[TREE] Move the files to target refactor location

This commit is contained in:
tqchen 2016-01-01 05:01:22 -08:00
parent 3128e1705b
commit 4adc4cf0b9
14 changed files with 0 additions and 889 deletions

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/*!
* Copyright 2014 by Contributors
* \file iterator.h
* \brief itertator interface
* \author Tianqi Chen
*/
#ifndef XGBOOST_UTILS_ITERATOR_H_
#define XGBOOST_UTILS_ITERATOR_H_
#include <cstdio>
namespace xgboost {
namespace utils {
/*!
* \brief iterator interface
* \tparam DType data type
*/
template<typename DType>
class IIterator {
public:
/*!
* \brief set the parameter
* \param name name of parameter
* \param val value of parameter
*/
virtual void SetParam(const char *name, const char *val) {}
/*! \brief initialize the iterator so that we can use the iterator */
virtual void Init(void) {}
/*! \brief set before first of the item */
virtual void BeforeFirst(void) = 0;
/*! \brief move to next item */
virtual bool Next(void) = 0;
/*! \brief get current data */
virtual const DType &Value(void) const = 0;
public:
/*! \brief constructor */
virtual ~IIterator(void) {}
};
} // namespace utils
} // namespace xgboost
#endif // XGBOOST_UTILS_ITERATOR_H_

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/*!
* Copyright 2014 by Contributors
* \file omp.h
* \brief header to handle OpenMP compatibility issues
* \author Tianqi Chen
*/
#ifndef XGBOOST_UTILS_OMP_H_
#define XGBOOST_UTILS_OMP_H_
#if defined(_OPENMP) && !defined(DISABLE_OPENMP)
#include <omp.h>
#else
#if !defined(DISABLE_OPENMP) && !defined(_MSC_VER)
// use pragma message instead of warning
#pragma message("Warning: OpenMP is not available,"\
"xgboost will be compiled into single-thread code."\
"Use OpenMP-enabled compiler to get benefit of multi-threading")
#endif
inline int omp_get_thread_num() { return 0; }
inline int omp_get_num_threads() { return 1; }
inline void omp_set_num_threads(int nthread) {}
inline int omp_get_num_procs() { return 1; }
#endif
// loop variable used in openmp
namespace xgboost {
#ifdef _MSC_VER
typedef int bst_omp_uint;
#else
typedef unsigned bst_omp_uint;
#endif
} // namespace xgboost
#endif // XGBOOST_UTILS_OMP_H_

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/*!
* Copyright 2014 by Contributors
* \file xgboost_random.h
* \brief PRNG to support random number generation
* \author Tianqi Chen: tianqi.tchen@gmail.com
*
* Use standard PRNG from stdlib
*/
#ifndef XGBOOST_UTILS_RANDOM_H_
#define XGBOOST_UTILS_RANDOM_H_
#include <cmath>
#include <cstdlib>
#include <vector>
#include <algorithm>
#include "./utils.h"
/*! namespace of PRNG */
namespace xgboost {
namespace random {
#ifndef XGBOOST_CUSTOMIZE_PRNG_
/*! \brief seed the PRNG */
inline void Seed(unsigned seed) {
srand(seed);
}
/*! \brief basic function, uniform */
inline double Uniform(void) {
return static_cast<double>(rand()) / (static_cast<double>(RAND_MAX)+1.0); // NOLINT(*)
}
/*! \brief return a real number uniform in (0,1) */
inline double NextDouble2(void) {
return (static_cast<double>(rand()) + 1.0) / (static_cast<double>(RAND_MAX)+2.0); // NOLINT(*)
}
/*! \brief return x~N(0,1) */
inline double Normal(void) {
double x, y, s;
do {
x = 2 * NextDouble2() - 1.0;
y = 2 * NextDouble2() - 1.0;
s = x*x + y*y;
} while (s >= 1.0 || s == 0.0);
return x * sqrt(-2.0 * log(s) / s);
}
#else
// include declarations, to be implemented
void Seed(unsigned seed);
double Uniform(void);
double Normal(void);
#endif
/*! \brief return a real number uniform in [0,1) */
inline double NextDouble(void) {
return Uniform();
}
/*! \brief return a random number in n */
inline uint32_t NextUInt32(uint32_t n) {
return (uint32_t)std::floor(NextDouble() * n);
}
/*! \brief return x~N(mu,sigma^2) */
inline double SampleNormal(double mu, double sigma) {
return Normal() * sigma + mu;
}
/*! \brief return 1 with probability p, coin flip */
inline int SampleBinary(double p) {
return NextDouble() < p;
}
template<typename T>
inline void Shuffle(T *data, size_t sz) {
if (sz == 0) return;
for (uint32_t i = (uint32_t)sz - 1; i > 0; i--) {
std::swap(data[i], data[NextUInt32(i + 1)]);
}
}
// random shuffle the data inside, require PRNG
template<typename T>
inline void Shuffle(std::vector<T> &data) { // NOLINT(*)
Shuffle(&data[0], data.size());
}
/*! \brief random number generator with independent random number seed*/
struct Random{
/*! \brief set random number seed */
inline void Seed(unsigned sd) {
this->rseed = sd;
#if defined(_MSC_VER) || defined(_WIN32)
::xgboost::random::Seed(sd);
#endif
}
/*! \brief return a real number uniform in [0,1) */
inline double RandDouble(void) {
// use rand instead of rand_r in windows, for MSVC it is fine since rand is threadsafe
// For cygwin and mingw, this can slows down parallelism,
// but rand_r is only used in objective-inl.hpp, won't affect speed in general
// todo, replace with another PRNG
#if defined(_MSC_VER) || defined(_WIN32) || defined(XGBOOST_STRICT_CXX98_)
return Uniform();
#else
return static_cast<double>(rand_r(&rseed)) / (static_cast<double>(RAND_MAX) + 1.0);
#endif
}
// random number seed
unsigned rseed;
};
} // namespace random
} // namespace xgboost
#endif // XGBOOST_UTILS_RANDOM_H_

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/*!
* Copyright by Contributors
* \file thread.h
* \brief this header include the minimum necessary resource
* for multi-threading that can be compiled in windows, linux, mac
* \author Tianqi Chen
*/
#ifndef XGBOOST_UTILS_THREAD_H_ // NOLINT(*)
#define XGBOOST_UTILS_THREAD_H_ // NOLINT(*)
#ifdef _MSC_VER
#include <windows.h>
#include <process.h>
#include "./utils.h"
namespace xgboost {
namespace utils {
/*! \brief simple semaphore used for synchronization */
class Semaphore {
public :
inline void Init(int init_val) {
sem = CreateSemaphore(NULL, init_val, 10, NULL);
utils::Check(sem != NULL, "create Semaphore error");
}
inline void Destroy(void) {
CloseHandle(sem);
}
inline void Wait(void) {
utils::Check(WaitForSingleObject(sem, INFINITE) == WAIT_OBJECT_0, "WaitForSingleObject error");
}
inline void Post(void) {
utils::Check(ReleaseSemaphore(sem, 1, NULL) != 0, "ReleaseSemaphore error");
}
private:
HANDLE sem;
};
/*! \brief mutex under windows */
class Mutex {
public:
inline void Init(void) {
utils::Check(InitializeCriticalSectionAndSpinCount(&mutex, 0x00000400) != 0,
"Mutex::Init fail");
}
inline void Lock(void) {
EnterCriticalSection(&mutex);
}
inline void Unlock(void) {
LeaveCriticalSection(&mutex);
}
inline void Destroy(void) {
DeleteCriticalSection(&mutex);
}
private:
friend class ConditionVariable;
CRITICAL_SECTION mutex;
};
// conditional variable that uses pthread
class ConditionVariable {
public:
// initialize conditional variable
inline void Init(void) {
InitializeConditionVariable(&cond);
}
// destroy the thread
inline void Destroy(void) {
// DeleteConditionVariable(&cond);
}
// wait on the conditional variable
inline void Wait(Mutex *mutex) {
utils::Check(SleepConditionVariableCS(&cond, &(mutex->mutex), INFINITE) != 0,
"ConditionVariable:Wait fail");
}
inline void Broadcast(void) {
WakeAllConditionVariable(&cond);
}
inline void Signal(void) {
WakeConditionVariable(&cond);
}
private:
CONDITION_VARIABLE cond;
};
/*! \brief simple thread that wraps windows thread */
class Thread {
private:
HANDLE thread_handle;
unsigned thread_id;
public:
inline void Start(unsigned int __stdcall entry(void*p), void *param) {
thread_handle = (HANDLE)_beginthreadex(NULL, 0, entry, param, 0, &thread_id);
}
inline int Join(void) {
WaitForSingleObject(thread_handle, INFINITE);
return 0;
}
};
/*! \brief exit function called from thread */
inline void ThreadExit(void *status) {
_endthreadex(0);
}
#define XGBOOST_THREAD_PREFIX unsigned int __stdcall
} // namespace utils
} // namespace xgboost
#else
// thread interface using g++
#include <semaphore.h>
#include <pthread.h>
#include <errno.h>
namespace xgboost {
namespace utils {
/*!\brief semaphore class */
class Semaphore {
#ifdef __APPLE__
private:
sem_t* semPtr;
char sema_name[20];
private:
inline void GenRandomString(char *s, const int len) {
static const char alphanum[] = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ";
for (int i = 0; i < len; ++i) {
s[i] = alphanum[rand() % (sizeof(alphanum) - 1)];
}
s[len] = 0;
}
public:
inline void Init(int init_val) {
sema_name[0] = '/';
sema_name[1] = 's';
sema_name[2] = 'e';
sema_name[3] = '/';
GenRandomString(&sema_name[4], 16);
if ((semPtr = sem_open(sema_name, O_CREAT, 0644, init_val)) == SEM_FAILED) {
perror("sem_open");
exit(1);
}
utils::Check(semPtr != NULL, "create Semaphore error");
}
inline void Destroy(void) {
if (sem_close(semPtr) == -1) {
perror("sem_close");
exit(EXIT_FAILURE);
}
if (sem_unlink(sema_name) == -1) {
perror("sem_unlink");
exit(EXIT_FAILURE);
}
}
inline void Wait(void) {
sem_wait(semPtr);
}
inline void Post(void) {
sem_post(semPtr);
}
#else
private:
sem_t sem;
public:
inline void Init(int init_val) {
if (sem_init(&sem, 0, init_val) != 0) {
utils::Error("Semaphore.Init:%s", strerror(errno));
}
}
inline void Destroy(void) {
if (sem_destroy(&sem) != 0) {
utils::Error("Semaphore.Destroy:%s", strerror(errno));
}
}
inline void Wait(void) {
if (sem_wait(&sem) != 0) {
utils::Error("Semaphore.Wait:%s", strerror(errno));
}
}
inline void Post(void) {
if (sem_post(&sem) != 0) {
utils::Error("Semaphore.Post:%s", strerror(errno));
}
}
#endif
};
// mutex that works with pthread
class Mutex {
public:
inline void Init(void) {
pthread_mutex_init(&mutex, NULL);
}
inline void Lock(void) {
pthread_mutex_lock(&mutex);
}
inline void Unlock(void) {
pthread_mutex_unlock(&mutex);
}
inline void Destroy(void) {
pthread_mutex_destroy(&mutex);
}
private:
friend class ConditionVariable;
pthread_mutex_t mutex;
};
// conditional variable that uses pthread
class ConditionVariable {
public:
// initialize conditional variable
inline void Init(void) {
pthread_cond_init(&cond, NULL);
}
// destroy the thread
inline void Destroy(void) {
pthread_cond_destroy(&cond);
}
// wait on the conditional variable
inline void Wait(Mutex *mutex) {
pthread_cond_wait(&cond, &(mutex->mutex));
}
inline void Broadcast(void) {
pthread_cond_broadcast(&cond);
}
inline void Signal(void) {
pthread_cond_signal(&cond);
}
private:
pthread_cond_t cond;
};
/*!\brief simple thread class */
class Thread {
private:
pthread_t thread;
public :
inline void Start(void * entry(void*), void *param) { // NOLINT(*)
pthread_attr_t attr;
pthread_attr_init(&attr);
pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
pthread_create(&thread, &attr, entry, param);
}
inline int Join(void) {
void *status;
return pthread_join(thread, &status);
}
};
inline void ThreadExit(void *status) {
pthread_exit(status);
}
} // namespace utils
} // namespace xgboost
#define XGBOOST_THREAD_PREFIX void *
#endif // Linux
#endif // XGBOOST_UTILS_THREAD_H_ NOLINT(*)

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/*!
* Copyright 2014 by Contributors
* \file thread_buffer.h
* \brief multi-thread buffer, iterator, can be used to create parallel pipeline
* \author Tianqi Chen
*/
#ifndef XGBOOST_UTILS_THREAD_BUFFER_H_
#define XGBOOST_UTILS_THREAD_BUFFER_H_
#include <vector>
#include <cstring>
#include <cstdlib>
#include "./utils.h"
// threading util could not run on solaris
#ifndef XGBOOST_STRICT_CXX98_
#include "./thread.h"
#endif
namespace xgboost {
namespace utils {
#if !defined(XGBOOST_STRICT_CXX98_)
/*!
* \brief buffered loading iterator that uses multithread
* this template method will assume the following parameters
* \tparam Elem element type to be buffered
* \tparam ElemFactory factory type to implement in order to use thread buffer
*/
template<typename Elem, typename ElemFactory>
class ThreadBuffer {
public:
/*!\brief constructor */
ThreadBuffer(void) {
this->init_end = false;
this->buf_size = 30;
}
~ThreadBuffer(void) {
if (init_end) this->Destroy();
}
/*!\brief set parameter, will also pass the parameter to factory */
inline void SetParam(const char *name, const char *val) {
using namespace std;
if (!strcmp( name, "buffer_size")) buf_size = atoi(val);
factory.SetParam(name, val);
}
/*!
* \brief initalize the buffered iterator
* \param param a initialize parameter that will pass to factory, ignore it if not necessary
* \return false if the initialization can't be done, e.g. buffer file hasn't been created
*/
inline bool Init(void) {
if (!factory.Init()) return false;
for (int i = 0; i < buf_size; ++i) {
bufA.push_back(factory.Create());
bufB.push_back(factory.Create());
}
this->init_end = true;
this->StartLoader();
return true;
}
/*!\brief place the iterator before first value */
inline void BeforeFirst(void) {
// wait till last loader end
loading_end.Wait();
// critical zone
current_buf = 1;
factory.BeforeFirst();
// reset terminate limit
endA = endB = buf_size;
// wake up loader for first part
loading_need.Post();
// wait til first part is loaded
loading_end.Wait();
// set current buf to right value
current_buf = 0;
// wake loader for next part
data_loaded = false;
loading_need.Post();
// set buffer value
buf_index = 0;
}
/*! \brief destroy the buffer iterator, will deallocate the buffer */
inline void Destroy(void) {
// wait until the signal is consumed
this->destroy_signal = true;
loading_need.Post();
loader_thread.Join();
loading_need.Destroy();
loading_end.Destroy();
for (size_t i = 0; i < bufA.size(); ++i) {
factory.FreeSpace(bufA[i]);
}
for (size_t i = 0; i < bufB.size(); ++i) {
factory.FreeSpace(bufB[i]);
}
bufA.clear(); bufB.clear();
factory.Destroy();
this->init_end = false;
}
/*!
* \brief get the next element needed in buffer
* \param elem element to store into
* \return whether reaches end of data
*/
inline bool Next(Elem &elem) { // NOLINT(*)
// end of buffer try to switch
if (buf_index == buf_size) {
this->SwitchBuffer();
buf_index = 0;
}
if (buf_index >= (current_buf ? endA : endB)) {
return false;
}
std::vector<Elem> &buf = current_buf ? bufA : bufB;
elem = buf[buf_index];
++buf_index;
return true;
}
/*!
* \brief get the factory object
*/
inline ElemFactory &get_factory(void) {
return factory;
}
inline const ElemFactory &get_factory(void) const {
return factory;
}
// size of buffer
int buf_size;
private:
// factory object used to load configures
ElemFactory factory;
// index in current buffer
int buf_index;
// indicate which one is current buffer
int current_buf;
// max limit of visit, also marks termination
int endA, endB;
// double buffer, one is accessed by loader
// the other is accessed by consumer
// buffer of the data
std::vector<Elem> bufA, bufB;
// initialization end
bool init_end;
// singal whether the data is loaded
bool data_loaded;
// signal to kill the thread
bool destroy_signal;
// thread object
Thread loader_thread;
// signal of the buffer
Semaphore loading_end, loading_need;
/*!
* \brief slave thread
* this implementation is like producer-consumer style
*/
inline void RunLoader(void) {
while (!destroy_signal) {
// sleep until loading is needed
loading_need.Wait();
std::vector<Elem> &buf = current_buf ? bufB : bufA;
int i;
for (i = 0; i < buf_size ; ++i) {
if (!factory.LoadNext(buf[i])) {
int &end = current_buf ? endB : endA;
end = i; // marks the termination
break;
}
}
// signal that loading is done
data_loaded = true;
loading_end.Post();
}
}
/*!\brief entry point of loader thread */
inline static XGBOOST_THREAD_PREFIX LoaderEntry(void *pthread) {
static_cast< ThreadBuffer<Elem, ElemFactory>* >(pthread)->RunLoader();
return NULL;
}
/*!\brief start loader thread */
inline void StartLoader(void) {
destroy_signal = false;
// set param
current_buf = 1;
loading_need.Init(1);
loading_end .Init(0);
// reset terminate limit
endA = endB = buf_size;
loader_thread.Start(LoaderEntry, this);
// wait until first part of data is loaded
loading_end.Wait();
// set current buf to right value
current_buf = 0;
// wake loader for next part
data_loaded = false;
loading_need.Post();
buf_index = 0;
}
/*!\brief switch double buffer */
inline void SwitchBuffer(void) {
loading_end.Wait();
// loader shall be sleep now, critcal zone!
current_buf = !current_buf;
// wake up loader
data_loaded = false;
loading_need.Post();
}
};
#else
// a dummy single threaded ThreadBuffer
// use this to resolve R's solaris compatibility for now
template<typename Elem, typename ElemFactory>
class ThreadBuffer {
public:
ThreadBuffer() : init_end_(false) {}
~ThreadBuffer() {
if (init_end_) {
factory_.FreeSpace(data_);
factory_.Destroy();
}
}
inline void SetParam(const char *name, const char *val) {
}
inline bool Init(void) {
if (!factory_.Init()) return false;
data_ = factory_.Create();
return (init_end_ = true);
}
inline void BeforeFirst(void) {
factory_.BeforeFirst();
}
inline bool Next(Elem &elem) { // NOLINT(*)
if (factory_.LoadNext(data_)) {
elem = data_; return true;
} else {
return false;
}
}
inline ElemFactory &get_factory() {
return factory_;
}
inline const ElemFactory &get_factory() const {
return factory_;
}
private:
// initialized
bool init_end_;
// current data
Elem data_;
// factory object used to load configures
ElemFactory factory_;
};
#endif // !defined(XGBOOST_STRICT_CXX98_)
} // namespace utils
} // namespace xgboost
#endif // XGBOOST_UTILS_THREAD_BUFFER_H_

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/*!
* Copyright 2014 by Contributors
* \file utils.h
* \brief simple utils to support the code
* \author Tianqi Chen
*/
#ifndef XGBOOST_UTILS_UTILS_H_
#define XGBOOST_UTILS_UTILS_H_
#define _CRT_SECURE_NO_WARNINGS
#include <cstdio>
#include <string>
#include <cstdlib>
#include <vector>
#include <stdexcept>
#ifndef XGBOOST_STRICT_CXX98_
#include <cstdarg>
#endif
#if !defined(__GNUC__)
#define fopen64 std::fopen
#endif
#ifdef _MSC_VER
// NOTE: sprintf_s is not equivalent to snprintf,
// they are equivalent when success, which is sufficient for our case
#define snprintf sprintf_s
#define vsnprintf vsprintf_s
#else
#ifdef _FILE_OFFSET_BITS
#if _FILE_OFFSET_BITS == 32
#pragma message("Warning: FILE OFFSET BITS defined to be 32 bit")
#endif
#endif
#ifdef __APPLE__
#define off64_t off_t
#define fopen64 std::fopen
#endif
extern "C" {
#include <sys/types.h>
}
#endif
#ifdef _MSC_VER
typedef unsigned char uint8_t;
typedef unsigned __int16 uint16_t;
typedef unsigned __int32 uint32_t;
typedef unsigned __int64 uint64_t;
typedef __int64 int64_t;
#else
#include <inttypes.h>
#endif
namespace xgboost {
/*! \brief namespace for helper utils of the project */
namespace utils {
/*! \brief error message buffer length */
const int kPrintBuffer = 1 << 12;
#ifndef XGBOOST_CUSTOMIZE_MSG_
/*!
* \brief handling of Assert error, caused by inappropriate input
* \param msg error message
*/
inline void HandleAssertError(const char *msg) {
fprintf(stderr, "AssertError:%s\n", msg);
exit(-1);
}
/*!
* \brief handling of Check error, caused by inappropriate input
* \param msg error message
*/
inline void HandleCheckError(const char *msg) {
throw std::runtime_error(msg);
}
inline void HandlePrint(const char *msg) {
printf("%s", msg);
}
#else
#ifndef XGBOOST_STRICT_CXX98_
// include declarations, some one must implement this
void HandleAssertError(const char *msg);
void HandleCheckError(const char *msg);
void HandlePrint(const char *msg);
#endif
#endif
#ifdef XGBOOST_STRICT_CXX98_
// these function pointers are to be assigned
extern "C" void (*Printf)(const char *fmt, ...);
extern "C" int (*SPrintf)(char *buf, size_t size, const char *fmt, ...);
extern "C" void (*Assert)(int exp, const char *fmt, ...);
extern "C" void (*Check)(int exp, const char *fmt, ...);
extern "C" void (*Error)(const char *fmt, ...);
#else
/*! \brief printf, print message to the console */
inline void Printf(const char *fmt, ...) {
std::string msg(kPrintBuffer, '\0');
va_list args;
va_start(args, fmt);
vsnprintf(&msg[0], kPrintBuffer, fmt, args);
va_end(args);
HandlePrint(msg.c_str());
}
/*! \brief portable version of snprintf */
inline int SPrintf(char *buf, size_t size, const char *fmt, ...) {
va_list args;
va_start(args, fmt);
int ret = vsnprintf(buf, size, fmt, args);
va_end(args);
return ret;
}
/*! \brief assert an condition is true, use this to handle debug information */
inline void Assert(bool exp, const char *fmt, ...) {
if (!exp) {
std::string msg(kPrintBuffer, '\0');
va_list args;
va_start(args, fmt);
vsnprintf(&msg[0], kPrintBuffer, fmt, args);
va_end(args);
HandleAssertError(msg.c_str());
}
}
/*!\brief same as assert, but this is intended to be used as message for user*/
inline void Check(bool exp, const char *fmt, ...) {
if (!exp) {
std::string msg(kPrintBuffer, '\0');
va_list args;
va_start(args, fmt);
vsnprintf(&msg[0], kPrintBuffer, fmt, args);
va_end(args);
HandleCheckError(msg.c_str());
}
}
/*! \brief report error message, same as check */
inline void Error(const char *fmt, ...) {
{
std::string msg(kPrintBuffer, '\0');
va_list args;
va_start(args, fmt);
vsnprintf(&msg[0], kPrintBuffer, fmt, args);
va_end(args);
HandleCheckError(msg.c_str());
}
}
#endif
/*! \brief replace fopen, report error when the file open fails */
inline std::FILE *FopenCheck(const char *fname, const char *flag) {
std::FILE *fp = fopen64(fname, flag);
Check(fp != NULL, "can not open file \"%s\"\n", fname);
return fp;
}
} // namespace utils
// easy utils that can be directly accessed in xgboost
/*! \brief get the beginning address of a vector */
template<typename T>
inline T *BeginPtr(std::vector<T> &vec) { // NOLINT(*)
if (vec.size() == 0) {
return NULL;
} else {
return &vec[0];
}
}
/*! \brief get the beginning address of a vector */
template<typename T>
inline const T *BeginPtr(const std::vector<T> &vec) {
if (vec.size() == 0) {
return NULL;
} else {
return &vec[0];
}
}
inline char* BeginPtr(std::string &str) { // NOLINT(*)
if (str.length() == 0) return NULL;
return &str[0];
}
inline const char* BeginPtr(const std::string &str) {
if (str.length() == 0) return NULL;
return &str[0];
}
} // namespace xgboost
#endif // XGBOOST_UTILS_UTILS_H_