--- /dev/null
+#ifndef myutils_h\r
+#define myutils_h\r
+\r
+#define RCE_MALLOC 0\r
+
+#include <stdio.h>\r
+#include <sys/types.h>\r
+#include <string>\r
+#include <string.h>\r
+#include <memory.h>\r
+#include <vector>\r
+#include <math.h>\r
+#include <stdarg.h>\r
+#include <cstdlib>\r
+#include <climits>\r
+\r
+#ifndef _MSC_VER\r
+#include <inttypes.h>\r
+#endif\r
+\r
+using namespace std;\r
+\r
+#ifdef _MSC_VER\r
+#include <crtdbg.h>\r
+#pragma warning(disable: 4996) // deprecated functions\r
+#define _CRT_SECURE_NO_DEPRECATE 1\r
+#endif\r
+\r
+#if defined(_DEBUG) && !defined(DEBUG)\r
+#define DEBUG 1\r
+#endif\r
+\r
+#if defined(DEBUG) && !defined(_DEBUG)\r
+#define _DEBUG 1\r
+#endif\r
+\r
+#ifndef NDEBUG\r
+#define DEBUG 1\r
+#define _DEBUG 1\r
+#endif\r
+\r
+typedef unsigned char byte;\r
+typedef unsigned short uint16;\r
+typedef unsigned uint32;\r
+typedef int int32;\r
+typedef double float32;\r
+typedef signed char int8;\r
+typedef unsigned char uint8;\r
+\r
+#ifdef _MSC_VER\r
+\r
+typedef __int64 int64;\r
+typedef unsigned __int64 uint64;\r
+\r
+#define INT64_PRINTF "lld"\r
+#define UINT64_PRINTF "llu"\r
+\r
+#define SIZE_T_PRINTF "u"\r
+#define OFF64_T_PRINTF "lld"\r
+\r
+#define INT64_PRINTFX "llx"\r
+#define UINT64_PRINTFX "llx"\r
+\r
+#define SIZE_T_PRINTFX "x"\r
+#define OFF64_T_PRINTFX "llx"\r
+\r
+#elif defined(__x86_64__)\r
+\r
+typedef long int64;\r
+typedef unsigned long uint64;\r
+\r
+#define INT64_PRINTF "ld"\r
+#define UINT64_PRINTF "lu"\r
+\r
+#define SIZE_T_PRINTF "lu"\r
+#define OFF64_T_PRINTF "ld"\r
+\r
+#define INT64_PRINTFX "lx"\r
+#define UINT64_PRINTFX "lx"\r
+\r
+#define SIZE_T_PRINTFX "lx"\r
+#define OFF64_T_PRINTFX "lx"\r
+\r
+#else\r
+\r
+typedef long long int64;\r
+typedef unsigned long long uint64;\r
+\r
+#define INT64_PRINTF "lld"\r
+#define UINT64_PRINTF "llu"\r
+\r
+#define SIZE_T_PRINTF "u"\r
+#define OFF64_T_PRINTF "lld"\r
+\r
+#define INT64_PRINTFX "llx"\r
+#define UINT64_PRINTFX "llx"\r
+\r
+#define SIZE_T_PRINTFX "x"\r
+#define OFF64_T_PRINTFX "llx"\r
+#endif\r
+\r
+#define d64 INT64_PRINTF\r
+#define u64 UINT64_PRINTF\r
+#define x64 UINT64_PRINTFX\r
+\r
+// const uint64 UINT64_MAX = (~((uint64) 0));\r
+\r
+void myassertfail(const char *Exp, const char *File, unsigned Line);\r
+#undef assert\r
+#ifdef NDEBUG\r
+#define assert(exp) ((void)0)\r
+#define myassert(exp) ((void)0)\r
+#else\r
+#define assert(exp) (void)( (exp) || (myassertfail(#exp, __FILE__, __LINE__), 0) )\r
+#define myassert(exp) (void)( (exp) || (myassertfail(#exp, __FILE__, __LINE__), 0) )\r
+#endif\r
+#define asserta(exp) (void)( (exp) || (myassertfail(#exp, __FILE__, __LINE__), 0) )\r
+\r
+#define ureturn(x) return (x)\r
+\r
+#define NotUsed(v) ((void *) &v)\r
+\r
+// pom=plus or minus, tof=true or false\r
+static inline char pom(bool Plus) { return Plus ? '+' : '-'; }\r
+static inline char tof(bool x) { return x ? 'T' : 'F'; }\r
+static inline char yon(bool x) { return x ? 'Y' : 'N'; }\r
+unsigned GetElapsedSecs();\r
+\r
+#if RCE_MALLOC\r
+\r
+void *rce_malloc(unsigned bytes, const char *FileName, int Line);\r
+void rce_free(void *p, const char *FileName, int LineNr);\r
+void rce_chkmem();\r
+\r
+void rce_dumpmem_(const char *FileName, int LineNr);\r
+#define rce_dumpmem() rce_dumpmem_(__FILE__, __LINE__)\r
+\r
+void rce_assertvalidptr_(void *p, const char *FileName, int LineNr);\r
+#define rce_assertvalidptr(p) rce_assertvalidptr_(p, __FILE__, __LINE__)\r
+\r
+void rce_dumpptr_(void *p, const char *FileName, int LineNr);\r
+#define rce_dumpptr(p) rce_dumpptr_(p, __FILE__, __LINE__)\r
+\r
+#define mymalloc(n) rce_malloc((n), __FILE__, __LINE__)\r
+#define myfree(p) rce_free(p, __FILE__, __LINE__)\r
+#define myfree2(p,n) rce_free(p, __FILE__, __LINE__)\r
+#define myalloc(t, n) (t *) rce_malloc((n)*sizeof(t), __FILE__, __LINE__)\r
+\r
+#else // RCE_MALLOC\r
+void *mymalloc(unsigned bytes);\r
+void myfree2(void *p, unsigned Bytes);\r
+void myfree(void *p);\r
+#define rce_chkmem() /* empty */\r
+#define myalloc(t, n) (t *) mymalloc((n)*sizeof(t))\r
+#endif // RCE_MALLOC\r
+\r
+#define SIZE(c) unsigned((c).size())\r
+\r
+bool myisatty(int fd);\r
+\r
+#ifdef _MSC_VER\r
+#define off_t __int64\r
+#endif\r
+\r
+FILE *OpenStdioFile(const string &FileName);\r
+FILE *CreateStdioFile(const string &FileName);\r
+bool CanSetStdioFilePos(FILE *f);\r
+void CloseStdioFile(FILE *f);\r
+void SetStdioFilePos(FILE *f, off_t Pos);\r
+void ReadStdioFile(FILE *f, off_t Pos, void *Buffer, unsigned Bytes);\r
+void ReadStdioFile(FILE *f, void *Buffer, unsigned Bytes);\r
+void WriteStdioFile(FILE *f, off_t Pos, const void *Buffer, unsigned Bytes);\r
+void WriteStdioFile(FILE *f, const void *Buffer, unsigned Bytes);\r
+bool ReadLineStdioFile(FILE *f, char *Line, unsigned Bytes);\r
+bool ReadLineStdioFile(FILE *f, string &Line);\r
+byte *ReadAllStdioFile(FILE *f, off_t &FileSize);\r
+byte *ReadAllStdioFile(const string &FileName, off_t &FileSize);\r
+void AppendStdioFileToFile(FILE *fFrom, FILE *fTo);\r
+void FlushStdioFile(FILE *f);\r
+bool StdioFileExists(const string &FileName);\r
+off_t GetStdioFilePos(FILE *f);\r
+off_t GetStdioFileSize(FILE *f);\r
+void LogStdioFileState(FILE *f);\r
+void RenameStdioFile(const string &FileNameFrom, const string &FileNameTo);\r
+void DeleteStdioFile(const string &FileName);\r
+\r
+void myvstrprintf(string &Str, const char *szFormat, va_list ArgList);\r
+void myvstrprintf(string &Str, const char *szFormat, ...);\r
+\r
+void SetLogFileName(const string &FileName);\r
+void Log(const char *szFormat, ...);\r
+\r
+void Die(const char *szFormat, ...);\r
+void Warning(const char *szFormat, ...);\r
+\r
+void ProgressStep(unsigned i, unsigned N, const char *Format, ...);\r
+void Progress(const char *szFormat, ...);\r
+void Progress(const string &Str);\r
+void ProgressLog(const char *szFormat, ...);\r
+void ProgressExit();\r
+\r
+char *mystrsave(const char *s);\r
+\r
+double GetPeakMemUseBytes();\r
+\r
+// Are two floats equal to within epsilon?\r
+const double epsilon = 0.01;\r
+inline bool feq(double x, double y, double epsilon)\r
+ {\r
+ if (fabs(x) > 10000)\r
+ epsilon = fabs(x)/10000;\r
+ if (fabs(x - y) > epsilon)\r
+ return false;\r
+ return true;\r
+ }\r
+\r
+inline bool feq(double x, double y)\r
+ {\r
+ if (x < -1e6 && y < -1e6)\r
+ return true;\r
+ double e = epsilon;\r
+ if (fabs(x) > 10000)\r
+ e = fabs(x)/10000;\r
+ if (fabs(x - y) > e)\r
+ return false;\r
+ return true;\r
+ }\r
+\r
+#define asserteq(x, y) assert(feq(x, y))\r
+#define assertaeq(x, y) asserta(feq(x, y))\r
+\r
+#define zero(a, n) memset(a, 0, n*sizeof(a[0]))\r
+\r
+void InitRand();\r
+unsigned randu32();\r
+void Split(const string &Str, vector<string> &Fields, char Sep = 0);\r
+double Pct(double x, double y);\r
+double GetMemUseBytes();\r
+const char *MemBytesToStr(double Bytes);\r
+const char *IntToStr(unsigned i);\r
+const char *FloatToStr(double d);\r
+const char *SecsToStr(double Secs);\r
+void Logu(unsigned u, unsigned w, unsigned prefixspaces = 2);\r
+void Logf(float x, unsigned w, unsigned prefixspaces = 2);\r
+const char *SecsToHHMMSS(int Secs);\r
+\r
+void MyCmdLine(int argc, char **argv);\r
+void CmdLineErr(const char *Format, ...);\r
+void Help();\r
+void GetCmdLine(string &s);\r
+\r
+#define FLAG_OPT(LongName) extern bool opt_##LongName; extern bool optset_##LongName;\r
+#define TOG_OPT(LongName, Default) extern bool opt_##LongName; extern bool optset_##LongName;\r
+#define INT_OPT(LongName, Default, Min, Max) extern int opt_##LongName; extern bool optset_##LongName;\r
+#define UNS_OPT(LongName, Default, Min, Max) extern unsigned opt_##LongName; extern bool optset_##LongName;\r
+#define FLT_OPT(LongName, Default, Min, Max) extern double opt_##LongName; extern bool optset_##LongName;\r
+#define STR_OPT(LongName, Default) extern string opt_##LongName; extern bool optset_##LongName;\r
+#define ENUM_OPT(LongName, Default, Values) extern int opt_##LongName; extern bool optset_##LongName;\r
+#include "myopts.h"\r
+#undef FLAG_OPT\r
+#undef TOG_OPT\r
+#undef INT_OPT\r
+#undef UNS_OPT\r
+#undef FLT_OPT\r
+#undef STR_OPT\r
+#undef ENUM_OPT\r
+\r
+extern const char *SVN_VERSION;\r
+extern const char *SVN_MODS;\r
+extern bool opt_quiet;
+extern bool opt_version;
+extern FILE *g_fLog;
+\r
+#endif // myutils_h\r
projects / mothur.git / blobdiff