C++ CCmdLine类代码示例

int main(int argc, _TCHAR* argv[])
//int _tmain(int argc, _TCHAR* argv[])
{
/*
    Power [-suspend | -hibernate]
*/
    CCmdLine cmdLine;
    cmdLine.SplitLine( argc, argv );

    if ( cmdLine.HasSwitch( "-suspend" ) ) {

        //::LockWorkStation(); // ËøÆÁ
        ::SetSuspendState( FALSE, FALSE, FALSE ); // ´ý»ú

    } else if ( cmdLine.HasSwitch( "-hibernate" ) ) {

        ::SetSuspendState( TRUE, FALSE, FALSE ); // ÐÝÃß

    }
    return 0;
}

/*
 * Get the file name from the command line arguments.
 * Show the help if required.
 */
bool GetOptions(int argc, char **argv, ConverterOptions &options)
{
	CCmdLine cmdLine;

	// parse argc,argv 
	// no switches were given on the command line, abort
	if (cmdLine.SplitLine(argc, argv) < 1)
	{
		ShowHelp();
		return false;
	}

	// test for the 'help' case
	if (cmdLine.HasSwitch(HELP_ARG))
	{
		ShowHelp();
		return false;
	}

	// get the required argument
	try
	{
		string str;
		str = cmdLine.GetArgument(INPUT_FILE_ARG, 0);
		options.fileName = str;

		str = cmdLine.GetArgument(VERSION_ARG, 0);
		options.version = (CELFileVersionType)(atoi(str.c_str()));
	}
	catch (...)
	{
		// one of the required arguments was missing, abort
		ShowHelp();
		return false;
	}
	return true;
}

// 初始化命令行参数
BOOL CUpdaterApp::_InitCmdline(int argc, LPTSTR* args)
{
	BOOL bReturn(FALSE);
	CCmdLine cmder;
	if (cmder.SplitLine(__argc, __targv) >= 2)
	{
		if (cmder.HasSwitch(_T("-PID")) && cmder.HasSwitch(_T("-H")))
		{
			m_dwProcessId = (DWORD)_ttoi(cmder.GetSafeArgument(_T("-PID"), 0, _T("0")));
			m_hWindowCtrl = (HWND)_ttoi(cmder.GetSafeArgument(_T("-H"), 0, _T("0")));
			bReturn = TRUE;
		}
		else
		{
			LOG(_T("命令行参数错误！"));
		}
	}
	else
	{
		LOG(_T("未指定命令行参数"));
	}
	return bReturn;
}

int main(int argc, char**argv)
#endif
{
#if defined WIN32
#ifndef _DEBUG
    CreateMutexA(0, FALSE, "Local\\Domoticz");
    if(GetLastError() == ERROR_ALREADY_EXISTS) {
        MessageBox(HWND_DESKTOP,"Another instance of Domoticz is already running!","Domoticz",MB_OK);
        return 1;
    }
#endif //_DEBUG
    bool bStartWebBrowser = true;
    RedirectIOToConsole();
#endif //WIN32

    szStartupFolder = "";
    szWWWFolder = "";
    szWebRoot = "";

    CCmdLine cmdLine;

    // parse argc,argv
#if defined WIN32
    cmdLine.SplitLine(__argc, __argv);
#else
    cmdLine.SplitLine(argc, argv);
    //ignore pipe errors
    signal(SIGPIPE, SIG_IGN);
#endif

    if (cmdLine.HasSwitch("-log"))
    {
        if (cmdLine.GetArgumentCount("-log") != 1)
        {
            _log.Log(LOG_ERROR, "Please specify an output log file");
            return 1;
        }
        logfile = cmdLine.GetSafeArgument("-log", 0, "domoticz.log");
        _log.SetOutputFile(logfile.c_str());
    }
    if (cmdLine.HasSwitch("-loglevel"))
    {
        if (cmdLine.GetArgumentCount("-loglevel") != 1)
        {
            _log.Log(LOG_ERROR, "Please specify logfile output level (0=All, 1=Status+Error, 2=Error)");
            return 1;
        }
        int Level = atoi(cmdLine.GetSafeArgument("-loglevel", 0, "").c_str());
        _log.SetVerboseLevel((_eLogFileVerboseLevel)Level);
    }
    if (cmdLine.HasSwitch("-notimestamps"))
    {
        _log.EnableLogTimestamps(false);
    }

    if (cmdLine.HasSwitch("-approot"))
    {
        if (cmdLine.GetArgumentCount("-approot") != 1)
        {
            _log.Log(LOG_ERROR, "Please specify a APP root path");
            return 1;
        }
        std::string szroot = cmdLine.GetSafeArgument("-approot", 0, "");
        if (szroot.size() != 0)
            szStartupFolder = szroot;
    }

    if (szStartupFolder == "")
    {
#if !defined WIN32
        char szStartupPath[255];
        getExecutablePathName((char*)&szStartupPath,255);
        szStartupFolder=szStartupPath;
        if (szStartupFolder.find_last_of('/')!=std::string::npos)
            szStartupFolder=szStartupFolder.substr(0,szStartupFolder.find_last_of('/')+1);
#else
#ifndef _DEBUG
        char szStartupPath[255];
        char * p;
        GetModuleFileName(NULL, szStartupPath, sizeof(szStartupPath));
        p = szStartupPath + strlen(szStartupPath);

        while (p >= szStartupPath && *p != '\\')
            p--;

        if (++p >= szStartupPath)
            *p = 0;
        szStartupFolder=szStartupPath;
        size_t start_pos = szStartupFolder.find("\\Release\\");
        if(start_pos != std::string::npos) {
            szStartupFolder.replace(start_pos, 9, "\\domoticz\\");
            _log.Log(LOG_STATUS,"%s",szStartupFolder.c_str());
        }
#endif
#endif
    }
    GetAppVersion();
    _log.Log(LOG_STATUS, "Domoticz V%s (c)2012-%d GizMoCuz", szAppVersion.c_str(), ActYear);
    _log.Log(LOG_STATUS, "Build Hash: %s, Date: %s", szAppHash.c_str(), szAppDate.c_str());

//.........这里部分代码省略.........

int main(int argc, char**argv)
#endif
{
#if defined WIN32
	CreateMutexA(0, FALSE, "Local\\Domoticz"); 
    if(GetLastError() == ERROR_ALREADY_EXISTS) { 
		MessageBox(HWND_DESKTOP,"Another instance of Domoticz is already running!","Domoticz",MB_OK);
        return -1; 
	}
	bool bStartWebBrowser=true;
	RedirectIOToConsole();
#endif

	szStartupFolder="";
	szWWWFolder="";
#if !defined WIN32
	char szStartupPath[255];
	getExecutablePathName((char*)&szStartupPath,255);
	szStartupFolder=szStartupPath;
	if (szStartupFolder.find_last_of('/')!=std::string::npos)
		szStartupFolder=szStartupFolder.substr(0,szStartupFolder.find_last_of('/')+1);
#else
	#ifndef _DEBUG
		char szStartupPath[255];
		char * p;
		GetModuleFileName(NULL, szStartupPath, sizeof(szStartupPath));
		p = szStartupPath + strlen(szStartupPath);

		while(p >= szStartupPath && *p != '\\')
			p--;

		if(++p >= szStartupPath)
			*p = 0;
		szStartupFolder=szStartupPath;
		size_t start_pos = szStartupFolder.find("\\Release\\");
		if(start_pos != std::string::npos) {
			szStartupFolder.replace(start_pos, 9, "\\domoticz\\");
			_log.Log(LOG_NORM,"%s",szStartupFolder.c_str());
		}
	#endif
#endif
	GetAppVersion();
	_log.Log(LOG_NORM,"Domoticz V%s (c)2012-2014 GizMoCuz",szAppVersion.c_str());

#if !defined WIN32
	//Check if we are running on a RaspberryPi
	std::string sLine = "";
	std::ifstream infile;

	infile.open("/proc/cpuinfo");
	if (infile.is_open())
	{
		while (!infile.eof())
		{
			getline(infile, sLine);
			if (sLine.find("BCM2708")!=std::string::npos)
			{
				_log.Log(LOG_NORM,"System: Raspberry Pi");
				bIsRaspberryPi=true;
				break;
			}
		}
		infile.close();
	}
	_log.Log(LOG_NORM,"Startup Path: %s", szStartupFolder.c_str());
#endif

	szWWWFolder=szStartupFolder+"www";

	CCmdLine cmdLine;

	// parse argc,argv 
#if defined WIN32
	cmdLine.SplitLine(__argc, __argv);
#else
	cmdLine.SplitLine(argc, argv);
#endif

	if ((cmdLine.HasSwitch("-h"))||(cmdLine.HasSwitch("--help"))||(cmdLine.HasSwitch("/?")))
	{
		_log.Log(LOG_NORM,szHelp);
		return 0;
	}

	if (cmdLine.HasSwitch("-startupdelay"))
	{
		if (cmdLine.GetArgumentCount("-startupdelay")!=1)
		{
			_log.Log(LOG_ERROR,"Please specify a startupdelay");
			return 0;
		}
		int DelaySeconds=atoi(cmdLine.GetSafeArgument("-startupdelay",0,"").c_str());
		_log.Log(LOG_NORM,"Startup delay... waiting %d seconds...",DelaySeconds);
		sleep_seconds(DelaySeconds);
	}

	if (cmdLine.HasSwitch("-www"))
	{
		if (cmdLine.GetArgumentCount("-www")!=1)
		{
//.........这里部分代码省略.........

int main(int argc, char* argv[]){
	CCmdLine cmdLine;
	
	cmdLine.SplitLine(argc, argv);

	if ( !(cmdLine.HasSwitch("-i") && cmdLine.HasSwitch("-o") && (cmdLine.HasSwitch("-pos") || cmdLine.HasSwitch("-f") || cmdLine.HasSwitch("-pbOnly"))) ){
		fprintf(stderr, "usage: %s -i <image> -o <output-directory> < -pos <x> <y> | -f <fixation-points-file> > [ -pb <probabilistic-boundary-prefix ] [ -flow <optical-flow-file> ] [ -sobel ]\n",argv[0]);
		fprintf(stderr, "OR \t %s -pbOnly -i <image> -o <output-probabilistic-boundary-prefix>\n",argv[0]);
		exit(1);
	}
	class segLayer frame1;
	char tmp[80];
	strcpy (tmp, cmdLine.GetArgument("-i", 0).c_str());

	int64 tic1,tic2,tic3,tic4;
	double ticFrequency = cvGetTickFrequency()*1000000;
	tic1=cvGetTickCount();

	IplImage *im=cvLoadImage(tmp), *im2;
	#ifdef CUDA_SUPPORT
	int maxWidth=640;
	#else
	int maxWidth=640;
	#endif
	bool resized=false;
	float scale=1;
	if(cvGetSize(im).width>maxWidth){
		scale=maxWidth/(double)(cvGetSize(im).width);
		printf("Image too big, resizing it for the segmentation...\n");
	    	int newHeight=(int)(cvGetSize(im).height*scale);
	    	im2=cvCreateImage( cvSize(maxWidth,newHeight), IPL_DEPTH_8U, 3 );
	    	cvResize(im,im2);
		resized=true;
	}else{
		im2=im;
	}
  	frame1.setImage(im2);

	if (cmdLine.HasSwitch("-pb")){
		strcpy (tmp, cmdLine.GetArgument("-pb", 0).c_str());
		frame1.readPbBoundary(tmp);
	}else{

		// Edge detection!
		if (cmdLine.HasSwitch("-sobel"))
	  		frame1.edgeSobel();
		else{
	#ifdef CUDA_SUPPORT
			if(!get_lock()){
				fprintf(stderr,"Impossible to get the lock...\n");
				exit(1);
			}
			frame1.edgeGPU(false);
			if(!release_lock()){
				fprintf(stderr,"Impossible to release the lock...\n");
				exit(1);
			}
	#else
			frame1.edgeCGTG();
	#endif
		}

		tic2=cvGetTickCount();

		if (cmdLine.HasSwitch("-flow")){
			strcpy (tmp, cmdLine.GetArgument("-flow", 0).c_str());
			IplImage *flow=cvLoadImage(tmp);
			IplImage *flow32 = cvCreateImage(cvGetSize(flow), IPL_DEPTH_32F,3);
			IplImage *flowU = cvCreateImage(cvGetSize(flow), IPL_DEPTH_32F,1);
	  		IplImage *flowV = cvCreateImage(cvGetSize(flow), IPL_DEPTH_32F,1);
			cvConvertScale(flow, flow32, 40/255.,-20);
			cvSplit(flow32,flowU,NULL,NULL,NULL);
			cvSplit(flow32,NULL,flowV,NULL,NULL);
			frame1.setU(flowU);
			frame1.setV(flowV);
			cvReleaseImage(&flow);
			cvReleaseImage(&flow32);
		}


		frame1.generatePbBoundary();
	}
	
	if (cmdLine.HasSwitch("-pbOnly")){
		strcpy (tmp, cmdLine.GetArgument("-o", 0).c_str());
		frame1.savePbBoundary(tmp);
	}else{
		frame1.allocateMemForContours();// Don't forget to allocate memory to store the region contours.
		//select fixation point!
		if(cmdLine.HasSwitch("-pos")){
			float x,y;
			sscanf(cmdLine.GetArgument("-pos", 0).c_str(),"%f",&x);
			sscanf(cmdLine.GetArgument("-pos", 1).c_str(),"%f",&y);
			frame1.assignFixPt((int)(x*scale), (int)(y*scale));
		}else{
			strcpy (tmp, cmdLine.GetArgument("-f", 0).c_str());
			frame1.readFixPts(tmp,scale);
		}
		//segment
		frame1.segmentAllFixs();		
//.........这里部分代码省略.........

int main(int argc, char* argv[])
{
	// Read parameters from console.
	CCmdLine cmdLine;

	if(cmdLine.SplitLine(argc, argv) < 5)
	{
		cerr << "Usage: ./bbnet -s score_file -n node -b bkg -f func_depth -o output" << endl;
		cerr << endl << "Additional parameter:" << endl;
		cerr << "-k\tPenalty parameter(logK, Default = 5.0)" << endl;
		cerr << "-c\tnumber of candidate motifs (Default=50)" << endl;
		cerr << "-d\tpositive negative (for prediction using BN)" << endl;
		cerr << "-l\toutput of all training samples' information." << endl;
		cerr << "-t\ttranslational(transcriptional) start sites.(Default = right end)" << endl;
		cerr << "-rb\tbit-string to determine which rules to include.(Default = 111110)" << endl;
		cerr << "-i\tUse mutual information instead of Bayesian score" << endl;
		cerr << endl << "Contact: \"Li Shen\"<[email protected]>" << endl;
		return 1;
	}

	string s, n, b, f, o;
	try
	{
		s = cmdLine.GetArgument("-s", 0);	// score file.
		n = cmdLine.GetArgument("-n", 0);	// node gene list file.
		b = cmdLine.GetArgument("-b", 0);	// bkg gene list file.
		f = cmdLine.GetArgument("-f", 0);	// func depth folder.
		o = cmdLine.GetArgument("-o", 0);	// results output file.
	}
	catch(int)
	{
		cerr << "Wrong arguments!" << endl;
		return 1;
	}

	if(cmdLine.HasSwitch("-i"))
		itag = true;

	//itag = true;
	//string s = "../gbnet/data/Beer/scor_test.list";
	//string n = "../gbnet/data/Beer/node.list";
	//string b = "../gbnet/data/Beer/bkg.list";
	//string f = "../gbnet/data/Beer/func";
	//string k = "0.015";
	//logK = atof(k.data());
	//string o = "../gbnet/data/Beer/bb_res_test2.txt";

	string k;	// Penalty parameter; logK value.
	if(!itag)
		k = cmdLine.GetSafeArgument("-k", 0, "5.0");
	else
		k = cmdLine.GetSafeArgument("-k", 0, "0.015");
	logK = atof(k.data());

	string c = cmdLine.GetSafeArgument("-c", 0, "50");	// number of candidate motifs. default = 50.
	motifcand = atoi(c.data());

	// Use prior counts for some motifs if specified.
	string p = cmdLine.GetSafeArgument("-p", 0, "0");	// prior counts.
	pricnt = atoi(p.data());
	if(pricnt > 0)	// read preferred motifs list from file.
	{
		prior = 1;
		string fPrim = cmdLine.GetSafeArgument("-p", 1, "primot.txt");
		vector<string> primv;
		if(get1stcol(fPrim, primv) < 0)
			return 1;
		for(size_t i = 0; i < primv.size(); i++)
			primo.insert(primv[i]);
	}

	// File names for positive, negative and left-out testing lists.
	string pos = cmdLine.GetSafeArgument("-d", 0, "");	// positive testing cases.
	string neg = cmdLine.GetSafeArgument("-d", 1, "");	// negative testing cases.
	string res = cmdLine.GetSafeArgument("-d", 2, "");	// left-out testing cases.
	vector<string> plst, nlst, rlst;	// positive, negative and left-out lists.
	if(pos != "" && neg != "")
	{
		if(get1stcol(pos, plst) < 0)
			return 1;
		if(get1stcol(neg, nlst) < 0)
			return 1;
	}
	if(res != "")
	{
		if(get1stcol(res, rlst) < 0)
			return 1;
	}

	// File for output of all training samples' information.
	string finfo = cmdLine.GetSafeArgument("-l", 0, "");

	// File to store all genes' translational/transcriptional start sites.
	string ftss = cmdLine.GetSafeArgument("-t", 0, "");
	if(ftss != "")
		loadtss(ftss, mtss);

	// A bit-string to determine which rules to include.
	rb = cmdLine.GetSafeArgument("-rb", 0, "111110");

//.........这里部分代码省略.........

/*! The main entrance to the program. */
int main(int argc, char * argv[])
{
	try
	{
		// Parse the command line arguments.
		CCmdLine cmdLine;
		if (cmdLine.SplitLine(argc, argv) < 1)
		{
			show_help();
			exit(-1);
		}

		string execId = cmdLine.GetArgument("-execid", 0);
		string celFile = cmdLine.GetSafeArgument("-cel", 0, "");
		string inFile = cmdLine.GetArgument("-in", 0);
		string outFile = cmdLine.GetArgument("-out", 0);
		string arrayType = cmdLine.GetArgument("-arrayType", 0);
		string algName = cmdLine.GetArgument("-algName", 0);
		string algVersion = cmdLine.GetArgument("-algVersion", 0);
		string programName = cmdLine.GetArgument("-programName", 0);
		string programVersion = cmdLine.GetArgument("-programVersion", 0);
		string programCompany = cmdLine.GetArgument("-programCompany", 0);

		vector<string> colNames;
		int n = cmdLine.GetArgumentCount("-colNames");
		for (int i=0; i<n; i++)
			colNames.push_back(cmdLine.GetArgument("-colNames", i));

		vector<string> colTypes;
		n = cmdLine.GetArgumentCount("-colTypes");
		for (int i=0; i<n; i++)
			colTypes.push_back(cmdLine.GetArgument("-colTypes", i));

		vector<string> paramNames;
		n = cmdLine.GetArgumentCount("-paramNames");
		for (int i=0; i<n; i++)
			paramNames.push_back(cmdLine.GetArgument("-paramNames", i));

		vector<string> paramValues;
		n = cmdLine.GetArgumentCount("-paramValues");
		for (int i=0; i<n; i++)
			paramValues.push_back(cmdLine.GetArgument("-paramValues", i));

		vector<string> sumNames;
		n = cmdLine.GetArgumentCount("-sumNames");
		for (int i=0; i<n; i++)
			sumNames.push_back(cmdLine.GetArgument("-sumNames", i));

		vector<string> sumValues;
		n = cmdLine.GetArgumentCount("-sumValues");
		for (int i=0; i<n; i++)
			sumValues.push_back(cmdLine.GetArgument("-sumValues", i));

		vector<string> extraNames;
		n = cmdLine.GetArgumentCount("-extraNames");
		for (int i=0; i<n; i++)
			extraNames.push_back(cmdLine.GetArgument("-extraNames", i));

		vector<string> extraValues;
		n = cmdLine.GetArgumentCount("-extraValues");
		for (int i=0; i<n; i++)
			extraValues.push_back(cmdLine.GetArgument("-extraValues", i));

		// Read the TSV input file
		int maxProbeSetNameLength = 0;

		// data collection is no longer used, so we have ReadData return the row count so that we can pass it into
		// CreateFileWithHeader call
		unsigned long rowCount = ReadData(inFile, maxProbeSetNameLength);

		// Create the CHP file.
		// Creates the header
		CreateFileWithHeader(execId, celFile, outFile, colNames, colTypes, rowCount, maxProbeSetNameLength,
			algName, algVersion, arrayType, programName, programVersion, programCompany, paramNames, paramValues,
			sumNames, sumValues, extraNames, extraValues);

		// add the body (data)
		AddFileBody(inFile,outFile, maxProbeSetNameLength, colTypes);
	}
	catch (string s)
	{
		cout << s << endl;
		show_help();
	}
	catch (int e)
	{
		cout << "Invalid argument" << endl;
		show_help();
	}
	catch (...)
	{
		cout << "Unknown error" << endl;
		show_help();
	}
	return 0;
}

int main(int argc, char* argv[])
{
        // Read in parameters from command line.
        CCmdLine cmdLine;

        if(cmdLine.SplitLine(argc, argv) < 3)
        {
                cerr << "Usage: ./gittar -m consensus_motif -e log_ratio_file -s promoter_sequence" << endl;
		cerr << "Additional parameters:" << endl;
		cerr << "[-mis] mismatches to consensus motif(Default=1)" << endl;
		cerr << "[-a] annotation file" << endl;
		cerr << "[-o] output(gene_and_other_info PSFM)" << endl;
		cerr << "[-v] verbose mode" << endl;
		cerr << "[-h] hyperprio parameters(hyper_samples=50 mu=2.0 sigma^2=1.0 flanking_length=7" << endl;
		cerr << "[-n] DO NOT use prio information(overide hyperprio parameters)" << endl;
		cerr << "[-g] Gibbs sampler parameters(starting_point=10 burn-in=100 window=100)" << endl;
		cerr << "[-misc] Miscellaneous parameters(stds_of_intial_target=4 skip_core_region=0 random_background=0 threshold_for_target=0.5 stds_enfore=1)" << endl;

                return 1;
        }

        string m, e, s;
        try
        {
                m = cmdLine.GetArgument("-m", 0);
                e = cmdLine.GetArgument("-e", 0);
                s = cmdLine.GetArgument("-s", 0);
        }
        catch(int)
        {
                cerr << "Wrong arguments!" << endl;
                return 1;
        }
	string mis = cmdLine.GetSafeArgument("-mis", 0, "1");	// mismatches.
	unsigned misallow = atoi(mis.data());
	string a = cmdLine.GetSafeArgument("-a", 0, "");	// gene annotation file.
	string o1 = cmdLine.GetSafeArgument("-o", 0, "");	// output gene and other information.
	string o2 = cmdLine.GetSafeArgument("-o", 1, "");	// output PSFM.
	
	// Hyper-prio parameters.
	HypePrio hypePrio;
	string v = cmdLine.GetSafeArgument("-h", 0, "50");
	hypePrio.V = atoi(v.data());
	string mu = cmdLine.GetSafeArgument("-h", 1, "2.0");
	hypePrio.MU = atof(mu.data());
	string sigma2 = cmdLine.GetSafeArgument("-h", 2, "1.0");
	hypePrio.SIGMA_2 = atof(sigma2.data());
	string flanking = cmdLine.GetSafeArgument("-h", 3, "7");
	hypePrio.FLANKING = atoi(flanking.data());

	// DO NOT use prior information? 
	if(cmdLine.HasSwitch("-n"))
		hypePrio.V = 1;

	// Gibbs-sampler parameters.
	string sta_pnt = cmdLine.GetSafeArgument("-g", 0, "10");
	STA_PNT = atoi(sta_pnt.data());
	string burn_in = cmdLine.GetSafeArgument("-g", 1, "100");
	BURN_IN = atoi(burn_in.data());
	string window = cmdLine.GetSafeArgument("-g", 2, "100");
	WINDOW = atoi(window.data());
 
	// Miscellaneous parameters.
	string iniv = cmdLine.GetSafeArgument("-misc", 0, "4");
	INIV = atoi(iniv.data());
	string skipcore	= cmdLine.GetSafeArgument("-misc", 1, "0");
	SKIPCORE = atoi(skipcore.data());
	string randbg = cmdLine.GetSafeArgument("-misc", 2, "0");
	RANDBG = atoi(randbg.data());
	VERBOSE = cmdLine.HasSwitch("-v");	// verbose mode switch.


	// Load data into memory.
	string motifSeq; // string of motif sequence.
	Expr expr; // hash table of expression values.
	Seq seq; // hash table of sequences.
	GeneAnno geneAnno; // hash table of gene annotation info.

	if(VERBOSE)
		cout << "Loading...motif...expression...sequence..." << endl;
	if(load_data(m, e, s, a, motifSeq, expr, seq, geneAnno)) // load data.
	{
		cerr << "Error occurs during data loading!" << endl;
		return 1;
	}
	if(VERBOSE)
		cout << "Data load complete!" << endl;

	// Normalize expression levels.
	double bkm = mean(expr);
	double bkstd = stnd(expr, bkm);
	if(VERBOSE)
		cout << "All gene mean: " << bkm << ", standard deviation: " << bkstd << endl;

	// Find all genes containing the motif with mismatch.
	VGene vGene;
	motifgene(motifSeq, hypePrio.FLANKING, expr, seq, misallow, vGene);
	if(VERBOSE)
		cout << "Total genes identified: " << vGene.size() << endl;
		
//.........这里部分代码省略.........

int
P300ClassifierMain( int argc, char **argv, QApplication& app )
{
  ConfigDialog dialog;

  CCmdLine    cmdLine;
  QString     arg_TrainingDataFiles;
  QString     arg_TestingDataFiles;
  QString     arg_inicfg;
  QStringList arg_TrainingDataFilesList;
  QStringList arg_TestingDataFilesList;
  bool        barg_TrainingDataFiles;
  bool        barg_TestingDataFiles;
  bool        barg_inicfg;

  cmdLine.SplitLine(argc, argv);

  barg_TrainingDataFiles     =cmdLine.HasSwitch("-TrainingDataFiles");
  barg_TestingDataFiles      =cmdLine.HasSwitch("-TestingDataFiles");
  barg_inicfg                =cmdLine.HasSwitch("-inicfg");

  //int co = cmdLine.GetArgumentCount("-TrainingDataFiles");
  if (barg_TrainingDataFiles)
  {
    for (int i=0; i<cmdLine.GetArgumentCount("-TrainingDataFiles"); i++)
    {
        arg_TrainingDataFiles = arg_TrainingDataFiles.fromStdString(cmdLine.GetArgument("-TrainingDataFiles",i));
        arg_TrainingDataFilesList.insert(i, arg_TrainingDataFiles);
    }
  }
  else
  {
      arg_TrainingDataFiles = "";
  }


  if (barg_TestingDataFiles)
  {
   for (int i=0; i<cmdLine.GetArgumentCount("-TestingDataFiles"); i++)
   {
       arg_TestingDataFiles = arg_TestingDataFiles.fromStdString(cmdLine.GetArgument("-TestingDataFiles",i));
       arg_TestingDataFilesList.insert(i, arg_TestingDataFiles);
   }
  }
  else
  {
    arg_TestingDataFiles = "";
  }

  if (barg_inicfg)
  {
    arg_inicfg = arg_inicfg.fromStdString(cmdLine.GetArgument("-inicfg",0));
  }
  else
  {
    arg_inicfg = "";
  }

  QString classifierOutputFile = cmdLine.GetSafeArgument( "-ClassifierOutputFile", 0, "" ).c_str();
  dialog.SetFiles(arg_TrainingDataFilesList, arg_TestingDataFilesList, arg_inicfg, classifierOutputFile);

  return dialog.exec();
}

//.........这里部分代码省略.........
    // Pour utilisation de RichEditCtrl
    AfxEnableControlContainer();
    AfxInitRichEdit();
    // InitCommonControlsEx() est requis sur Windows XP si le manifeste de l'application
    // spécifie l'utilisation de ComCtl32.dll version 6 ou ultérieure pour activer les
    // styles visuels.  Dans le cas contraire, la création de fenêtres échouera.
    INITCOMMONCONTROLSEX InitCtrls;
    InitCtrls.dwSize = sizeof(InitCtrls);
    // À définir pour inclure toutes les classes de contrôles communs à utiliser
    // dans votre application.
    InitCtrls.dwICC = ICC_WIN95_CLASSES;
    InitCommonControlsEx(&InitCtrls);

    InitContextMenuManager();
    InitShellManager();
    InitKeyboardManager();
    InitTooltipManager();
    CMFCToolTipInfo ttParams;
    ttParams.m_bVislManagerTheme = TRUE;
    GetTooltipManager()->SetTooltipParams(AFX_TOOLTIP_TYPE_ALL, RUNTIME_CLASS(CMFCToolTipCtrl), &ttParams);

    // enregistrement Scintilla
#ifndef SCINTILLA_DLL
    Scintilla_RegisterClasses(AfxGetInstanceHandle());
    Scintilla_LinkLexers();
#endif

// Supprime pour la gestion multi-lingues
//    CWinAppEx::InitInstance();


    // Initialisation standard
    // Si vous n'utilisez pas ces fonctionnalités et que vous souhaitez réduire la taille
    // de votre exécutable final, vous devez supprimer ci-dessous
    // les routines d'initialisation spécifiques dont vous n'avez pas besoin.
    // Changez la clé de Registre sous laquelle nos paramètres sont enregistrés
    // TODO : modifiez cette chaîne avec des informations appropriées,
    // telles que le nom de votre société ou organisation
    SetRegistryKey(m_versionInfos.GetCompanyName().c_str());

    //First free the string allocated by MFC at CWinApp startup.
    //The string is allocated before InitInstance is called.
    free((void*)m_pszProfileName);
    //Change the name of the .INI file.
    //The CWinApp destructor will free the memory.
    // Ce nom est utilise pour la sauvegarde des parametres
    strReg = m_versionInfos.GetProductName() + "MFCFP";
    m_pszProfileName = _tcsdup(strReg.c_str());

    LoadStdProfileSettings(4);  // Charge les options de fichier INI standard (y compris les derniers fichiers utilisés)
    // Inscrire les modèles de document de l'application. Ces modèles
    //  lient les documents, fenêtres frame et vues entre eux
    
    // creation du manager de doc specifique afin de gerer specifiquement les repertoires
    // de sauvegarde des diffents documents.
    // cf http://www.codeguru.com/cpp/w-d/dislog/commondialogs/article.php/c1967
    m_pDocManager = new COngTVDocManager;

    // Creation doc template pour les scripts LUA (uniquement si DLL scintilla disponible)
    if (NULL != m_hSciDLL)
    {
        m_pNewLuaDocTemplate = new CMultiDocTemplate( IDR_LUATYPE
                                                    , RUNTIME_CLASS(CLuaDoc)
                                                    , RUNTIME_CLASS(CLuaChildFrame)
                                                    , RUNTIME_CLASS(CLuaView)
                                                    );
        if (!m_pNewLuaDocTemplate)
            return FALSE;
        AddDocTemplate(m_pNewLuaDocTemplate);
    }

    // Installe la police DINA
    HRSRC hRes   = FindResource(NULL, MAKEINTRESOURCE(IDR_DINA), _T("DINA"));
    PVOID lpFont = LockResource(LoadResource(NULL, hRes)); 
    DWORD dwSize = SizeofResource(NULL, hRes), cFonts = 0;
    m_hDinaFont = AddFontMemResourceEx(lpFont, dwSize, NULL, &cFonts);
    ASSERT(cFonts > 0);

    // crée la fenêtre frame MDI principale
    CMainFrame* pMainFrame = new CMainFrame;
    // On parse la ligne de commande
    CCmdLine cmdLine;
    cmdLine.SplitLine(__argc, __argv);
    // On indique le fichier de configuration ("" par defaut)
    std::string configFileName = cmdLine.GetSafeArgument("-cnx", 0, "");
    pMainFrame->SetConfigFile(configFileName);

    m_pMainWnd = pMainFrame;
    if (!pMainFrame || !pMainFrame->LoadFrame(IDR_MAINFRAME))
    {
        delete pMainFrame;
        return FALSE;
    }

    // La fenêtre principale a été initialisée et peut donc être affichée et mise à jour
    pMainFrame->ShowWindow(m_nCmdShow);
    pMainFrame->UpdateWindow();

    return TRUE;
}

int MainEntry(HINSTANCE hInstance,
                     HINSTANCE hPrevInstance,
                     LPSTR     lpCmdLine,
                     int       nCmdShow)
{
	MSG msg;
	ULONG_PTR           gdiplusToken;
	GdiplusStartupInput gdiplusStartupInput;
	BOOL bConsoleAttached = FALSE;

	// Set locale
	char *locale = setlocale(LC_ALL, ".936");

	// Startup GDI+
	Status status = GdiplusStartup(&gdiplusToken, &gdiplusStartupInput, NULL);
	if (status != Ok)
		return FALSE;

	// set options by command line
	CCmdLine cmdline;
	if (cmdline.SplitLine(__argc, __argv) > 0)
	{
		if (cmdline.HasSwitch("-width"))
			g_nScreenWidth = atoi(cmdline.GetArgument("-width", 0).c_str());
		if (cmdline.HasSwitch("-height"))
			g_nScreenHeight = atoi(cmdline.GetArgument("-height", 0).c_str());

		if (cmdline.HasSwitch("-d"))
		{
			if (AttachConsole(ATTACH_PARENT_PROCESS))
			{
				bConsoleAttached = TRUE;
				freopen("CONIN$", "r", stdin);
				freopen("CONOUT$", "w", stdout);
				freopen("CONOUT$", "w", stderr);
			}
		}

		if (cmdline.HasSwitch("-appid"))
		{
			xsStrCpyN(g_szAppId, cmdline.GetArgument("-appid", 0).c_str(), sizeof(g_szAppId));
		}
	}

	xsTcsCpy((xsTChar *)g_szTitle, xsT("XSKit"));
	xsTcsCpy((xsTChar *)g_szWindowClass, xsT("XSKitMainWnd"));

	RegisterWndClass(hInstance);

	if (!InitInstance (hInstance, nCmdShow))
	{
		if (bConsoleAttached)
			FreeConsole();
		return FALSE;
	}

	while (GetMessage(&msg, NULL, 0, 0))
	{
		TranslateMessage(&msg);
		DispatchMessage(&msg);
	}
	xsPalGuiUninit();

	if (bConsoleAttached)
		FreeConsole();
	// Shutdown GDI+
	GdiplusShutdown(gdiplusToken);

	return msg.wParam;
}

int main(int argc, char *argv[]){
	Fgwas_params p;

    CCmdLine cmdline;
    if (cmdline.SplitLine(argc, argv) < 1){
        printopts();
        exit(1);
    }
    //get the input file
    if (cmdline.HasSwitch("-i")) p.infile = cmdline.GetArgument("-i", 0).c_str();
    else{
    	cerr << "ERROR: missing input file (-i)\n";
        printopts();
        exit(1);
    }
    //get the output file
    if (cmdline.HasSwitch("-o")) p.outstem = cmdline.GetArgument("-o", 0);
    if (cmdline.HasSwitch("-pcond")) printcond = true;
    if (cmdline.HasSwitch("-v")) {
     	p.V.clear();
     	vector<string> strs;
     	string s = cmdline.GetArgument("-v", 0);
     	boost::split(strs, s ,boost::is_any_of(","));
     	for (int i  = 0; i < strs.size(); i++) {
     		p.V.push_back( atof(strs[i].c_str()) );
     	}
     }
    //LD file
    if (cmdline.HasSwitch("-ld")) {
    	p.overlap = true;
    	p.ldfile = cmdline.GetArgument("-ld", 0);
    	if (cmdline.HasSwitch("-nhap")) p.Nhap = atoi(cmdline.GetArgument("-nhap", 0).c_str());
    	else{
    		cerr << "ERROR: inputing LD matrix, -nhap flag\n";
    	   	printopts();
    	   	exit(1);
    	}
    }
    else if (cmdline.HasSwitch("-cor")){
    	//cerr << "WARNING: including correlation, did you mean to include an LD file?\n";
    	//printopts();
    	//exit(1);
    }
    if (cmdline.HasSwitch("-rev")) p.rev = true;
    if (cmdline.HasSwitch("-numbered")) p.numberedseg = true;
    //set K
    if (cmdline.HasSwitch("-k")) p.K = atoi(cmdline.GetArgument("-k", 0).c_str());
    if (cmdline.HasSwitch("-bed")) {
    	p.bedseg = true;
    	p.segment_bedfile = cmdline.GetArgument("-bed", 0);
    }

    if (cmdline.HasSwitch("-noprint")) p.print = false;

    //names of the phenotypes, expecting header like NAME1_Z NAME1_V NAME2_Z NAME2_V
    if (cmdline.HasSwitch("-phenos")){
     	p.pairwise = true;
     	p.pheno1 = cmdline.GetArgument("-phenos", 0);
     	p.pheno2 = cmdline.GetArgument("-phenos", 1);
     }
    else{
    	cerr << "ERROR: missing phenotypes (-pheno)\n";
        printopts();
        exit(1);
    }
    /*
    if (cmdline.HasSwitch("-w")){
    	vector<string> strs;
    	string s = cmdline.GetArgument("-w", 0);
    	boost::split(strs, s ,boost::is_any_of("+"));
    	for (int i  = 0; i < strs.size(); i++) {
    		p.wannot.push_back( strs[i] );
    	}
    }
    if (cmdline.HasSwitch("-dists")){
     	vector<string> strs;
     	string s = cmdline.GetArgument("-dists", 0);
     	boost::split(strs, s ,boost::is_any_of("+"));
     	for (int i  = 0; i < strs.size(); i++) {
     		vector<string> strs2;
     		boost::split(strs2, strs[i], boost::is_any_of(":"));
     		p.dannot.push_back( strs2[0] );
     		p.distmodels.push_back(strs2[1]);
     	}
     }
    if (cmdline.HasSwitch("-drop")){
    	p.dropchr = true;
    	string s = cmdline.GetArgument("-drop", 0);
    	p.chrtodrop = s;
    }


    if (cmdline.HasSwitch("-dens")) {
    	p.segannot.push_back(cmdline.GetArgument("-dens", 0));
    	p.loquant = atof(cmdline.GetArgument("-dens", 1).c_str());
    	p.hiquant = atof(cmdline.GetArgument("-dens", 2).c_str());
    }
    */
    if (cmdline.HasSwitch("-fine")) p.finemap = true;
    if (cmdline.HasSwitch("-mcmc")) p.MCMC = true;
//.........这里部分代码省略.........

void GameComponent::ParseCommandLine( LPTSTR lpCmdLine )
{
	m_CmdLineParse.clear();
	if( _tcscmp( "", lpCmdLine ) != 0 )
	{
		CCmdLine CmdLine;
		CmdLine.SplitLine( lpCmdLine );

		if( CmdLine.HasSwitch( "-multiplier" ) )
		{
			m_iMultiplier = _ttoi( CmdLine.GetSafeArgument( "-multiplier", 0, DEFAULT_Multiplier.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: multiplier\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-creditstart" ) )
		{
			m_iCreditStart = _ttoi( CmdLine.GetSafeArgument( "-creditstart", 0, DEFAULT_CreditStart.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: creditstart\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-creditcont" ) )
		{
			m_iCreditCont = _ttoi( CmdLine.GetSafeArgument( "-creditcont", 0, DEFAULT_CreditCont.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: creditcont\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-freeplay" ) )
		{
			m_bFreeplay = !(DEFAULT_Freeplay);
			StdString parseLine = _T("Cmd line argument: freeplay\n");
			m_CmdLineParse.push_back(parseLine);
		}
		else
		{
			m_bFreeplay = DEFAULT_Freeplay;
		}

		if( CmdLine.HasSwitch( "-time" ) )
		{
			m_iPlayTime = _ttoi( CmdLine.GetSafeArgument( "-time", 0, DEFAULT_PlayTime.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: time\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-contime" ) )
		{
			m_iContTime = _ttoi( CmdLine.GetSafeArgument( "-contime", 0, DEFAULT_ContTime.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: contime\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-language" ) )
		{
			m_iLanguage = _ttoi( CmdLine.GetSafeArgument( "-language", 0, DEFAULT_ContTime.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: language\n");
			m_CmdLineParse.push_back(parseLine);
		}

		if( CmdLine.HasSwitch( "-violence" ) )
		{
			m_iViolence = _ttoi( CmdLine.GetSafeArgument( "-violence", 0, DEFAULT_Violence.c_str() ).c_str() );
			StdString parseLine = _T("Cmd line argument: violence\n");
			m_CmdLineParse.push_back(parseLine);
		}

		// in free play mode some things need to be zeroed out
		if (m_bFreeplay)
		{
			m_iCreditStart = 0;
			m_iCreditCont = 0;
			m_iMultiplier = 0;			
		}
	}
}

//--------------------------------------------------------------------------------
BOOL CSecurityServerApp::InitInstance()
	{
	BOOL b = ::SetPriorityClass(::GetCurrentProcess(), HIGH_PRIORITY_CLASS);

	if (!AfxSocketInit())
		{
		AfxMessageBox(IDP_SOCKETS_INIT_FAILED);
		return FALSE;
		}

	g_hSingletonMutex = ::CreateMutex(NULL, FALSE, "MCMSSecurityServerSingletonMutex");
	if(g_hSingletonMutex == NULL || GetLastError() == ERROR_ALREADY_EXISTS)
		{
#ifndef _NOT_A_SERVICE
		g_service.AddToMessageLog(_T("SecurityServer already running."));
#endif
		TRACE("SecurityServer already running\n");
		return FALSE;
		}

	// create an invisible window
	m_pMainWnd = new CWnd;
	m_pMainWnd->CreateEx(0, AfxRegisterWndClass(NULL), NULL, 0, 0, 0, 0, 0, NULL, NULL);

	AfxEnableControlContainer();

#ifdef _NOT_A_SERVICE

	m_pSystem = new CSecuritySystem;
	m_pSystem->GetIOSubSystem()->CreateLogFile("C:\\SStest.log", false);
	m_pSystem->GetIOSubSystem()->SetTraceLevel(IOMASK_1|IOMASK_2|IOMASK_3|IOMASK_4|IOMASK_5|IOMASK_6);

	m_pServiceThread = ::AfxBeginThread((AFX_THREADPROC) ServiceThread, (LPVOID) this);
	return TRUE;

#else
	CCmdLine cmdLine;

	int nIndex;
	if(cmdLine.HasParam('I', nIndex) || cmdLine.HasParam("-install", nIndex))
		g_service.InstallService();
	else
		if(cmdLine.HasParam('R', nIndex) || cmdLine.HasParam("-remove", nIndex))
			g_service.RemoveService();
		else
			if(cmdLine.HasParam('E', nIndex) || cmdLine.HasParam("-end", nIndex) || cmdLine.HasParam("-stop", nIndex))
				g_service.EndService();
			else
				{
				// must start the system first
				m_pSystem = new CSecuritySystem;
				if(m_pSystem->GetResultCode() != CResult::noErr)
					g_service.AddToMessageLog(_T("Exception occured during SecurityServer startup.  Check license file validity."));

				CSSConfigPerformance config;
				m_pSystem->GetIOSubSystem()->SetTraceLevel(config.m_nTraceLevel);

				m_pServiceThread = ::AfxBeginThread((AFX_THREADPROC) ServiceThread, (LPVOID) this);
				::Sleep(1000);
				g_service.ReportStatus(SERVICE_RUNNING);
				// dont destroy the window cuz we'll need it
				return TRUE;
				}

	// we dont need this window
	delete m_pMainWnd;
	m_pMainWnd = NULL;

	return FALSE;
#endif // _DEBUG
	}