src/stdafx.h

/*****************************************************************************
* This file is provided under the Creative Commons Attribution 3.0 license.
*
* You are free to share, copy, distribute, transmit, or adapt this work
* PROVIDED THAT you attribute the work to the authors listed below.
* For more information, please see the following web page:
* http://creativecommons.org/licenses/by/3.0/
*
* This file is a component of the Sleipnir library for functional genomics,
* authored by:
* Curtis Huttenhower (chuttenh@princeton.edu)
* Mark Schroeder
* Maria D. Chikina
* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
*
* If you use this library, the included executable tools, or any related
* code in your work, please cite the following publication:
* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
* Olga G. Troyanskaya.
* "The Sleipnir library for computational functional genomics"
*****************************************************************************/
#ifndef STDAFX_H
#define STDAFX_H

#include <assert.h>
#include <float.h>
#include <limits.h>
#include <math.h>
#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <unistd.h>
#ifdef _MSC_VER
#include <fcntl.h>
#include <io.h>
#include <winsock2.h>

#define socklen_t   int
#else // _MSC_VER
#include <dirent.h>
#include <errno.h>
#include <fcntl.h>
#define __STDC_LIMIT_MACROS
#include <netinet/in.h>
#include <signal.h>
#include <stdarg.h>
#include <sys/mman.h>
#include <sys/socket.h>
#include <sys/time.h>
#include <omp.h>

#define _isnan              isnan
#define _lseek              lseek
#define _read               read
#define _write              write
#define closesocket         close
#define SOCKET              int
#define strcpy_s(a,b,c)     strcpy(a,c)
#define strncpy_s(a,b,c,d)  strncpy(a,c,d)


inline char* _mktemp_s( char* szTemplate, size_t iSize ) {

    return mktemp( szTemplate ); }

inline size_t GetTickCount( ) {
    struct timeval  sTime;

    gettimeofday( &sTime, NULL );
    return ( ( sTime.tv_sec * 1000000 ) + sTime.tv_usec ); }

inline int sprintf_s( char* szDest, size_t iSize, const char* szFormat,
    ... ) {
    va_list valArgs;

    va_start( valArgs, szFormat );
    return vsprintf( szDest, szFormat, valArgs ); }

inline size_t max( size_t iOne, size_t iTwo ) {

    return ( ( iOne > iTwo ) ? iOne : iTwo ); }
#endif // _MSC_VER

#pragma warning (disable: 4267)
#include <algorithm>
#include <fstream>
#include <iostream>
#include <map>
#include <queue>
#include <set>
#include <sstream>
#include <vector>
using namespace std;

#ifndef USE_LOG4CPP_STUB
#include <log4cpp/Category.hh>
#include <log4cpp/OstreamAppender.hh>
using namespace log4cpp;
#endif // USE_LOG4CPP_STUB

#if _MSC_VER
#include <windows.h>
#include <psapi.h>
#else // _MSC_VER
#define ios_base    ios
#define UINT        unsigned int
#endif // _MSC_VER

namespace pnl { }
using namespace pnl;

namespace Sleipnir {

#ifdef USE_LOG4CPP_STUB

struct Priority {
    enum PriorityLevel {
        EMERG   = 0, 
        FATAL   = 0,
        ALERT   = 1,
        CRIT    = 2,
        ERROR   = 3, 
        WARN    = 4,
        NOTICE  = 5,
        INFO    = 6,
        DEBUG   = 7,
        NOTSET  = 8
    };

    const static char* c_aszPriorityLevels[];
};

struct Category {

    static void shutdown( ) { }

    static void log4cpp( const char* szTag, const char* szFormat, va_list& valArgs ) {

        fprintf( stderr, "%d ", time( NULL ) );
        fprintf( stderr, szTag );
        fprintf( stderr, " : " );
        vfprintf( stderr, szFormat, valArgs );
        fprintf( stderr, "\n" ); }

    void error( const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( "ERROR", szFormat, valArgs ); }

    void info( const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( "INFO", szFormat, valArgs ); }

    void notice( const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( "NOTICE", szFormat, valArgs ); }

    void warn( const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( "WARN", szFormat, valArgs ); }

    void debug( const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( "DEBUG", szFormat, valArgs ); }

    void log( Priority::PriorityLevel ePriority, const char* szFormat, ... ) const {
        va_list valArgs;

        va_start( valArgs, szFormat );
        log4cpp( Priority::c_aszPriorityLevels[ ePriority ], szFormat, valArgs ); }

    bool isDebugEnabled( ) const {

        return true; }

    bool isInfoEnabled( ) const {

        return true; }

    bool isNoticeEnabled( ) const {

        return true; }
};

#endif // USE_LOG4CPP_STUB

#ifdef USE_LOG4CPP_STUB
inline Category& g_CatSleipnir( ) {
    static Category s_CatSleipnir;

    return s_CatSleipnir; }
#else // USE_LOG4CPP_STUB
extern const char   c_szSleipnir[];

inline Category& g_CatSleipnir( ) {
    static Category&    s_CatSleipnir   = Category::getInstance( c_szSleipnir );

    return s_CatSleipnir; }
#endif // USE_LOG4CPP_STUB

}

#endif // STDAFX_H