/usr/include/libGkArrays-2.1.0/largebinvect.cxx is in libgkarrays-dev 2.1.0+dfsg-1.
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The actual contents of the file can be viewed below.
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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 *
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* 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> *
* *
* Programmeurs *
* /Progammers: *
* 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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* Ce logiciel est régi par la licence CeCILL-C soumise au droit français et *
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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_CXX__
#define __LARGEBINVECT_CXX__
#include "largebinvect.hxx"
using std::ostream;
template <typename CountWordSize>
CountWordSize LargeBinVect<CountWordSize>::GetDataArrayLength() const {
CountWordSize w = length/8 + ((length % 8) > 0);
return w;
}
template <typename CountWordSize>
unsigned char LargeBinVect<CountWordSize>::GetDataArrayEndingMask() const {
unsigned char mask = (length % 8 ? 255 << (8 - (length % 8)) : 255);
return mask;
}
template <typename CountWordSize>
unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) {
unsigned char *array;
if (!w) {
return NULL;
}
if ((array = (unsigned char *) malloc(w*sizeof(unsigned char))) == NULL) {
throw std::bad_alloc();
}
if (value >= 0) {
memset(array, value, w*sizeof(unsigned char));
}
return array;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc)
: length(length) {
CountWordSize w = GetDataArrayLength();
unsigned char mask = GetDataArrayEndingMask();
data = MyCalloc(w, (value ? 255 : 0));
if (w) {
data[w - 1] |= ~mask;
}
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) {
length = strlen(binary_string);
if (length != (long unsigned int) length) {
throw BinVectOverflow();
}
CountWordSize w = GetDataArrayLength();
unsigned char mask = GetDataArrayEndingMask();
data = MyCalloc(w, 0);
for (CountWordSize i = 0; i < length; i++) {
if (binary_string[i] == '1') {
unsigned char m = 1 << (7 - (i%8));
data[i/8] |= m;
}
}
if (w) {
data[w - 1] |= ~mask;
}
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc)
: length(v.length) {
CountWordSize w = v.GetDataArrayLength();
data = MyCalloc(w);
for (CountWordSize i = 0; i < w; i++) {
data[i] = v.data[i];
}
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::~LargeBinVect() {
if (data) {
free(data);
}
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc) {
if (this != &v) {
if (data) {
free(data);
}
length = v.length;
CountWordSize w = v.GetDataArrayLength();
data = MyCalloc(w);
for (CountWordSize i = 0; i < w; i++) {
data[i] = v.data[i];
}
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator~() const {
LargeBinVect<CountWordSize> bv(*this);
CountWordSize w = bv.GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
bv.data[i] ^= 255;
}
unsigned char mask = GetDataArrayEndingMask();
if (w) {
bv.data[w - 1] |= ~mask;
}
return bv;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator^(const LargeBinVect<CountWordSize> &v) const {
assert(v.length == length);
LargeBinVect<CountWordSize> bv(*this);
CountWordSize w = bv.GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
bv.data[i] ^= v.data[i];
}
unsigned char mask = GetDataArrayEndingMask();
if (w) {
bv.data[w - 1] |= ~mask;
}
return bv;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator|(const LargeBinVect<CountWordSize> &v) const {
assert(v.length == length);
LargeBinVect<CountWordSize> bv(*this);
CountWordSize w = bv.GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
bv.data[i] |= v.data[i];
}
return bv;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator&(const LargeBinVect<CountWordSize> &v) const {
assert(v.length == length);
LargeBinVect<CountWordSize> bv(*this);
CountWordSize w = bv.GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
bv.data[i] &= v.data[i];
}
return bv;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator<<(const CountWordSize s) const {
LargeBinVect<CountWordSize> v(*this);
v<<=s;
return v;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator>>(const CountWordSize s) const {
LargeBinVect<CountWordSize> v(*this);
v>>=s;
return v;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator^=(const LargeBinVect<CountWordSize> &v) {
assert(v.length == length);
CountWordSize w = GetDataArrayLength();
unsigned char mask = GetDataArrayEndingMask();
for (CountWordSize i = 0; i < w; i++) {
data[i] ^= v.data[i];
}
if (w) {
data[w - 1] |= ~mask;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator|=(const LargeBinVect<CountWordSize> &v) {
assert(v.length == length);
CountWordSize w = GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
data[i] |= v.data[i];
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator&=(const LargeBinVect<CountWordSize> &v) {
assert(v.length == length);
CountWordSize w = GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
data[i] &= v.data[i];
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator<<=(const CountWordSize s) {
CountWordSize w = GetDataArrayLength();
unsigned char m = ~(255>>s);
unsigned char mask = GetDataArrayEndingMask();
for (CountWordSize i = 0; i < w - 1; i++) {
if (i) {
data[i - 1] |= (data[i] & m) >> (8-s);
}
data[i] <<= s;
}
if (w) {
if (w - 1) {
data[w - 2] |= (data[w - 1] & m & mask) >> (8-s);
}
data[w - 1] &= mask;
data[w - 1] <<= s;
data[w - 1] |= ~mask;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator>>=(const CountWordSize s) {
CountWordSize w = GetDataArrayLength();
unsigned char m = ~(255<<s);
unsigned char mask = GetDataArrayEndingMask();
if (!w) {
return *this;
}
data[w - 1] &= mask;
data[w - 1] >>= s;
for (CountWordSize i = w - 2; (i >= 0) && (i < w - 1); i--) {
data[i + 1] |= (data[i] & m) << (8-s);
data[i] >>= s;
}
data[w - 1] |= ~mask;
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
if ((b < 0) || (b > length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "b=" << (unsigned long int) b
<< " should be >= 0 and <= " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
CountWordSize l = (lg > length ? length : lg);
if (b+l > length) {
l = length - b;
}
assert(l <= length || l == 0);
LargeBinVect<CountWordSize> bv(l);
for (CountWordSize i = 0; i < l; i++) {
bv.SetBit(i, GetBit(i+b));
}
return bv;
}
template <typename CountWordSize>
unsigned long int LargeBinVect<CountWordSize>::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
if ((b < 0) || (b > length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "b=" << (unsigned long int) b
<< " should be >= 0 and <= " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
unsigned long int r = 0;
CountWordSize l = b + (lg > sizeof(unsigned long int)*8 ? sizeof(unsigned long int)*8 : lg);
// std::cerr << "1: b = " << (unsigned int) b
// << ", l = " << (unsigned int) l
// << std::endl;
if ((l > length) || (l < b)) {
l = length;
}
// std::cerr << "2: b = " << (unsigned int) b
// << ", l = " << (unsigned int) l
// << std::endl;
assert(l <= length || l == 0);
for (CountWordSize i = b; i < l; i++) {
r <<= 1;
r |= GetBit(i);
// std::cerr << "i = " << (unsigned int) i
// << ", GetBit(i) = " << GetBit(i)
// << ", r = " << r
// << std::endl;
}
return r;
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator[](const CountWordSize i) const throw (std::out_of_range) {
if ((i < 0) || (i >= length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "i=" << (unsigned long int) i
<< " should be >= 0 and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
return (128&(data[i/8]<<(i%8)));
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator==(const LargeBinVect<CountWordSize> &v) const {
if (length != v.length) {
return false;
}
const CountWordSize w = GetDataArrayLength();
for (CountWordSize i = 0; i < w; i++) {
if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
return false;
}
}
return true;
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator!=(const LargeBinVect<CountWordSize> &v) const {
return !(*this == v);
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator<(const LargeBinVect<CountWordSize> &v) const {
const CountWordSize &lg = (length > v.length ? v.length : length);
const CountWordSize w = lg/8;
CountWordSize i;
for (i = 0; i < w; i++) {
if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
return (data[i] < v.data[i]);
}
}
if (lg%8) {
unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
if ((data[i]&mask) ^ (v.data[i]&mask)) { // True if they differ by at least one bit
return ((data[i]&mask) < (v.data[i]&mask));
}
}
return (length < v.length);
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator>(const LargeBinVect<CountWordSize> &v) const {
return v < *this;
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator<=(const LargeBinVect<CountWordSize> &v) const {
const CountWordSize &lg = (length > v.length ? v.length : length);
const CountWordSize w = lg/8;
CountWordSize i;
for (i = 0; i < w; i++) {
if (data[i] ^ v.data[i]) { // True if they differ by at least one bit
return (data[i] < v.data[i]);
}
}
if (lg%8) {
unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
if ((data[i]&mask) ^ (v.data[i]&mask)) { // True if they differ by at least one bit
return ((data[i]&mask) < (v.data[i]&mask));
}
}
return (length <= v.length);
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::operator>=(const LargeBinVect<CountWordSize> &v) const {
return v <= *this;
}
template <typename CountWordSize>
bool LargeBinVect<CountWordSize>::GetBit(const CountWordSize i) const throw (std::out_of_range) {
if ((i < 0) || (i >= length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "i=" << (unsigned long int) i
<< " should be >= 0 and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
return (data[i/8] & (1 << (7-(i%8))));
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) {
if ((i < 0) || (i >= length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "i=" << (unsigned long int) i
<< " should be >= 0 and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
if (value) {
data[i/8] |= (1 << (7-(i%8)));
} else {
data[i/8] &= ~(1 << (7-(i%8)));
}
return *this;
}
// Set Bits between positions i and j (>= 0, < length) to value
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) {
if ((i < 0) || (i >= length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "i=" << (unsigned long int) i
<< " should be >= 0 and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
if ((j < i) || (j >= length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "j=" << (unsigned long int) j
<< " should be >= " << i << " and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
long unsigned int v = value;
// cerr << "i / 8 = " << (unsigned int) i <<" / 8 = " << i / 8 << " et i % 8 = " << i % 8 << endl;
// cerr << "j / 8 = " << (unsigned int) j <<" / 8 = " << j / 8 << " et j % 8 = " << j % 8 << endl;
if ((j / 8) > (i / 8)) {
// cerr << "cas 1" << endl;
if ((j + 1) % 8) {
// cerr << "cas 1A" << endl;
unsigned char mask = ~(255 << (j % 8 + 1));
unsigned char clear_mask = ~(255 << (7 - (j % 8)));
// cerr << "clearing mask = " << bitset<8>(clear_mask) << ", setting mask = " << bitset<8>(mask) << endl;
// cerr << "data["<<(unsigned int) j<<" / 8] = " << bitset<8>(data[j / 8]) << endl;
data[j / 8] &= clear_mask;
// cerr << "clearing => " << bitset<8>(data[j / 8]) << endl;
data[j / 8] |= ((char) v & mask) << (7 - (j % 8));
// cerr << "setting with " << bitset<8>(((char) v & mask)) << "<<" << 7 - (j % 8) << " => " << bitset<8>(data[j / 8]) << endl;
v >>= (j % 8 + 1);
// cerr << "shifting value by " << j % 8 + 1 << " bits => " << bitset<8>(v) << endl;
}
for (CountWordSize x = j / 8 - ((j + 1) % 8 != 0); x > i / 8; x--) {
// cerr << "cas 1B for data[x = " << (unsigned int) x << "]" << endl;
data[x] = (char) v & 255;
v >>= 8;
// cerr << "shifting value by 8 bits => " << bitset<8>(v) << endl;
}
// cerr << "cas 1C" << endl;
unsigned char mask = 255 << (8 - (i % 8));
// cerr << "clearing mask = " << bitset<8>(mask) << ", setting mask = " << bitset<8>(~mask) << endl;
// cerr << "data[" << (unsigned int) i <<" / 8] = " << bitset<8>(data[i / 8]) << endl;
data[i / 8] &= mask;
// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
data[i / 8] |= (char) v & ~mask;
// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
} else {
// cerr << "cas 2" << endl;
if (i / 8 == length / 8) {
// cerr << "cas 2A" << endl;
unsigned char mask = ~(255 << (j - i + 1));
unsigned char clear_mask = ~(mask << (8 - (length % 8)));
// cerr << "clearing mask is " << bitset<8>(clear_mask) << endl;
data[i / 8] &= clear_mask;
// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
// cerr << "value setting mask = " << bitset<8>(mask) << endl;
// cerr << "result of masking will be shifted by " << (8 - (length % 8)) << " positions" << endl;
data[i / 8] |= (v & mask) << (8 - (length % 8));
// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
} else {
// cerr << "cas 2B" << endl;
unsigned char clearing_mask = ~((255 >> (i % 8)) & (255 << (7 - (j % 8))));
unsigned char setting_mask = ~(255 << (j - i + 1));
// cerr << "clearing mask = " << bitset<8>(clearing_mask) << ", setting mask = " << bitset<8>(setting_mask) << endl;
// cerr << "data[" << (unsigned int) i <<" / 8] = " << bitset<8>(data[i / 8]) << endl;
data[i / 8] &= clearing_mask;
// cerr << "clearing => " << bitset<8>(data[i / 8]) << endl;
data[i / 8] |= ((char) v & setting_mask) << (7 - (j % 8));
// cerr << "setting => " << bitset<8>(data[i / 8]) << endl;
}
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Clear(const bool value) {
unsigned char mask = GetDataArrayEndingMask();
CountWordSize w = GetDataArrayLength();
if (w) {
memset(data, (value ? 255 : 0), w*sizeof(unsigned char));
data[w - 1] |= ~mask;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::RandomInit() {
unsigned char mask = GetDataArrayEndingMask();
CountWordSize w = GetDataArrayLength();
if (w) {
for (CountWordSize i = 0; i < w; i++) {
data[i] = (unsigned char) random();
}
data[w - 1] |= ~mask;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) {
CountWordSize old_w = GetDataArrayLength();
unsigned char mask = GetDataArrayEndingMask();
this->length = length;
CountWordSize w = GetDataArrayLength();
if (!w) { // If length is 0 ;-)
free(data);
data = NULL;
return *this;
}
if (old_w) {
if (value) {
data[old_w - 1] |= ~mask;
} else {
data[old_w - 1] &= mask;
}
}
if ((data = (unsigned char *) realloc(data, w*sizeof(unsigned char))) == NULL) {
throw std::bad_alloc();
}
if (w > old_w) {
memset(data+old_w, (value ? 255 : 0), (w-old_w)*sizeof(unsigned char));
}
mask = GetDataArrayEndingMask();
data[w - 1] |= ~mask;
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) {
if (length == CountWordSize(~0)) {
throw BinVectOverflow();
}
return Resize(length+1, value);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) {
if (length == CountWordSize(~0)) {
throw BinVectOverflow();
}
Resize(length+1) >>= 1;
if (value) {
data[0] |= 128;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc) {
if ((length + v.length < length) || (length + v.length < v.length)) {
throw BinVectOverflow();
}
if (!v.length) {
return *this;
}
CountWordSize old_w = GetDataArrayLength();
unsigned char mask = GetDataArrayEndingMask();
CountWordSize app_w = v.GetDataArrayLength();
unsigned int shift = (length%8);
Resize(length + v.length);
if (shift) {
assert(old_w);
assert(app_w);
old_w--;
data[old_w] &= mask;
mask = v.GetDataArrayEndingMask();
v.data[app_w - 1] &= mask;
for (CountWordSize i = 0; i < app_w - 1; i++) {
data[old_w + i] |= v.data[i] >> shift;
data[old_w + i + 1] |= v.data[i] << (8 - shift);
}
data[old_w + app_w - 1] |= v.data[app_w - 1] >> shift;
if (old_w + app_w == GetDataArrayLength() - 1) {
data[old_w + app_w] |= v.data[app_w - 1] << (8 - shift);
}
} else {
for (CountWordSize i = 0; i < app_w; i++) {
data[old_w + i] = v.data[i];
}
mask = GetDataArrayEndingMask();
data[old_w + app_w - 1] |= ~mask;
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator++() throw (BinVectOverflow, std::bad_alloc) {
CountWordSize w = GetDataArrayLength();
unsigned char mask = ~GetDataArrayEndingMask();
++mask;
while (mask && w--) {
unsigned char old = data[w];
data[w] += mask;
mask = (data[w] < old);
}
if (mask) {
Prepend(true);
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator++(int) throw (BinVectOverflow, std::bad_alloc) {
LargeBinVect<CountWordSize> ret(*this);
++(*this);
return ret;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator--() throw (BinVectOverflow) {
CountWordSize w = GetDataArrayLength();
unsigned char mask = ~GetDataArrayEndingMask();
++mask;
while (mask && w--) {
unsigned char old = data[w];
data[w] -= mask;
mask = (data[w] > old);
}
if (mask) {
throw BinVectOverflow();
}
return *this;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator--(int) throw (BinVectOverflow, std::bad_alloc) {
LargeBinVect<CountWordSize> ret(*this);
--(*this);
return ret;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) {
if ((i < 0) || (i > length)) {
std::stringstream msg;
msg << __FILE__ << ":"
<< __PRETTY_FUNCTION__ << ":"
<< __LINE__ << ":"
<< "i=" << (unsigned long int) i
<< " should be >= 0 and < " << (unsigned long int) length;
throw std::out_of_range(msg.str());
}
if (i == length) {
return LargeBinVect<CountWordSize>();
} else {
LargeBinVect<CountWordSize> bv = (*this)(i, length - i);
Resize(i);
return bv;
}
}
template <typename CountWordSize>
CountWordSize LargeBinVect<CountWordSize>::GetLonguestCommonPrefix(const LargeBinVect<CountWordSize> &v) const {
const CountWordSize &lg = (length > v.length ? v.length : length);
const CountWordSize w = lg/8;
CountWordSize i;
for (i = 0; i < w; i++) {
unsigned char m = data[i] ^ v.data[i];
CountWordSize p;
if (m) { // True if they differ by at least one bit
for (p = i*8; !(128 & m); p++) {
m <<= 1;
}
return p;
}
}
if (lg%8) {
unsigned char mask = (length > v.length ? v.GetDataArrayEndingMask() : GetDataArrayEndingMask());
unsigned char m = (data[i] & mask) ^ (v.data[i] & mask);
CountWordSize p;
if (m) { // True if they differ by at least one bit
for (p = i*8; !(128 & m); p++) {
m <<= 1;
}
return p;
}
}
return lg;
}
template <typename CountWordSize>
CountWordSize LargeBinVect<CountWordSize>::GetLonguestCommonSuffix(const LargeBinVect<CountWordSize> &v) const {
if (length > v.length) {
return v.GetLonguestCommonSuffix(*this);
} else { // length <= v.length
const CountWordSize delta = v.length - length;
for (CountWordSize i = length - 1; (i >= 0) && (i < length); i--) {
if (GetBit(i) != v.GetBit(i+delta)) {
return length - i - 1;
}
}
return length;
}
}
template <typename CountWordSize>
char * LargeBinVect<CountWordSize>::ToString() const {
char* tmp;
tmp = new char [length + 1];
const CountWordSize w = length / 8;
unsigned char m;
for (CountWordSize i = 0; i < w; i++) {
m = data[i];
for (unsigned char b = 0; b < 8; b++) {
tmp[i*8+b] = ((128 & m) ? '1' : '0');
m<<=1;
}
}
if (length % 8) {
m = data[w];
for (unsigned char b = 0; b < length % 8; b++) {
tmp[w*8+b] = ((128 & m) ? '1' : '0');
m<<=1;
}
}
tmp[length]=0;
return tmp;
}
template <typename CountWordSize>
CountWordSize LargeBinVect<CountWordSize>::GetLength() const {
return length;
}
// Cast operators
template <typename CountWordSize, typename target_type>
target_type cast(const LargeBinVect<CountWordSize> &v) {
target_type r = 0;
CountWordSize i = sizeof(target_type)*8;
if (i > v.GetLength()) {
i = v.GetLength();
}
for (; i > 0; i--) {
r <<= 1;
r |= v.GetBit(v.GetLength() - i);
}
return r;
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator char() const {
return cast<CountWordSize, char>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator unsigned char() const {
return cast<CountWordSize, unsigned char>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator short int() const {
return cast<CountWordSize, short int>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator unsigned short int() const {
return cast<CountWordSize, unsigned short int>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator int() const {
return cast<CountWordSize, int>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator unsigned int() const {
return cast<CountWordSize, unsigned int>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator long int() const {
return cast<CountWordSize, long int>(*this);
}
template <typename CountWordSize>
LargeBinVect<CountWordSize>::operator unsigned long int() const {
return cast<CountWordSize, unsigned long int>(*this);
}
template <typename CountWordSize>
std::ostream &operator<<(std::ostream &os, const LargeBinVect<CountWordSize> &v) {
char *tmp = v.ToString();
os << tmp;
delete [] tmp;
return os;
}
#ifdef TEST_LARGEBINVECT
// Compile this test program with the following command line:
// g++ largebinvect.cxx -DTEST_LARGEBINVECT -o test_largebinvect -Wall -ansi -pedantic -O4
using std::cout;
using std::endl;
#include <bitset>
template <typename CountWordSize>
void TestLargeBinVectors(char *title, CountWordSize max_test_length) {
cout << "Testing class LargeBinVect<" << title << ">" << endl;
cout << "SizeOf(" << title << ") = "
<< sizeof(CountWordSize) << "Bytes (= "
<< 8*sizeof(CountWordSize) << "bits)" << endl << endl;
const char *binary_string1 = "1001010111010001011110100010101";
const char *binary_string2 = "10010101110100010101";
cout << "Building a short binvect from string '" << binary_string1 << "'" << endl;
LargeBinVect<CountWordSize> * v1 = new LargeBinVect<CountWordSize>(binary_string1);
cout << "=> '" << *v1 << "' of length " << (unsigned long int) v1->GetLength() << endl;
LargeBinVect<CountWordSize> * v2 = new LargeBinVect<CountWordSize>(binary_string2);
cout << "=> '" << *v2 << "' of length " << (unsigned long int) v2->GetLength() << endl;
cout << "Compute the longuest common prefix (size 18) between" << endl;
cout << "bv1='" << *v1 << "'" << endl;
cout << "bv2='" << *v2 << "'" << endl;
cout << "It returns " << (unsigned long int)v1->GetLonguestCommonPrefix(*v2);
cout << " which should also be " << (unsigned long int)v2->GetLonguestCommonPrefix(*v1) << endl;
cout << "Compute the longuest common suffix (size 13) between" << endl;
cout << "bv1='" << *v1 << "'" << endl;
cout << "bv2='" << *v2 << "'" << endl;
cout << "It returns " << (unsigned long int)v1->GetLonguestCommonSuffix(*v2);
cout << " which should also be " << (unsigned long int)v2->GetLonguestCommonSuffix(*v1) << endl;
cout << endl;
cout << "Resizing bv1 to 78 bits (filling with 0)" << endl;
cout << "bv1 was ='" << *v1 << "'" << endl;
v1->Resize(78);
cout << "bv1 is ='" << *v1 << "'" << endl;
cout << "Resizing bv2 to 35 bits (filling with 1)" << endl;
cout << "bv2 was ='" << *v2 << "'" << endl;
v2->Resize(35, 1);
cout << "bv2 is ='" << *v2 << "'" << endl;
cout << "Resizing bv1 to 35 bits ([not] filling with 1)" << endl;
cout << "bv1 was ='" << *v1 << "'" << endl;
v1->Resize(35, 1);
cout << "bv1 is ='" << *v1 << "'" << endl;
cout << "Resizing bv2 to 13 bits ([not] filling with 0)" << endl;
cout << "bv2 was ='" << *v2 << "'" << endl;
v2->Resize(13);
cout << "bv2 is ='" << *v2 << "'" << endl;
cout << "Resizing bv2 to 20 bits (filling with 0)" << endl;
cout << "bv2 was ='" << *v2 << "'" << endl;
v2->Resize(20);
cout << "bv2 is ='" << *v2 << "'" << endl;
cout << endl;
*v2 = LargeBinVect<CountWordSize>("1000000010000000100000001000000010000000100000001000000010000000");
cout << "Testing cast operators" << endl;
cout << "casting " << *v2 << " to char:" << (int) ((char) *v2)
<< ", which should be -128" << endl;
cout << "casting " << *v2 << " to unsigned char:" << (unsigned int) (unsigned char) *v2
<< ", which should be 128" << endl;
cout << "casting " << *v2 << " to short:" << (short int) *v2
<< ", which should be -32640" << endl;
cout << "casting " << *v2 << " to unsigned short:" << (unsigned short int) *v2
<< ", which should be 32896" << endl;
cout << "casting " << *v2 << " to int:" << (int) *v2
<< ", which should be -2139062144" << endl;
cout << "casting " << *v2 << " to unsigned int:" << (unsigned int) *v2
<< ", which should be 2155905152" << endl;
cout << "casting " << *v2 << " to long:" << (long int) *v2
<< ", which should be -9187201950435737472" << endl;
cout << "casting " << *v2 << " to unsigned long:" << (unsigned long int) *v2
<< ", which should be 9259542123273814144" << endl;
cout << endl;
cout << "Deleting the binvectors" << endl;
delete v1;
delete v2;
cout << endl;
cout << "Creating empty binvector" << endl;
v1 = new LargeBinVect<CountWordSize>();
cout << "LargeBinVect is '" << *v1 << "'" << endl;
cout << "Preincrementing '" << *v1 << "'" << endl;
cout << "=> '" << ++(*v1) << "'" << endl;
cout << "Postincrementing '" << (*v1)++ << "'" << endl;
cout << "=> '" << *v1 << "'" << "'" << endl;
cout << "Incrementing '" << *v1 << "'" << endl;
cout << "=> '" << ++(*v1) << "'" << endl;
cout << "Incrementing '" << *v1 << "'" << endl;
cout << "=> '" << ++(*v1) << "'" << endl;
cout << "Appending '111111111111111' to '" << *v1 << "'" << endl;
*v1 += LargeBinVect<CountWordSize>("111111111111111");
cout << "=> '" << *v1 << "'" << endl;
cout << "Incrementing '" << *v1 << "'" << endl;
cout << "=> '" << ++(*v1) << "'" << endl;
cout << "Predecrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Postdecrementing '" << (*v1)-- << "'" << endl;
cout << "=> '" << *v1 << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Resizing '" << *v1 << "' to 3 bits" << endl;
v1->Resize(3);
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << "Decrementing '" << *v1 << "'" << endl;
cout << "=> '" << --(*v1) << "'" << endl;
cout << endl;
cout << "Deleting the binvector" << endl;
delete v1;
cout << "===" << endl;
for (CountWordSize i = 1; i < max_test_length; i*=2) {
cout << endl;
cout << "Make 0-filled binvect of length " << (unsigned long int) i << endl;
LargeBinVect<CountWordSize> bv(i);
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Overwrite (operator=) the binvect with a 1-filled one of same length" << endl;
bv = LargeBinVect<CountWordSize>(i, 1);
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Clearing the binvect with 0" << endl;
bv.Clear();
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Clearing the binvect with 1" << endl;
bv.Clear(1);
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
long unsigned int r = rand();
cout << "Setting the bit range from " << i / 3
<< " to " << 3 * i / 4
<< " with the value " << std::bitset<20>(r) << endl;
bv.SetBitRange(i / 3, 3 * i / 4, r);
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Setting even bits to 0" << endl;
cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
for (CountWordSize b = 0; b < i; b+=2) {
bv.SetBit(b, 0);
}
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Left Shifting (Self assignment) binvect by 3" << endl;
cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
bv <<= 3;
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Right Shifting (Self assignment) binvect by 4" << endl;
cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
bv >>= 4;
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << "Assigning its inversed bit values" << endl;
cout << "was '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
bv = ~bv;
cout << "=> '" << bv << "' of length " << (unsigned long int) bv.GetLength() << endl;
cout << endl;
cout << "Generating a random bitvector having same length" << endl;
LargeBinVect<CountWordSize> rbv(i);
rbv.RandomInit();
cout << "=> '" << rbv << "' of length " << (unsigned long int) rbv.GetLength() << endl;
cout << "Performing XOR between bv and rbv" << endl;
LargeBinVect<CountWordSize> res = (bv ^ rbv);
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Performing OR between bv and rbv" << endl;
res = (bv | rbv);
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Performing AND between bv and rbv" << endl;
res = (bv & rbv);
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Using the copy constructor" << endl;
v1 = new LargeBinVect<CountWordSize>(res);
cout << "res='" << res << "'" << endl;
cout << "=> '" << *v1 << "' of length " << (unsigned long int) v1->GetLength() << endl;
delete v1;
cout << "Performing Self Assignment XOR between copy of bv and rbv" << endl;
res = bv;
res ^= rbv;
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Performing Self Assignment OR between copy of bv and rbv" << endl;
res = bv;
res |= rbv;
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Performing Self Assignment AND between copy of bv and rbv" << endl;
res = bv;
res &= rbv;
cout << "bv ='" << bv << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Build prefix of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
res = rbv(0, rbv.GetLength()/3);
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "Testing between rbv < res" << endl;
cout << "=> " << (rbv < res ? "true" : "false") << endl;
cout << "Testing between rbv <= res" << endl;
cout << "=> " << (rbv <= res ? "true" : "false") << endl;
cout << "Testing between rbv > res" << endl;
cout << "=> " << (rbv > res ? "true" : "false") << endl;
cout << "Testing between rbv >= res" << endl;
cout << "=> " << (rbv >= res ? "true" : "false") << endl;
cout << "Testing between rbv == res" << endl;
cout << "=> " << (rbv == res ? "true" : "false") << endl;
cout << "Testing between rbv != res" << endl;
cout << "=> " << (rbv != res ? "true" : "false") << endl;
CountWordSize p = 0;
if (res.GetLength()) {
p = rand() % res.GetLength();
cout << "Spin bit at position " << (unsigned long int) p << " in res (using GetBit, SetBit and operator[])" << endl;
cout << "res["<<(unsigned long int) p<<"] was " << res[p];
res.SetBit(p, !res.GetBit(p));
cout << " and now is " << res[p]<<endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
}
cout << endl;
cout << "Computing the longuest common prefix between res and rbv should give " << (res.GetLength() ? (unsigned long int) p : 0) << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "It returns " << (unsigned long int)res.GetLonguestCommonPrefix(rbv);
cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonPrefix(res) << endl;
cout << endl;
cout << "Build suffix of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
res = rbv(rbv.GetLength() - rbv.GetLength()/3 - 1, rbv.GetLength()/3);
cout << "rbv='" << rbv << "'" << endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
if (res.GetLength()) {
p = rand() % res.GetLength();
cout << "Spin bit at position " << (unsigned long int) p << " in res (using GetBit, SetBit and operator[])" << endl;
cout << "res["<<(unsigned long int) p<<"] was " << res[p];
res.SetBit(p, !res.GetBit(p));
cout << " and now is " << res[p]<<endl;
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
}
cout << endl;
cout << "Computing the longuest common suffix between res and rbv" << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "It returns " << (unsigned long int)res.GetLonguestCommonSuffix(rbv);
cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonSuffix(res) << endl;
cout << endl;
cout << "Build centered factor of rbv of length " << (unsigned long int) rbv.GetLength()/3 << endl;
res = rbv(rbv.GetLength()/3, rbv.GetLength()/3);
cout << "=> '" << res << "' of length " << (unsigned long int) res.GetLength() << endl;
cout << "Compute the longuest common prefix between res and rbv." << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "It returns " << (unsigned long int)res.GetLonguestCommonPrefix(rbv);
cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonPrefix(res) << endl;
cout << "Compute the longuest common suffix between res and rbv." << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "It returns " << (unsigned long int)res.GetLonguestCommonSuffix(rbv);
cout << " which should also be " << (unsigned long int)rbv.GetLonguestCommonSuffix(res) << endl;
cout << "===" << endl;
cout << "Append longuest common prefix between res and rbv to the longuest common suffix between res and rbv." << endl;
cout << "res='" << res << "'" << endl;
cout << "rbv='" << rbv << "'" << endl;
cout << "* res.GetLength() = " << (unsigned long int)res.GetLength() << endl;
cout << "* res.GetLonguestCommonSuffix(rbv) = " << (unsigned long int) res.GetLonguestCommonSuffix(rbv) << endl;
cout << "* res.GetLength() - res.GetLonguestCommonSuffix(rbv) = " << (unsigned long int)(res.GetLength() - res.GetLonguestCommonSuffix(rbv)) << endl;
bv = res(res.GetLength() - res.GetLonguestCommonSuffix(rbv));
res = res(0, res.GetLonguestCommonPrefix(rbv));
cout << "longuest common prefix is '" << res << "'" << endl;
cout << "longuest common suffix is '" << bv << "'" << endl;
res += bv;
cout << "res is ='" << res << "'" << endl;
cout << "===" << endl;
res = rbv;
cout << "Append a 0 to res." << endl;
cout << "res='" << res << "'" << endl;
cout << "now='" << res.Append(0) << "'" << endl;
cout << "Append a 1 to res." << endl;
cout << "res='" << res << "'" << endl;
cout << "now='" << res.Append(1) << "'" << endl;
cout << "Prepend a 0 to res." << endl;
cout << "res='" << res << "'" << endl;
cout << "now='" << res.Prepend(0) << "'" << endl;
cout << "Prepend a 1 to res." << endl;
cout << "res='" << res << "'" << endl;
cout << "now='" << res.Prepend(1) << "'" << endl;
cout << "Split res at position " << (unsigned long int) i/3 << "." << endl;
cout << "res='" << res << "'" << endl;
rbv = res.Split(i/3);
cout << "now='" << res << "'" << endl;
cout << "suf='" << rbv << "'" << endl;
}
}
int main(int argc, char** argv) {
TestLargeBinVectors<unsigned char>((char *)"unsigned char", 128);
TestLargeBinVectors<unsigned int>((char *)"unsigned int", 1000000);
TestLargeBinVectors<long unsigned int>((char *)"long unsigned int", 1000000);
return 0;
}
#endif
#endif
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