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* *
* Copyright © 2010-2013 -- IRB/INSERM *
* (Institut de Recherches en Biothérapie / *
* Institut National de la Santé et de la Recherche *
* Médicale) *
* LIFL/INRIA *
* (Laboratoire d'Informatique Fondamentale de *
* Lille / Institut National de Recherche en *
* Informatique et Automatique) *
* LIRMM/CNRS *
* (Laboratoire d'Informatique, de Robotique et de *
* Microélectronique de Montpellier / *
* Centre National de la Recherche Scientifique) *
* LITIS *
* (Laboratoire d'Informatique, du Traitement de *
* l'Information et des Systèmes). *
* *
* *
* Auteurs/Authors: Nicolas PHILIPPE <nicolas.philippe@lirmm.fr> *
* Mikaël SALSON <mikael.salson@lifl.fr> *
* Thierry LECROQ <thierry.lecroq@univ-rouen.fr> *
* Martine LÉONARD <Martine.Leonard@univ-rouen.fr> *
* Éric RIVALS <eric.rivals@lirmm.fr> *
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* Alban MANCHERON <alban.mancheron@lirmm.fr> *
* *
* Contact: Gk-Arrays list <crac-gkarrays@lists.gforge.inria.fr> *
* *
* ------------------------------------------------------------------------- *
* *
* Ce fichier fait partie de la librairie Gk-arrays. *
* *
* La librairie Gk-arrays a pour objectif d'indexer de grands ensembles de *
* lectures de séquences issues du séquençage haut-débit. *
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* ------------------------------------------------------------------------- *
* *
* This File is part of the Gk-arrays library. *
* *
* The Gk-arrays library aims at indexing k-factors from a huge set of *
* sequencing reads. *
* *
* This software is governed by the CeCILL-C license under French law and *
* abiding by the rules of distribution of free software. You can use, *
* modify and/ or redistribute the software under the terms of the CeCILL-C *
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******************************************************************************/
#ifndef __LARGEBINVECT_HXX__
#define __LARGEBINVECT_HXX__
#include "binvect.hxx"
template <typename CountWordSize = unsigned char>
class LargeBinVect {
private:
unsigned char *data;
CountWordSize length;
// Get the data internal array length
CountWordSize GetDataArrayLength() const;
// Get the last unsigned char mask for the internal array
unsigned char GetDataArrayEndingMask() const;
public:
// Constructors
LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc);
LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc);
LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
// Destructors
~LargeBinVect();
// Operators
inline LargeBinVect<CountWordSize> &operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
// Bitwise NOT
inline LargeBinVect<CountWordSize> operator~() const;
// Bitwise XOR
inline LargeBinVect<CountWordSize> operator^(const LargeBinVect<CountWordSize> &v) const;
// Bitwise OR
inline LargeBinVect<CountWordSize> operator|(const LargeBinVect<CountWordSize> &v) const;
// Bitwise AND
inline LargeBinVect<CountWordSize> operator&(const LargeBinVect<CountWordSize> &v) const;
// Right to Left shift by 's' bits
inline LargeBinVect<CountWordSize> operator<<(const CountWordSize s) const;
// Left to Right shift by 's' bits
inline LargeBinVect<CountWordSize> operator>>(const CountWordSize s) const;
// Bitwise XOR with self assignment
inline LargeBinVect<CountWordSize> &operator^=(const LargeBinVect<CountWordSize> &v);
// Bitwise OR with self assignment
inline LargeBinVect<CountWordSize> &operator|=(const LargeBinVect<CountWordSize> &v);
// Bitwise AND with self assignment
inline LargeBinVect<CountWordSize> &operator&=(const LargeBinVect<CountWordSize> &v);
// Right to Left shift by 's' bits with self assignment
inline LargeBinVect<CountWordSize> &operator<<=(const CountWordSize s);
// Left to Right shift by 's' bits with self assignment
inline LargeBinVect<CountWordSize> &operator>>=(const CountWordSize s);
// Sub-LargeBinVector starting at position b (>= 0) and
// of length lg (or to the end)
inline LargeBinVect<CountWordSize> operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
// Optimized already casted version
inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
// [ReadOnly] Access bit at position i (>= 0, < length)
inline bool operator[](const CountWordSize i) const throw (std::out_of_range);
// Bitwise equality. False if *this and v doesn't have the same length.
inline bool operator==(const LargeBinVect<CountWordSize> &v) const;
// Bitwise inequality. True if *this and v doesn't have the same length.
inline bool operator!=(const LargeBinVect<CountWordSize> &v) const;
// less than lexicographic operator
inline bool operator<(const LargeBinVect<CountWordSize> &v) const;
// greater than lexicographic operator
inline bool operator>(const LargeBinVect<CountWordSize> &v) const;
// less than or equal to lexicographic operator
inline bool operator<=(const LargeBinVect<CountWordSize> &v) const;
// greater than or equal to lexicographic operator
inline bool operator>=(const LargeBinVect<CountWordSize> &v) const;
// equivalent to operator[]
inline bool GetBit(const CountWordSize i) const throw (std::out_of_range);
// Set Bit at position i (>= 0, < length) to value
inline LargeBinVect<CountWordSize> &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range);
// Set Bits between positions i and j (>= 0, < length) to value
inline LargeBinVect<CountWordSize> &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range);
// Clear the bit vector and set all bits to value
inline LargeBinVect<CountWordSize> &Clear(const bool value = 0);
// set each bit of the vector to a random value
inline LargeBinVect<CountWordSize> &RandomInit();
// Resize the bit vector according to length and set all extra bits to value (if any)
inline LargeBinVect<CountWordSize> &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc);
// Append a bit to the vector and set its value to value
inline LargeBinVect<CountWordSize> &Append(const bool value) throw (BinVectOverflow, std::bad_alloc);
// Prepend a bit to the vector and set its value to value
inline LargeBinVect<CountWordSize> &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc);
// Concatenate v to the current binary vector
inline LargeBinVect<CountWordSize> &operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc);
// Pre-Increment the current binary vector by 1
inline LargeBinVect<CountWordSize> &operator++() throw (BinVectOverflow, std::bad_alloc);
// Post-Increment the current binary vector by 1
inline LargeBinVect<CountWordSize> operator++(int) throw (BinVectOverflow, std::bad_alloc);
// Pre-Decrement the current binary vector by 1
inline LargeBinVect<CountWordSize> &operator--() throw (BinVectOverflow);
// Post-Decrement the current binary vector by 1
inline LargeBinVect<CountWordSize> operator--(int) throw (BinVectOverflow, std::bad_alloc);
// Split the bit vector at position i.
// Current object is set to the prefix of length i and the remaining suffix is returned.
inline LargeBinVect<CountWordSize> Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc);
// Get longuest common prefix length.
inline CountWordSize GetLonguestCommonPrefix(const LargeBinVect<CountWordSize> &v) const;
// Get longuest common suffix length.
inline CountWordSize GetLonguestCommonSuffix(const LargeBinVect<CountWordSize> &v) const;
// Get bit vector length.
inline CountWordSize GetLength() const;
// Convert to ascii
inline char *ToString() const;
// Cast operators
inline operator char() const;
inline operator unsigned char() const;
inline operator short int() const;
inline operator unsigned short int() const;
inline operator int() const;
inline operator unsigned int() const;
inline operator long int() const;
inline operator unsigned long int() const;
};
template <typename CountWordSize>
std::ostream &operator<<(std::ostream &os, const LargeBinVect<CountWordSize> &v);
#include "largebinvect.cxx"
#endif
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