool showUndistorted = false;
bool videofile = false;
int delay = 1000;
clock_t prevTimestamp = 0;
int mode = DETECTION;
int cameraId = 0;
vector<vector<Point2f> > imagePoints;
vector<string> imageList;
if ( getOpt(argc, argv, &boardSize, &squareSize, &nframes, &aspectRatio, &delay, &flags, &writeExtrinsics, &writePoints, &flipVertical, &showUndistorted, &videofile, &cameraId, inputFilename, outputFilename) != 0)
return -1;
if( inputFilename )
{
if( !videofile && readStringList(inputFilename, imageList) )
mode = CAPTURING;
else
capture.open(inputFilename);
}
else
capture.open(cameraId);
if( !capture.isOpened() && imageList.empty() )
return fprintf(stderr, "Could not initialize video (%d) capture\n", cameraId ), -2;
if( !imageList.empty() )
nframes = (int)imageList.size();
if( capture.isOpened() )
printf("%s", liveCaptureHelp);
namedWindow("Image View", 1);
bool qrfound = false;
int qr_pixel_size;
struct quirc *q;
q = quirc_new();
for(i = 0;;i++)
{
Mat view, viewGray;
bool blink = false;
if( capture.isOpened() )
{
Mat view0;
capture >> view0;
view0.copyTo(view);
}
else if( i < (int)imageList.size() )
/**
* Make sure that our options are sane. Call Err::errAbort if not.
*/
void DmetEngine::checkOptionsImp() {
defineStates();
setLibFileOpt("cdf-file");
setLibFileOpt("spf-file");
setLibFileOpt("special-snps");
setLibFileOpt("chrX-probes");
setLibFileOpt("chrY-probes");
setLibFileOpt("reference-input");
setLibFileOpt("probeset-ids");
setLibFileOpt("probeset-ids-reported");
setLibFileOpt("region-model");
setLibFileOpt("probeset-model");
setLibFileOpt("cn-region-gt-probeset-file");
if (getOpt("out-dir") == "") {Err::errAbort("Must specify an output directory.");}
if (getOpt("temp-dir") == "") {
setOpt("temp-dir", Fs::join(getOpt("out-dir"),"temp"));
}
string cdfFile = getOpt("cdf-file");
string spfFile = getOpt("spf-file");
string specialSnps = getOpt("special-snps");
string chrXProbes = getOpt("chrX-probes");
string chrYProbes = getOpt("chrY-probes");
if(getOpt("sample-type") == "plasmid") {
setOpt("run-cn-engine","false");
} else {
setOpt("run-cn-engine",getOpt("run-cn-engine"));
}
string refOut = getOpt("reference-output");
string batchName = getOpt("batch-name");
if(refOut == "") {
if (batchName.empty() != true)
Err::errAbort("You cannot provide a batch-name when running in single sample mode. batch-name is only valid when output-reference is specified.");
} else {
if (batchName.empty() == true)
Err::errAbort("You must define the batch-name parameter");
if(Fs::isReadable(refOut))
if(Fs::rm(refOut, false) != APT_OK)
Err::errAbort("Unable to remove existing reference-output file '" + refOut + "'");
}
///@todo check chip type in reference file
///@todo check reference file version
/* Read in cel file list from other file if specified. */
vector<string> celFiles;
EngineUtil::getCelFiles(celFiles, this);
if(celFiles.size() == 0)
Err::errAbort("No cel files specified.");
setOpt("cels",celFiles);
// Build a consent file if vector of markers was passed in
vector<string> consented = getOptVector("report");
if(consented.size() > 0) {
FsPath probeset_path;
probeset_path.setPath(getOpt("out-dir"),"probesets-reported","txt");
//probeset_path.ensureWriteableDirPath();
Fs::ensureWriteableDirPath(getOpt("out-dir", false));
writeProbesetList(probeset_path.asUnixPath(), consented);
setOpt("probeset-ids-reported", probeset_path.asUnixPath());
} else {
setOpt("probeset-ids-reported", getOpt("probeset-ids-reported"));
}
if(cdfFile == "" && spfFile == "")
Err::errAbort("Must specify either a cdf file or spf (simple probe format) file.");
if (chrXProbes != "" && chrYProbes == "")
Err::errAbort("Must provide a chrY Probe File when providing a chrX Probe File.");
if (chrXProbes == "" && chrYProbes != "")
Err::errAbort("Must provide a chrX Probe File when providing a chrY Probe File.");
// Check chip types
vector<string> chipTypesInLayout;
/* Get the intial info about the chip and check cel files to make sure
they match. */
colrow_t numRows = 0, numCols = 0;
int probeCount=0, probeSetCount=0;
if(cdfFile != "")
EngineUtil::getCdfChipType(chipTypesInLayout, numRows, numCols, probeCount, probeSetCount, cdfFile);
else if(spfFile != "")
EngineUtil::getSpfChipType(chipTypesInLayout, numRows, numCols, probeCount, probeSetCount, spfFile);
else
Err::errAbort("Must specify either a cdf file or spf (simple probe format) file.");
setOpt("num-rows", ToStr(numRows));
setOpt("num-cols", ToStr(numCols));
setOpt("probe-count", ToStr(probeCount));
if(chipTypesInLayout.empty() || chipTypesInLayout[0] == "" || probeCount == 0)
Err::errAbort("Problem determining ChipType in file: " +
( cdfFile != "" ? cdfFile : spfFile));
/* Did the user "force" a set of chip types via options? */
vector<string> chipTypesSupplied = getOptVector("chip-type");
/* Figure out what chip type to report */
if(chipTypesSupplied.size() > 0) {
setOpt("chip-type", chipTypesSupplied);
} else if(chipTypesInLayout.size() > 0) {
setOpt("chip-type", chipTypesInLayout);
} else {
Err::errAbort("Unable to figure out a chip type.");
}
/* Do Chip Type Check */
if(!getOptBool("force")) {
vector<string> chipTypeJustPrimary;
vector<string> chipTypesToCheck;
if(chipTypesSupplied.size() > 0) {
chipTypesToCheck = chipTypesSupplied;
EngineUtil::checkChipTypeVectors(chipTypesSupplied, chipTypesInLayout);
} else {
chipTypesToCheck = chipTypesInLayout;
}
chipTypeJustPrimary.push_back(chipTypesToCheck[0]);
EngineUtil::checkCelChipTypes(chipTypesToCheck, probeCount, celFiles, numRows, numCols);
// Check special SNPs files
if (specialSnps != "") {
EngineUtil::checkTsvFileChipType(specialSnps, chipTypeJustPrimary);
}
// And other files
if (chrXProbes != "") {
EngineUtil::checkTsvFileChipType(chrXProbes, chipTypesToCheck);
}
if (chrYProbes != "") {
EngineUtil::checkTsvFileChipType(chrYProbes, chipTypesToCheck);
}
} // end if(!force)
}
/**
* Compute the CN state
*/
void DmetEngine::computeCnState() {
DmetCopyNumberEngine engine;
engine.setOpt("out-dir",Fs::join(getOpt("out-dir"),"adc"));
engine.setOpt("force",getOpt("force"));
engine.setOpt("verbose",getOpt("verbose"));
engine.setOpt("set-analysis-name", getOpt("set-analysis-name"));
engine.setOpt("command-line", getOpt("command-line"));
engine.setOpt("exec-guid", getOpt("exec-guid"));
engine.setOpt("program-name", getOpt("program-name"));
engine.setOpt("program-company", getOpt("program-company"));
engine.setOpt("program-version", getOpt("program-version"));
engine.setOpt("program-cvs-id", getOpt("program-cvs-id"));
engine.setOpt("version-to-report", getOpt("version-to-report"));
engine.setOpt("a5-output", "true");
engine.setOpt("text-output", "true");
engine.setOpt("region-model", getOpt("region-model"));
engine.setOpt("cn-region-gt-probeset-file", getOpt("cn-region-gt-probeset-file"));
engine.setOpt("probeset-model", getOpt("probeset-model"));
engine.setOpt("a5-summaries",
Fs::join(getOpt("out-dir"), "aps",
getOpt("set-analysis-name") + ".summary.a5"));
if(m_ArgvPosCN > 0)
engine.parseArgv(m_argv, m_ArgvPosCN);
engine.run();
}