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common.hpp
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common.hpp
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// common.hpp
/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* Author: Vyacheslav Brover
*
* File Description:
* Common utilities
*
*/
#ifndef COMMON_HPP_64052 // random number
#define COMMON_HPP_64052
#ifdef _MSC_VER
#pragma warning (disable : 4061) // enumerator ... in switch of enum ... is not explicitly handled by a case label
#pragma warning (disable : 4290) // C++ exception specification ignored except to indicate a function is not __declspec(nothrow)
#pragma warning (disable : 4365) // conversion from 'type_1' to 'type_2', signed/unsigned mismatch (bool -> size_t)
#pragma warning (disable : 4503) // decorated name length exceeded, name was truncated
#pragma warning (disable : 4514) // '...': unreferenced inline function has been removed
#pragma warning (disable : 4521) // multiple copy constructors specified
#pragma warning (disable : 4522) // multiple assignment operators specified
#pragma warning (disable : 4592) // symbol will be dynamically initialized (implementation limitation)
#pragma warning (disable : 4625) // copy constructor was implicitly defined as deleted
#pragma warning (disable : 4626) // assignment operator was implicitly defined as deleted
#pragma warning (disable : 4710) // function not inlined
#pragma warning (disable : 4800) // 'const char *': forcing value to bool 'true' or 'false' (performance warning)
#pragma warning (disable : 4820) // '...' bytes padding added after data member '...'
#pragma warning (disable : 5026) // move constructor was implicitly defined as deleted
#pragma warning (disable : 5027) // move assignment operator was implicitly defined as deleted
#pragma warning (disable : 4005) // macro redefinition
#define _HAS_ITERATOR_DEBUGGING 0
#pragma warning (default : 4005)
#endif
#include <cassert>
#include <cstring>
#include <cmath>
#include <string>
#include <stdexcept>
#include <limits>
#include <array>
#include <list>
#include <vector>
#include <stack>
#include <set>
#include <map>
#include <unordered_set>
#include <unordered_map>
#include <iostream>
#include <fstream>
#include <sstream>
#include <iomanip>
#include <memory>
#include <algorithm>
#include <thread>
#ifdef _MSC_VER
#pragma warning(push)
#pragma warning(disable:4265)
#endif
#include <mutex>
#ifdef _MSC_VER
#pragma warning(pop)
#endif
using namespace std;
namespace Common_sp
{
bool initCommon ();
// Module initialization
// Invoked automaticallly
// Numeric types
typedef unsigned char uchar;
typedef unsigned int uint;
typedef unsigned long ulong;
// Numeric constants
constexpr size_t no_index = numeric_limits<size_t>::max ();
static_assert ((size_t) 0 - 1 == no_index);
constexpr double NaN = numeric_limits<double>::quiet_NaN ();
// Global variables
extern vector<string> programArgs;
extern string programName;
string getCommandLine ();
extern ostream* logPtr;
extern bool qc_on;
extern ulong seed_global;
// >= 1
// Errors
constexpr const char* error_caption ("*** ERROR ***");
[[noreturn]] void errorExit (const char* msg,
bool segmFault = false);
// Input: programArgs, programName, logptr
// Update: *logPtr
// Invokes: if segmFault then abort() else exit(1)
void errorExitStr (const string &msg);
// For debugger: should not be inline
// Invokes: beep()
[[noreturn]] void throwf (const string &s);
// For debugger: should not be inline
// Invokes: throw logic_error
void sleepNano (long nanoSec);
void beep ();
// Requires: !isRedirected()
// SHLVL = 1 ??
// Comparison templates
template <typename T>
inline void swapGreater (T &a, T &b)
{ if (a > b)
swap (a, b);
}
template <typename T>
inline bool maximize (T &a, T b)
{ if (a < b) { a = b; return true; } return false; }
template <typename T>
inline bool minimize (T &a, T b)
{ if (a > b) { a = b; return true; } return false; }
template <typename T>
inline T difference (T a, T b)
{ if (a > b) return a - b; return b - a; }
template <typename T /*:number*/>
inline bool between (T x, T low, T high)
{ return x >= low && x < high; }
template <typename T/*:number*/>
inline bool betweenEqual (T x, T low, T high)
{ return x >= low && x <= high; }
template <typename T>
inline bool lessPtr (const T* x,
const T* y)
{ return *x < *y; }
typedef int (*CompareInt) (const void*, const void*);
// Pointer templates
template <typename T>
inline T* var_cast (const T* t)
{ return const_cast <T*> (t); }
template <typename T>
inline T& var_cast (const T &t)
{ return const_cast <T&> (t); }
template <typename T, typename S>
inline T const_static_cast (const S* s)
{ return static_cast <T> (const_cast <S*> (s)); }
template <typename T, typename S>
inline T const_static_cast (const S &s)
{ return static_cast <T> (const_cast <S&> (s)); }
template <typename T>
inline T* checkPtr (T* t)
{ if (t)
return t;
throwf ("Dereferencing nullptr");
return nullptr;
}
// Container templates
template <typename T>
inline void sort (T &t)
{ std::sort (t. begin (), t. end ()); }
template <typename T, typename StrictlyLess>
inline void sort (T &t,
const StrictlyLess &strictlyLess)
{ std::sort (t. begin (), t. end (), strictlyLess); }
template <typename T, typename U>
bool intersects (const T &t,
const U &u)
{ if (u. empty ())
return false;
for (const auto& x : t)
if (u. find (static_cast <typename U::value_type> (x)) != u. end ())
return true;
return false;
}
template <typename T>
unordered_set<T> setIntersect (const unordered_set<T> &s1,
const unordered_set<T> &s2)
{ const unordered_set<T>* s1_ = & s1;
const unordered_set<T>* s2_ = & s2;
if (s1. size () > s2. size ())
swap (s1_, s2_);
unordered_set<T> res; res. rehash (s1_->size ());
for (const T& t : *s1_)
if (contains (*s2_, t))
res. insert (t);
return res;
}
template <typename T, typename U>
bool containsSubset (const T &t,
const U &u)
{ for (const auto& x : u)
if (t. find (static_cast <typename U::value_type> (x)) == t. end ())
return false;
return true;
}
template <typename T>
unordered_set<T> getSetMinus (const unordered_set<T> &s1,
const unordered_set<T> &s2)
{ unordered_set<T> res; res. rehash (s1. size ());
for (const T& t : s1)
if (! contains (s2, t))
res. insert (t);
return res;
}
template <typename T, typename U>
void setMinus (T &t,
const U &u)
{ for (const auto& x : u)
t. erase (x);
}
template <typename Key, typename Value, typename KeyParent>
inline bool contains (const map <Key, Value> &m,
const KeyParent& key)
{ return m. find (key) != m. end (); }
template <typename Key, typename Value, typename KeyParent>
inline bool contains (const unordered_map <Key, Value> &m,
const KeyParent& key)
{ return m. find (key) != m. end (); }
template <typename Key, typename KeyParent>
inline bool contains (const unordered_set <Key> &m,
const KeyParent& key)
{ return m. find (key) != m. end (); }
template <typename T, size_t N>
size_t indexOf (const array<T,N> &arr, const T item)
{ for (size_t i = 0; i < N; i++)
if (arr [i] == item)
return i;
return no_index;
}
template <typename T, size_t N>
inline bool contains (const array<T,N> &arr, const T item)
{ return indexOf (arr, item) != no_index; }
template <typename Key, typename Value, typename KeyParent>
bool find (const map <Key, Value> &m,
const KeyParent& key,
Value &value)
// Return: success
// Output: value, if Return
{ const auto& it = m. find (key);
if (it == m. end ())
return false;
value = it->second;
return true;
}
template <typename Key, typename Value, typename KeyParent>
bool find (const unordered_map <Key, Value> &m,
const KeyParent& key,
Value &value)
// Return: success
// Output: value, if Return
{ const auto& it = m. find (key);
if (it == m. end ())
return false;
value = it->second;
return true;
}
template <typename Key, typename Value, typename Hash, typename KeyParent>
bool find (const unordered_map <Key, Value, Hash> &m,
const KeyParent& key,
Value &value)
// Return: success
// Output: value, if Return
{ const auto& it = m. find (key);
if (it == m. end ())
return false;
value = it->second;
return true;
}
template <typename Key, typename Value, typename KeyParent>
const Value* findPtr (const map <Key, Value> &m,
const KeyParent& key)
{ const auto& it = m. find (key);
if (it == m. end ())
return nullptr;
return & it->second;
}
template <typename Key, typename Value, typename KeyParent>
const Value* findPtr (const unordered_map <Key, Value> &m,
const KeyParent& key)
{ const auto& it = m. find (key);
if (it == m. end ())
return nullptr;
return & it->second;
}
template <typename Key, typename Value, typename KeyParent>
const Value* findPtr (const map <Key, const Value* /*!nullptr*/> &m,
const KeyParent& key)
{ const Value* value;
if (find (m, key, value))
return value;
return nullptr;
}
template <typename Key, typename Value, typename KeyParent>
const Value* findPtr (const unordered_map <Key, const Value* /*!nullptr*/> &m,
const KeyParent& key)
{ const Value* value;
if (find (m, key, value))
return value;
return nullptr;
}
template <typename Key, typename Value>
const Value& findMake (map <Key, const Value* /*!nullptr*/> &m,
const Key& key)
{ if (! contains (m, key))
m [key] = new Value ();
return * m [key];
}
template <typename Key, typename Value>
const Value& findMake (unordered_map <Key, const Value* /*!nullptr*/> &m,
const Key& key)
{ if (! contains (m, key))
m [key] = new Value ();
return * m [key];
}
template <typename T, typename UnaryPredicate>
inline size_t count_if (T &t, UnaryPredicate pred)
{ return (size_t) std::count_if (t. begin (), t. end (), pred); }
template <typename To, typename From>
inline void insertAll (To &to,
const From &from)
{
#pragma GCC diagnostic ignored "-Waggressive-loop-optimizations"
to. insert (to. begin (), from. begin (), from. end ());
#pragma GCC diagnostic warning "-Waggressive-loop-optimizations"
}
template <typename To, typename From>
inline void insertIter (To &to,
From &&from)
{ for (auto&& x : from)
to. insert (std::move (x));
}
template <typename To, typename From>
inline void insertIter (To &to,
const From &from)
{ for (const auto& x : from)
to. insert (x);
}
template <typename From, typename What>
inline void eraseIter (From &from,
const What &what)
{ for (const auto& x : what)
if (contains (from, x))
from. erase (x);
}
template <typename T /*container*/>
void save (ostream &os,
const T &container,
char sep)
{ bool first = true;
for (const auto& t : container)
{ if (! first)
os << sep;
os << t;
first = false;
}
}
// KeyValue
typedef map<string/*key*/,string/*value*/> KeyValue;
inline string find (const KeyValue& kv,
const string& key)
{ const auto& it = kv. find (key);
if (it == kv. end ())
throw runtime_error ("Key \"" + key + "\" is not found");
return it->second;
}
// hash
extern hash<string> str_hash;
extern hash<size_t> size_hash;
// PAR
constexpr size_t small_hash_class_max = 1000;
constexpr size_t large_hash_class_max = small_hash_class_max * 100;
inline size_t str2hash_class (const string &s,
bool large_hash)
{ return str_hash (s) % (large_hash
? large_hash_class_max
: small_hash_class_max
);
}
// bool
inline void toggle (bool &b)
{ b = ! b; }
inline int getSign (bool b)
{ return b ? 1 : -1; }
inline bool boolPow (bool x, bool power)
{ return power ? x : ! x; }
inline string yesNo (bool x)
{ return x ? "Y" : "N"; }
// ebool: extended bool
enum ebool {efalse = false,
etrue = true,
enull = true + 1};
inline ebool toEbool (bool b)
{ return b ? etrue : efalse; }
inline bool operator<= (ebool a, ebool b)
{ static constexpr char rank [3/*ebool*/] = {0, 2, 1};
return rank [a] <= rank [b];
}
inline void toggle (ebool &b)
{ if (b == etrue)
b = efalse;
else if (b == efalse)
b = etrue;
}
inline string ebool2txt (ebool choice,
const string &yes,
const string &no,
const string &ambig)
{ switch (choice)
{ case etrue: return yes;
case efalse: return no;
default: return ambig;
}
}
// char
inline bool isChar (long long n)
{ return between<long long> (n, -128, 128); }
inline bool isAlpha (char c)
{ return strchr ("abcdefghijklmnopqrstuvwxyz", tolower (c)); }
// isalpha() is locale-specific
inline bool isDigit (char c)
{ return strchr ("0123456789", c); }
// isdigit() is locale-specific
inline bool isLetter (char c)
{ return isAlpha (c) || isDigit (c) || c == '_'; }
inline char toUpper (char c)
{ return (char) toupper (c); }
inline char toLower (char c)
{ return (char) tolower (c); }
inline bool isUpper (char c)
{ return toUpper (c) == c; }
inline bool isLower (char c)
{ return toLower (c) == c; }
inline bool printable (char c)
{ return between (c, ' ', (char) 127); }
inline bool nonPrintable (long c)
{ return between<long> (c, '\x001', ' '); }
string nonPrintable2str (char c);
inline bool isDelimiter (char c)
{ return c != ' '
&& printable (c)
&& ! isLetter (c);
}
inline bool isSpace (char c)
{ return c > '\0' && c <= ' ' && isspace (c); }
string to_url (const string &s);
// char*
inline const char* nvl (const char* s,
const char* nullS = "-")
{ return s ? s : nullS; }
// string
extern const string noString;
#ifndef _MSC_VER
inline string getEnv (const string& name)
{ if (const char* p = getenv (name. c_str ()))
return p;
return noString;
}
#endif
inline string ifS (bool cond,
const string &s)
{ return cond ? s : noString; }
inline string nvl (const string& s,
const string& nullS = "-")
{ return s. empty () ? nullS : s; }
inline string appendS (const string &s,
const string &suffix)
{ return s. empty () ? noString : (s + suffix); }
inline string prependS (const string &s,
const string &prefix)
{ return s. empty () ? noString : (prefix + s); }
inline void add (string &to,
const string &delimiter,
const string &what)
{ if (! to. empty ())
to += delimiter;
to += what;
}
inline bool isQuoted (const string &s,
char quote = '\"')
{ return ! s. empty () && s [0] == quote && s [s. size () - 1] == quote; }
string strQuote (const string &s,
char quote = '\"');
inline string unQuote (const string &s)
{ return s. substr (1, s. size () - 2); }
bool strBlank (const string &s);
bool getScientific (string numberS,
bool &hasPoint,
streamsize &decimals);
template <typename T>
string toString (const T &t)
{ ostringstream oss;
oss << t;
return oss. str ();
}
template <typename T>
T str2 (const string &s)
{ static_assert (numeric_limits<T>::max() > 256, "str2 does not work on chars");
T i;
istringstream iss (s);
iss >> i;
if ( Common_sp::strBlank (s)
|| ! iss. eof ()
|| iss. fail ()
)
throw runtime_error ("Cannot convert " + strQuote (s) + " to number");
return i;
}
template <typename T>
bool str2 (const string &s,
T &t)
{ try { t = str2<T> (s); return true; }
catch (...) { return false; }
}
void commaize (string &s);
// ' ' --> ','
inline bool isLeftBlank (const string &s,
size_t spaces)
{ size_t i = 0;
while (i < s. size () && i < spaces && s [i] == ' ')
i++;
return i == spaces;
}
string pad (const string &s,
size_t size,
ebool right);
// right: enull - center
bool goodName (const string &name);
bool isIdentifier (const string& name,
bool dashInName);
// Return: true. !empty(), !dashInName => (c \in mame => isLetter(c))
bool isNatural (const string& name,
bool leadingZeroAllowed);
void strUpper (string &s);
void strLower (string &s);
bool isUpper (const string &s);
bool isLower (const string &s);
inline string strUpper1 (const string &s)
{ if (s. empty ())
return s;
return toUpper (s [0]) + s. substr (1);
}
inline bool charInSet (char c,
const string &charSet)
{ return charSet. find (c) != string::npos; }
size_t stringNotInSet (const string &s,
const string &charSet);
// Return: index in s which is not in charSet; may be no_index
size_t strCountSet (const string &s,
const string &charSet);
void strDeleteSet (string &s,
const string &charSet);
inline bool isLeft (const string &s,
const string &left)
{ return s. substr (0, left. size ()) == left; }
bool isRight (const string &s,
const string &right);
bool trimPrefix (string &s,
const string &prefix);
// Return: success
bool trimSuffix (string &s,
const string &suffix);
// Return: success
void trimSuffixNonAlphaNum (string &s);
bool trimTailAt (string &s,
const string &tailStart);
// Return: trimmed
// Update: s
void trimLeading (string &s);
void trimTrailing (string &s);
inline void trim (string &s)
{ trimTrailing (s);
trimLeading (s);
}
void trimLeading (string &s,
char c);
// Invokes: isSpace()
void trimTrailing (string &s,
char c);
// Invokes: isSpace()
inline void trim (string &s,
char c)
{ trimTrailing (s, c);
trimLeading (s, c);
}
inline bool strNull (const string &s)
{ if (strBlank (s))
return true;
string s1 (s);
trim (s1);
strUpper (s1);
return s1 == "NULL"
|| s1 == "NA"
|| s1 == "N/A";
}
inline bool contains (const string &hay,
const string &needle)
{ return hay. find (needle) != string::npos; }
inline bool contains (const string &hay,
char needle)
{ return hay. find (needle) != string::npos; }
size_t containsWord (const string& hay,
const string& needle);
// Return: position of needle in hay; string::npos if needle does not exist
struct StringMatch
{
enum Type {part, word, whole};
};
bool matches (const string &hay,
const string &needle,
StringMatch::Type type);
void replace (string &s,
char from,
char to);
void replace (string &s,
const string &fromAnyChars,
char to);
void replaceStr (string &s,
const string &from,
const string &to);
// Replaces "from" by "to" in s from left to right
// The replacing "to" is skipped if it contains "from"
// Requires: !from.empty()
string to_c (const string &s);
// " --> \", etc.
void collapseSpace (string &s);
// " " --> " "
void visualizeTrailingSpaces (string &s);
// Invokes: nonPrintable2str(' ')
string str2streamWord (const string &s,
size_t wordNum);
// Return: May be empty()
// Input: wordNum: 0-based
string str2sql (const string &s);
// Return: ' s ' (replacing ' by '')
string findSplit (string &s,
char c = ' ');
// Return: prefix of s+c before c
// Update: s
string rfindSplit (string &s,
char c = ' ');
// Return: suffix of c+s after c
// Update: s
void reverse (string &s);
size_t strMonth2num (const string& month);
// Input: month: "Jan", "Feb", ... (3 characters)
// Bit operations
inline bool contains (uint who,
uint what)
{ return (who & what) == what; }
inline uchar reverse (uchar b)
{ return uchar (numeric_limits<uchar>::max () - b); }
size_t byte2first (uchar b);
// Return: First 1-bit, 0-based
size_t utf8_len (char first);
// Return: 0 - first is ASCII
// 1 - first is UTF-8 not first byte
// else - first is UTF-8 first byte and value is the number of UTF-8 bytes
// Integer operations
inline void advance (size_t &index,
size_t size)
// Update: index: < size
{ index++; if (index == size) index = 0; }
template <typename T/*:integer*/>
inline bool even (T x)
{ static_assert (numeric_limits<T>::is_integer);
return x % 2 == 0;
}
inline bool divisible (size_t n,
size_t divisor)
{ return ! (n % divisor); }
inline uint remainder (int n, uint div)
{ if (const int rem = n % (int) div)
return (uint) (rem > 0 ? rem : (rem + (int) div));
return 0;
}
inline uint gcd (uint a,
uint b)
// Greatest common divisor
// Euclid's algorithm
{ if (! b)
return a;
if (a < b)
return gcd (b, a);
return gcd (b, a % b);
}
size_t powInt (size_t a,
size_t b);
// Return: a^b
// Time: O(log(b))
struct Rand
// Numerical Recipes in C, p. 279
{
static const long /*actually ulong*/ max_;
private:
long seed {0};
// 0 < seed < max_
public:
explicit Rand (ulong seed_arg = 1)
{ setSeed (seed_arg); }
void setSeed (ulong seed_arg)
{ seed = (long) (seed_arg % (ulong) max_);
qc ();
}
// Input: seed_arg > 0
ulong get (ulong max);
// Return: in 0 .. max - 1
// Input: 0 < max <= max_
ulong get ()
{ return get ((ulong) max_); }
double getProb ()
{ return (double) get ((ulong) max_) / ((double) max_ - 1); }
// Return: [0,1]
private:
void qc () const;
void run ();
};
// Hexadecimal
inline bool isHex (char c)
{ return isDigit (c) || strchr ("ABCDEF", toUpper (c)); }
inline uchar hex2uchar (char c)
{ return uchar (isDigit (c) ? (c - '0') : (toUpper (c) - 'A' + 10)); }
inline string uchar2hex (uchar c)
{ constexpr char hex [16] = {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F'};
string res (" ");
res [0] = hex [c / 16];
res [1] = hex [c % 16];
return res;
}
string unpercent (const string &s);
// '%HH' -> char
struct DisjointCluster
// Cormen, Leiserson, Rivest, Introduction to Algorithms, p. 449
{
protected:
DisjointCluster* parentDC {nullptr};
// !nullptr
// Tree
// = this <=> root
size_t rankDC {0};
// Upper bound on the height of *this
// (Height = max. # arcs between *this and a leaf)
public:
protected:
DisjointCluster ()
{ init (); }
public:
void init ()
{ rankDC = 0;
parentDC = this;
}
void merge (DisjointCluster &other);