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hisat-3n/ds.h
Yaossg 5e601d0401 initial commit
2025-01-18 21:09:52 +08:00

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/*
* Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
*
* This file is part of Bowtie 2.
*
* Bowtie 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Bowtie 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef DS_H_
#define DS_H_
#include <algorithm>
#include <stdexcept>
#include <utility>
#include <stdint.h>
#include <string.h>
#include <limits>
#include "assert_helpers.h"
#include "threading.h"
#include "random_source.h"
#include "btypes.h"
//added by Joe Paggi to implement EList.push_back_array
#include <cstring>
/**
* Tally how much memory is allocated to certain
*/
class MemoryTally {
public:
MemoryTally() : tot_(0), peak_(0) {
memset(tots_, 0, 256 * sizeof(uint64_t));
memset(peaks_, 0, 256 * sizeof(uint64_t));
}
/**
* Tally a memory allocation of size amt bytes.
*/
void add(int cat, uint64_t amt);
/**
* Tally a memory free of size amt bytes.
*/
void del(int cat, uint64_t amt);
/**
* Return the total amount of memory allocated.
*/
uint64_t total() { return tot_; }
/**
* Return the total amount of memory allocated in a particular
* category.
*/
uint64_t total(int cat) { return tots_[cat]; }
/**
* Return the peak amount of memory allocated.
*/
uint64_t peak() { return peak_; }
/**
* Return the peak amount of memory allocated in a particular
* category.
*/
uint64_t peak(int cat) { return peaks_[cat]; }
#ifndef NDEBUG
/**
* Check that memory tallies are internally consistent;
*/
bool repOk() const {
uint64_t tot = 0;
for(int i = 0; i < 256; i++) {
assert_leq(tots_[i], peaks_[i]);
tot += tots_[i];
}
assert_eq(tot, tot_);
return true;
}
#endif
protected:
MUTEX_T mutex_m;
uint64_t tots_[256];
uint64_t tot_;
uint64_t peaks_[256];
uint64_t peak_;
};
extern MemoryTally gMemTally;
/**
* A simple fixed-length array of type T, automatically freed in the
* destructor.
*/
template<typename T>
class AutoArray {
public:
AutoArray(size_t sz, int cat = 0) : cat_(cat) {
t_ = NULL;
t_ = new T[sz];
gMemTally.add(cat_, sz);
memset(t_, 0, sz * sizeof(T));
sz_ = sz;
}
~AutoArray() {
if(t_ != NULL) {
delete[] t_;
gMemTally.del(cat_, sz_);
}
}
T& operator[](size_t sz) {
return t_[sz];
}
const T& operator[](size_t sz) const {
return t_[sz];
}
size_t size() const { return sz_; }
private:
int cat_;
T *t_;
size_t sz_;
};
/**
* A wrapper for a non-array pointer that associates it with a memory
* category for tracking purposes and calls delete on it when the
* PtrWrap is destroyed.
*/
template<typename T>
class PtrWrap {
public:
explicit PtrWrap(
T* p,
bool freeable = true,
int cat = 0) :
cat_(cat),
p_(NULL)
{
init(p, freeable);
}
explicit PtrWrap(int cat = 0) :
cat_(cat),
p_(NULL)
{
reset();
}
void reset() {
free();
init(NULL);
}
~PtrWrap() { free(); }
void init(T* p, bool freeable = true) {
assert(p_ == NULL);
p_ = p;
freeable_ = freeable;
if(p != NULL && freeable_) {
gMemTally.add(cat_, sizeof(T));
}
}
void free() {
if(p_ != NULL) {
if(freeable_) {
delete p_;
gMemTally.del(cat_, sizeof(T));
}
p_ = NULL;
}
}
inline T* get() { return p_; }
inline const T* get() const { return p_; }
private:
int cat_;
T *p_;
bool freeable_;
};
/**
* A wrapper for an array pointer that associates it with a memory
* category for tracking purposes and calls delete[] on it when the
* PtrWrap is destroyed.
*/
template<typename T>
class APtrWrap {
public:
explicit APtrWrap(
T* p,
size_t sz,
bool freeable = true,
int cat = 0) :
cat_(cat),
p_(NULL)
{
init(p, sz, freeable);
}
explicit APtrWrap(int cat = 0) :
cat_(cat),
p_(NULL)
{
reset();
}
void reset() {
free();
init(NULL, 0);
}
~APtrWrap() { free(); }
void init(T* p, size_t sz, bool freeable = true) {
assert(p_ == NULL);
p_ = p;
sz_ = sz;
freeable_ = freeable;
if(p != NULL && freeable_) {
gMemTally.add(cat_, sizeof(T) * sz_);
}
}
void free() {
if(p_ != NULL) {
if(freeable_) {
delete[] p_;
gMemTally.del(cat_, sizeof(T) * sz_);
}
p_ = NULL;
}
}
inline T* get() { return p_; }
inline const T* get() const { return p_; }
private:
int cat_;
T *p_;
bool freeable_;
size_t sz_;
};
/**
* An EList<T> is an expandable list with these features:
*
* - Payload type is a template parameter T.
* - Initial size can be specified at construction time, otherwise
* default of 128 is used.
* - When allocated initially or when expanding, the new[] operator is
* used, which in turn calls the default constructor for T.
* - All copies (e.g. assignment of a const T& to an EList<T> element,
* or during expansion) use operator=.
* - When the EList<T> is resized to a smaller size (or cleared, which
* is like resizing to size 0), the underlying containing is not
* reshaped. Thus, ELists<T>s never release memory before
* destruction.
*
* And these requirements:
*
* - Payload type T must have a default constructor.
*
* For efficiency reasons, ELists should not be declared on the stack
* in often-called worker functions. Best practice is to declare
* ELists at a relatively stable layer of the stack (such that it
* rarely bounces in and out of scope) and let the worker function use
* it and *expand* it only as needed. The effect is that only
* relatively few allocations and copies will be incurred, and they'll
* occur toward the beginning of the computation before stabilizing at
* a "high water mark" for the remainder of the computation.
*
* A word about multidimensional lists. One way to achieve a
* multidimensional lists is to nest ELists. This works, but it often
* involves a lot more calls to the default constructor and to
* operator=, especially when the outermost EList needs expanding, than
* some of the alternatives. One alternative is use a most specialized
* container that still uses ELists but knows to use xfer instead of
* operator= when T=EList.
*
* The 'cat_' fiends encodes a category. This makes it possible to
* distinguish between object subgroups in the global memory tally.
*
* Memory allocation is lazy. Allocation is only triggered when the
* user calls push_back, expand, resize, or another function that
* increases the size of the list. This saves memory and also makes it
* easier to deal with nested ELists, since the default constructor
* doesn't set anything in stone.
*/
template <typename T, int S = 128>
class EList {
public:
/**
* Allocate initial default of S elements.
*/
explicit EList() :
cat_(0), allocCat_(-1), list_(NULL), sz_(S), cur_(0) { }
/**
* Allocate initial default of S elements.
*/
explicit EList(int cat) :
cat_(cat), allocCat_(-1), list_(NULL), sz_(S), cur_(0)
{
assert_geq(cat, 0);
}
/**
* Initially allocate given number of elements; should be > 0.
*/
explicit EList(size_t isz, int cat = 0) :
cat_(cat), allocCat_(-1), list_(NULL), sz_(isz), cur_(0)
{
assert_geq(cat, 0);
}
/**
* Copy from another EList using operator=.
*/
EList(const EList<T, S>& o) :
cat_(0), allocCat_(-1), list_(NULL), sz_(0), cur_(0)
{
*this = o;
}
/**
* Copy from another EList using operator=.
*/
explicit EList(const EList<T, S>& o, int cat) :
cat_(cat), allocCat_(-1), list_(NULL), sz_(0), cur_(0)
{
*this = o;
assert_geq(cat, 0);
}
/**
* Destructor.
*/
~EList() { free(); }
/**
* Make this object into a copy of o by allocat
*/
EList<T, S>& operator=(const EList<T, S>& o) {
assert_eq(cat_, o.cat());
if(o.cur_ == 0) {
// Nothing to copy
cur_ = 0;
return *this;
}
if(list_ == NULL) {
// cat_ should already be set
lazyInit();
}
if(sz_ < o.cur_) expandNoCopy(o.cur_ + 1);
assert_geq(sz_, o.cur_);
cur_ = o.cur_;
for(size_t i = 0; i < cur_; i++) {
list_[i] = o.list_[i];
}
return *this;
}
/**
* Transfer the guts of another EList into this one without using
* operator=, etc. We have to set EList o's list_ field to NULL to
* avoid o's destructor from deleting list_ out from under us.
*/
void xfer(EList<T, S>& o) {
// What does it mean to transfer to a different-category list?
assert_eq(cat_, o.cat());
// Can only transfer into an empty object
free();
allocCat_ = cat_;
list_ = o.list_;
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = NULL;
o.sz_ = o.cur_ = 0;
o.allocCat_ = -1;
}
//Added by Joe
void swap(EList<T, S>& o) {
assert_eq(cat_, o.cat());
T* temp_l = list_;
size_t temp_sz = sz_;
size_t temp_cur = cur_;
list_ = o.list_;
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = temp_l;
o.sz_ = temp_sz;
o.cur_ = temp_cur;
}
/**
* Return number of elements.
*/
inline size_t size() const { return cur_; }
/**
* Return number of elements allocated.
*/
inline size_t capacity() const { return sz_; }
/**
* Return the total size in bytes occupied by this list.
*/
size_t totalSizeBytes() const {
return 2 * sizeof(int) +
2 * sizeof(size_t) +
cur_ * sizeof(T);
}
/**
* Return the total capacity in bytes occupied by this list.
*/
size_t totalCapacityBytes() const {
return 2 * sizeof(int) +
2 * sizeof(size_t) +
sz_ * sizeof(T);
}
/**
* Ensure that there is sufficient capacity to expand to include
* 'thresh' more elements without having to expand.
*/
inline void ensure(size_t thresh) {
if(list_ == NULL) lazyInit();
expandCopy(cur_ + thresh);
}
/**
* Ensure that there is sufficient capacity to include 'newsz' elements.
* If there isn't enough capacity right now, expand capacity to exactly
* equal 'newsz'.
*/
inline void reserveExact(size_t newsz) {
if(list_ == NULL) lazyInitExact(newsz);
expandCopyExact(newsz);
}
/**
* Return true iff there are no elements.
*/
inline bool empty() const { return cur_ == 0; }
/**
* Return true iff list hasn't been initialized yet.
*/
inline bool null() const { return list_ == NULL; }
/**
* Add an element to the back and immediately initialize it via
* operator=.
*/
void push_back(const T& el) {
if(list_ == NULL) lazyInit();
if(cur_ == sz_) expandCopy(sz_+1);
list_[cur_++] = el;
}
void nullify() {
free();
}
/**
* Add an element to the back. No intialization is done.
*/
void expand() {
if(list_ == NULL) lazyInit();
if(cur_ == sz_) expandCopy(sz_+1);
cur_++;
}
/**
* Add an element to the back. No intialization is done.
*/
void fill(size_t begin, size_t end, const T& v) {
assert_leq(begin, end);
assert_leq(end, cur_);
for(size_t i = begin; i < end; i++) {
list_[i] = v;
}
}
/**
* Add an element to the back. No intialization is done.
*/
void fill(const T& v) {
for(size_t i = 0; i < cur_; i++) {
list_[i] = v;
}
}
/**
* Set all bits in specified range of elements in list array to 0.
*/
void fillZero(size_t begin, size_t end) {
assert_leq(begin, end);
memset(&list_[begin], 0, sizeof(T) * (end-begin));
}
/**
* Set all bits in the list array to 0.
*/
void fillZero() {
memset(list_, 0, sizeof(T) * cur_);
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resizeNoCopy(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) expandNoCopy(sz);
cur_ = sz;
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resizeNoCopyExact(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) expandNoCopyExact(sz);
cur_ = sz;
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) {
expandCopy(sz);
}
cur_ = sz;
}
/**
* If size is less than requested size, resize up to exactly sz and set
* cur_ to requested sz.
*/
void resizeExact(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInitExact(sz);
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) expandCopyExact(sz);
cur_ = sz;
}
/**
* Erase element at offset idx.
*/
void erase(size_t idx) {
assert_lt(idx, cur_);
for(size_t i = idx; i < cur_-1; i++) {
list_[i] = list_[i+1];
}
cur_--;
}
/**
* Erase range of elements starting at offset idx and going for len.
*/
void erase(size_t idx, size_t len) {
assert_geq(len, 0);
if(len == 0) {
return;
}
assert_lt(idx, cur_);
for(size_t i = idx; i < cur_-len; i++) {
list_[i] = list_[i+len];
}
cur_ -= len;
}
/**
* Insert value 'el' at offset 'idx'
*/
void insert(const T& el, size_t idx) {
if(list_ == NULL) lazyInit();
assert_leq(idx, cur_);
if(cur_ == sz_) expandCopy(sz_+1);
for(size_t i = cur_; i > idx; i--) {
list_[i] = list_[i-1];
}
list_[idx] = el;
cur_++;
}
/**
* Insert contents of list 'l' at offset 'idx'
*/
void insert(const EList<T>& l, size_t idx) {
if(list_ == NULL) lazyInit();
assert_lt(idx, cur_);
if(l.cur_ == 0) return;
if(cur_ + l.cur_ > sz_) expandCopy(cur_ + l.cur_);
for(size_t i = cur_ + l.cur_ - 1; i > idx + (l.cur_ - 1); i--) {
list_[i] = list_[i - l.cur_];
}
for(size_t i = 0; i < l.cur_; i++) {
list_[i+idx] = l.list_[i];
}
cur_ += l.cur_;
}
/**
* push first l_size objects of T array l to top of stack
* added by Joe Paggi
*/
void push_back_array(const T* l, size_t l_size) {
if(list_ == NULL) lazyInit();
if(l_size == 0) return;
if(cur_ + l_size > sz_) expandCopy(cur_ + l_size);
size_t bytes = l_size * sizeof(T);
std::memcpy(list_ + cur_, l, bytes);
cur_ += l_size;
}
/**
* Remove an element from the top of the stack.
*/
void pop_back() {
assert_gt(cur_, 0);
cur_--;
}
/**
* Make the stack empty.
*/
void clear() {
cur_ = 0; // re-use stack memory
// Don't clear heap; re-use it
}
/**
* Get the element on the top of the stack.
*/
inline T& back() {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Reverse list elements.
*/
void reverse() {
if(cur_ > 1) {
size_t n = cur_ >> 1;
for(size_t i = 0; i < n; i++) {
T tmp = list_[i];
list_[i] = list_[cur_ - i - 1];
list_[cur_ - i - 1] = tmp;
}
}
}
/**
* Get the element on the top of the stack, const version.
*/
inline const T& back() const {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the frontmost element (bottom of stack).
*/
inline T& front() {
assert_gt(cur_, 0);
return list_[0];
}
/**
* Get the element on the bottom of the stack, const version.
*/
inline const T& front() const { return front(); }
inline T* begin() {
assert_gt(cur_, 0);
return &list_[0];
}
inline const T* begin() const { return begin(); }
inline T* end() { return begin() + cur_; }
inline const T* end() const { return begin() + cur_; }
/**
* Return true iff this list and list o contain the same elements in the
* same order according to type T's operator==.
*/
bool operator==(const EList<T, S>& o) const {
if(size() != o.size()) {
return false;
}
for(size_t i = 0; i < size(); i++) {
if(!(get(i) == o.get(i))) {
return false;
}
}
return true;
}
/**
* Return true iff this list contains all of the elements in o according to
* type T's operator==.
*/
bool isSuperset(const EList<T, S>& o) const {
if(o.size() > size()) {
// This can't be a superset if the other set contains more elts
return false;
}
// For each element in o
for(size_t i = 0; i < o.size(); i++) {
bool inthis = false;
// Check if it's in this
for(size_t j = 0; j < size(); j++) {
if(o[i] == (*this)[j]) {
inthis = true;
break;
}
}
if(!inthis) {
return false;
}
}
return true;
}
/**
* Return a reference to the ith element.
*/
inline T& operator[](size_t i) {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline const T& operator[](size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline T& get(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element.
*/
inline const T& get(size_t i) const {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
T& getSlow(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
const T& getSlow(size_t i) const {
return operator[](i);
}
/**
* Sort some of the contents.
*/
void sortPortion(size_t begin, size_t num) {
assert_leq(begin+num, cur_);
if(num < 2) return;
std::sort(list_ + begin, list_ + begin + num);
}
/**
* Shuffle a portion of the list.
*/
void shufflePortion(size_t begin, size_t num, RandomSource& rnd) {
assert_leq(begin+num, cur_);
if(num < 2) return;
size_t left = num;
for(size_t i = begin; i < begin + num - 1; i++) {
uint32_t rndi = rnd.nextU32() % left;
if(rndi > 0) {
std::swap(list_[i], list_[i + rndi]);
}
left--;
}
}
/**
* Sort contents
*/
void sort() {
sortPortion(0, cur_);
}
/**
* Return true iff every element is < its successor. Only operator< is
* used.
*/
bool sorted() const {
for(size_t i = 1; i < cur_; i++) {
if(!(list_[i-1] < list_[i])) {
return false;
}
}
return true;
}
/**
* Delete element at position 'idx'; slide subsequent chars up.
*/
void remove(size_t idx) {
assert_lt(idx, cur_);
assert_gt(cur_, 0);
for(size_t i = idx; i < cur_-1; i++) {
list_[i] = list_[i+1];
}
cur_--;
}
/**
* Return a pointer to the beginning of the buffer.
*/
T *ptr() { return list_; }
/**
* Return a const pointer to the beginning of the buffer.
*/
const T *ptr() const { return list_; }
/**
* Set the memory category for this object.
*/
void setCat(int cat) {
// What does it mean to set the category after the list_ is
// already allocated?
assert(null());
assert_gt(cat, 0); cat_ = cat;
}
/**
* Return memory category.
*/
int cat() const { return cat_; }
/**
* Perform a binary search for the first element that is not less
* than 'el'. Return cur_ if all elements are less than el.
*/
size_t bsearchLoBound(const T& el) const {
size_t hi = cur_;
size_t lo = 0;
while(true) {
if(lo == hi) {
return lo;
}
size_t mid = lo + ((hi-lo)>>1);
assert_neq(mid, hi);
if(list_[mid] < el) {
if(lo == mid) {
return hi;
}
lo = mid;
} else {
hi = mid;
}
}
}
private:
/**
* Initialize memory for EList.
*/
void lazyInit() {
assert(list_ == NULL);
list_ = alloc(sz_);
}
/**
* Initialize exactly the prescribed number of elements for EList.
*/
void lazyInitExact(size_t sz) {
assert_gt(sz, 0);
assert(list_ == NULL);
sz_ = sz;
list_ = alloc(sz);
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
T *alloc(size_t sz) {
T* tmp = new T[sz];
assert(tmp != NULL);
gMemTally.add(cat_, sz);
allocCat_ = cat_;
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
assert_neq(-1, allocCat_);
assert_eq(allocCat_, cat_);
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
sz_ = cur_ = 0;
}
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements. Size
* increases quadratically with number of expansions. Copy old contents
* into new buffer using operator=.
*/
void expandCopy(size_t thresh) {
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
expandCopyExact(newsz);
}
/**
* Expand the list_ buffer until it has exactly 'newsz' elements. Copy
* old contents into new buffer using operator=.
*/
void expandCopyExact(size_t newsz) {
if(newsz <= sz_) return;
T* tmp = alloc(newsz);
assert(tmp != NULL);
size_t cur = cur_;
if(list_ != NULL) {
for(size_t i = 0; i < cur_; i++) {
// Note: operator= is used
tmp[i] = list_[i];
}
free();
}
list_ = tmp;
sz_ = newsz;
cur_ = cur;
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Size increases quadratically with number of expansions. Don't copy old
* contents into the new buffer.
*/
void expandNoCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
expandNoCopyExact(newsz);
}
/**
* Expand the list_ buffer until it has exactly 'newsz' elements. Don't
* copy old contents into the new buffer.
*/
void expandNoCopyExact(size_t newsz) {
assert(list_ != NULL);
assert_gt(newsz, 0);
free();
T* tmp = alloc(newsz);
assert(tmp != NULL);
list_ = tmp;
sz_ = newsz;
assert_gt(sz_, 0);
}
int cat_; // memory category, for accounting purposes
int allocCat_; // category at time of allocation
T *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
/**
* An ELList<T> is an expandable list of lists with these features:
*
* - Payload type of the inner list is a template parameter T.
* - Initial size can be specified at construction time, otherwise
* default of 128 is used.
* - When allocated initially or when expanding, the new[] operator is
* used, which in turn calls the default constructor for EList<T>.
* - Upon expansion, instead of copies, xfer is used.
* - When the ELList<T> is resized to a smaller size (or cleared,
* which is like resizing to size 0), the underlying containing is
* not reshaped. Thus, ELLists<T>s never release memory before
* destruction.
*
* And these requirements:
*
* - Payload type T must have a default constructor.
*
*/
template <typename T, int S1 = 128, int S2 = 128>
class ELList {
public:
/**
* Allocate initial default of 128 elements.
*/
explicit ELList(int cat = 0) :
cat_(cat), list_(NULL), sz_(S2), cur_(0)
{
assert_geq(cat, 0);
}
/**
* Initially allocate given number of elements; should be > 0.
*/
explicit ELList(size_t isz, int cat = 0) :
cat_(cat), list_(NULL), sz_(isz), cur_(0)
{
assert_gt(isz, 0);
assert_geq(cat, 0);
}
/**
* Copy from another ELList using operator=.
*/
ELList(const ELList<T, S1, S2>& o) :
cat_(0), list_(NULL), sz_(0), cur_(0)
{
*this = o;
}
/**
* Copy from another ELList using operator=.
*/
explicit ELList(const ELList<T, S1, S2>& o, int cat) :
cat_(cat), list_(NULL), sz_(0), cur_(0)
{
*this = o;
assert_geq(cat, 0);
}
/**
* Destructor.
*/
~ELList() { free(); }
/**
* Make this object into a copy of o by allocating enough memory to
* fit the number of elements in o (note: the number of elements
* may be substantially less than the memory allocated in o) and
* using operator= to copy them over.
*/
ELList<T, S1, S2>& operator=(const ELList<T, S1, S2>& o) {
assert_eq(cat_, o.cat());
if(list_ == NULL) {
lazyInit();
}
if(o.cur_ == 0) {
cur_ = 0;
return *this;
}
if(sz_ < o.cur_) expandNoCopy(o.cur_ + 1);
assert_geq(sz_, o.cur_);
cur_ = o.cur_;
for(size_t i = 0; i < cur_; i++) {
// Note: using operator=, not xfer
assert_eq(list_[i].cat(), o.list_[i].cat());
list_[i] = o.list_[i];
}
return *this;
}
/**
* Transfer the guts of another EList into this one without using
* operator=, etc. We have to set EList o's list_ field to NULL to
* avoid o's destructor from deleting list_ out from under us.
*/
void xfer(ELList<T, S1, S2>& o) {
assert_eq(cat_, o.cat());
list_ = o.list_; // list_ is an array of EList<T>s
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = NULL;
o.sz_ = o.cur_ = 0;
}
/**
* Return number of elements.
*/
inline size_t size() const { return cur_; }
/**
* Return true iff there are no elements.
*/
inline bool empty() const { return cur_ == 0; }
/**
* Return true iff list hasn't been initialized yet.
*/
inline bool null() const { return list_ == NULL; }
/**
* Add an element to the back. No intialization is done.
*/
void expand() {
if(list_ == NULL) lazyInit();
if(cur_ == sz_) expandCopy(sz_+1);
cur_++;
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) {
expandCopy(sz);
}
cur_ = sz;
}
/**
* Make the stack empty.
*/
void clear() {
cur_ = 0; // re-use stack memory
// Don't clear heap; re-use it
}
/**
* Get the element on the top of the stack.
*/
inline EList<T, S1>& back() {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the element on the top of the stack, const version.
*/
inline const EList<T, S1>& back() const {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the frontmost element (bottom of stack).
*/
inline EList<T, S1>& front() {
assert_gt(cur_, 0);
return list_[0];
}
/**
* Get the element on the bottom of the stack, const version.
*/
inline const EList<T, S1>& front() const { return front(); }
/**
* Return a reference to the ith element.
*/
inline EList<T, S1>& operator[](size_t i) {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline const EList<T, S1>& operator[](size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline EList<T, S1>& get(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element.
*/
inline const EList<T, S1>& get(size_t i) const {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
EList<T, S1>& getSlow(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
const EList<T, S1>& getSlow(size_t i) const {
return operator[](i);
}
/**
* Return a pointer to the beginning of the buffer.
*/
EList<T, S1> *ptr() { return list_; }
/**
* Set the memory category for this object and all children.
*/
void setCat(int cat) {
assert_gt(cat, 0);
cat_ = cat;
if(cat_ != 0) {
for(size_t i = 0; i < sz_; i++) {
assert(list_[i].null());
list_[i].setCat(cat_);
}
}
}
/**
* Return memory category.
*/
int cat() const { return cat_; }
protected:
/**
* Initialize memory for EList.
*/
void lazyInit() {
assert(list_ == NULL);
list_ = alloc(sz_);
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
EList<T, S1> *alloc(size_t sz) {
assert_gt(sz, 0);
EList<T, S1> *tmp = new EList<T, S1>[sz];
gMemTally.add(cat_, sz);
if(cat_ != 0) {
for(size_t i = 0; i < sz; i++) {
assert(tmp[i].ptr() == NULL);
tmp[i].setCat(cat_);
}
}
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
}
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Copy old contents into new buffer
* using operator=.
*/
void expandCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
EList<T, S1>* tmp = alloc(newsz);
if(list_ != NULL) {
for(size_t i = 0; i < cur_; i++) {
assert_eq(cat_, tmp[i].cat());
tmp[i].xfer(list_[i]);
assert_eq(cat_, tmp[i].cat());
}
free();
}
list_ = tmp;
sz_ = newsz;
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Don't copy old contents over.
*/
void expandNoCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
free();
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
EList<T, S1>* tmp = alloc(newsz);
list_ = tmp;
sz_ = newsz;
assert_gt(sz_, 0);
}
int cat_; // memory category, for accounting purposes
EList<T, S1> *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
/**
* An ELLList<T> is an expandable list of expandable lists with these
* features:
*
* - Payload type of the innermost list is a template parameter T.
* - Initial size can be specified at construction time, otherwise
* default of 128 is used.
* - When allocated initially or when expanding, the new[] operator is
* used, which in turn calls the default constructor for ELList<T>.
* - Upon expansion, instead of copies, xfer is used.
* - When the ELLList<T> is resized to a smaller size (or cleared,
* which is like resizing to size 0), the underlying containing is
* not reshaped. Thus, ELLLists<T>s never release memory before
* destruction.
*
* And these requirements:
*
* - Payload type T must have a default constructor.
*
*/
template <typename T, int S1 = 128, int S2 = 128, int S3 = 128>
class ELLList {
public:
/**
* Allocate initial default of 128 elements.
*/
explicit ELLList(int cat = 0) :
cat_(cat), list_(NULL), sz_(S3), cur_(0)
{
assert_geq(cat, 0);
}
/**
* Initially allocate given number of elements; should be > 0.
*/
explicit ELLList(size_t isz, int cat = 0) :
cat_(cat), list_(NULL), sz_(isz), cur_(0)
{
assert_geq(cat, 0);
assert_gt(isz, 0);
}
/**
* Copy from another ELLList using operator=.
*/
ELLList(const ELLList<T, S1, S2, S3>& o) :
cat_(0), list_(NULL), sz_(0), cur_(0)
{
*this = o;
}
/**
* Copy from another ELLList using operator=.
*/
explicit ELLList(const ELLList<T, S1, S2, S3>& o, int cat) :
cat_(cat), list_(NULL), sz_(0), cur_(0)
{
*this = o;
assert_geq(cat, 0);
}
/**
* Destructor.
*/
~ELLList() { free(); }
/**
* Make this object into a copy of o by allocating enough memory to
* fit the number of elements in o (note: the number of elements
* may be substantially less than the memory allocated in o) and
* using operator= to copy them over.
*/
ELLList<T, S1, S2, S3>& operator=(const ELLList<T, S1, S2, S3>& o) {
assert_eq(cat_, o.cat());
if(list_ == NULL) lazyInit();
if(o.cur_ == 0) {
cur_ = 0;
return *this;
}
if(sz_ < o.cur_) expandNoCopy(o.cur_ + 1);
assert_geq(sz_, o.cur_);
cur_ = o.cur_;
for(size_t i = 0; i < cur_; i++) {
// Note: using operator=, not xfer
assert_eq(list_[i].cat(), o.list_[i].cat());
list_[i] = o.list_[i];
}
return *this;
}
/**
* Transfer the guts of another EList into this one without using
* operator=, etc. We have to set EList o's list_ field to NULL to
* avoid o's destructor from deleting list_ out from under us.
*/
void xfer(ELLList<T, S1, S2, S3>& o) {
assert_eq(cat_, o.cat());
list_ = o.list_; // list_ is an array of EList<T>s
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = NULL;
o.sz_ = o.cur_ = 0;
}
/**
* Return number of elements.
*/
inline size_t size() const { return cur_; }
/**
* Return true iff there are no elements.
*/
inline bool empty() const { return cur_ == 0; }
/**
* Return true iff list hasn't been initialized yet.
*/
inline bool null() const { return list_ == NULL; }
/**
* Add an element to the back. No intialization is done.
*/
void expand() {
if(list_ == NULL) lazyInit();
if(cur_ == sz_) expandCopy(sz_+1);
cur_++;
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) expandCopy(sz);
cur_ = sz;
}
/**
* Make the stack empty.
*/
void clear() {
cur_ = 0; // re-use stack memory
// Don't clear heap; re-use it
}
/**
* Get the element on the top of the stack.
*/
inline ELList<T, S1, S2>& back() {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the element on the top of the stack, const version.
*/
inline const ELList<T, S1, S2>& back() const {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the frontmost element (bottom of stack).
*/
inline ELList<T, S1, S2>& front() {
assert_gt(cur_, 0);
return list_[0];
}
/**
* Get the element on the bottom of the stack, const version.
*/
inline const ELList<T, S1, S2>& front() const { return front(); }
/**
* Return a reference to the ith element.
*/
inline ELList<T, S1, S2>& operator[](size_t i) {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline const ELList<T, S1, S2>& operator[](size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline ELList<T, S1, S2>& get(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element.
*/
inline const ELList<T, S1, S2>& get(size_t i) const {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
ELList<T, S1, S2>& getSlow(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
const ELList<T, S1, S2>& getSlow(size_t i) const {
return operator[](i);
}
/**
* Return a pointer to the beginning of the buffer.
*/
ELList<T, S1, S2> *ptr() { return list_; }
/**
* Set the memory category for this object and all children.
*/
void setCat(int cat) {
assert_gt(cat, 0);
cat_ = cat;
if(cat_ != 0) {
for(size_t i = 0; i < sz_; i++) {
assert(list_[i].null());
list_[i].setCat(cat_);
}
}
}
/**
* Return memory category.
*/
int cat() const { return cat_; }
protected:
/**
* Initialize memory for EList.
*/
void lazyInit() {
assert(null());
list_ = alloc(sz_);
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
ELList<T, S1, S2> *alloc(size_t sz) {
assert_gt(sz, 0);
ELList<T, S1, S2> *tmp = new ELList<T, S1, S2>[sz];
gMemTally.add(cat_, sz);
if(cat_ != 0) {
for(size_t i = 0; i < sz; i++) {
assert(tmp[i].ptr() == NULL);
tmp[i].setCat(cat_);
}
}
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
}
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Copy old contents into new buffer
* using operator=.
*/
void expandCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
ELList<T, S1, S2>* tmp = alloc(newsz);
if(list_ != NULL) {
for(size_t i = 0; i < cur_; i++) {
assert_eq(cat_, tmp[i].cat());
tmp[i].xfer(list_[i]);
assert_eq(cat_, tmp[i].cat());
}
free();
}
list_ = tmp;
sz_ = newsz;
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Don't copy old contents over.
*/
void expandNoCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
free();
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
ELList<T, S1, S2>* tmp = alloc(newsz);
list_ = tmp;
sz_ = newsz;
assert_gt(sz_, 0);
}
int cat_; // memory category, for accounting purposes
ELList<T, S1, S2> *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
/**
* Expandable set using a heap-allocated sorted array.
*
* Note that the copy constructor and operator= routines perform
* shallow copies (w/ memcpy).
*/
template <typename T>
class ESet {
public:
/**
* Allocate initial default of 128 elements.
*/
ESet(int cat = 0) :
cat_(cat),
list_(NULL),
sz_(0),
cur_(0)
{
if(sz_ > 0) {
list_ = alloc(sz_);
}
}
/**
* Initially allocate given number of elements; should be > 0.
*/
ESet(size_t isz, int cat = 0) :
cat_(cat),
list_(NULL),
sz_(isz),
cur_(0)
{
assert_gt(isz, 0);
if(sz_ > 0) {
list_ = alloc(sz_);
}
}
/**
* Copy from another ESet.
*/
ESet(const ESet<T>& o, int cat = 0) :
cat_(cat), list_(NULL)
{
assert_eq(cat_, o.cat());
*this = o;
}
/**
* Destructor.
*/
~ESet() { free(); }
/**
* Copy contents of given ESet into this ESet.
*/
ESet& operator=(const ESet<T>& o) {
assert_eq(cat_, o.cat());
sz_ = o.sz_;
cur_ = o.cur_;
free();
if(sz_ > 0) {
list_ = alloc(sz_);
memcpy(list_, o.list_, cur_ * sizeof(T));
} else {
list_ = NULL;
}
return *this;
}
/**
* Return number of elements.
*/
size_t size() const { return cur_; }
/**
* Return the total size in bytes occupied by this set.
*/
size_t totalSizeBytes() const {
return sizeof(int) + cur_ * sizeof(T) + 2 * sizeof(size_t);
}
/**
* Return the total capacity in bytes occupied by this set.
*/
size_t totalCapacityBytes() const {
return sizeof(int) + sz_ * sizeof(T) + 2 * sizeof(size_t);
}
/**
* Return true iff there are no elements.
*/
bool empty() const { return cur_ == 0; }
/**
* Return true iff list isn't initialized yet.
*/
bool null() const { return list_ == NULL; }
/**
* Insert a new element into the set in sorted order.
*/
bool insert(const T& el) {
size_t i = 0;
if(cur_ == 0) {
insert(el, 0);
return true;
}
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
if(i < cur_ && list_[i] == el) return false;
insert(el, i);
return true;
}
/**
* Return true iff this set contains 'el'.
*/
bool contains(const T& el) const {
if(cur_ == 0) {
return false;
}
else if(cur_ == 1) {
return el == list_[0];
}
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
return i != cur_ && list_[i] == el;
}
/**
* Remove element from set.
*/
void remove(const T& el) {
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
assert(i != cur_ && list_[i] == el);
erase(i);
}
/**
* Get
*/
T& get(const T& el) {
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
assert(i != cur_ && list_[i] == el);
return list_[i];
}
const T& get(const T& el) const {
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
assert(i != cur_ && list_[i] == el);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline T& operator[](size_t i) {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline const T& operator[](size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz <= cur_) return;
if(sz_ < sz) expandCopy(sz);
}
/**
* Clear set without deallocating (or setting) anything.
*/
void clear() { cur_ = 0; }
/**
* Return memory category.
*/
int cat() const { return cat_; }
/**
* Set the memory category for this object.
*/
void setCat(int cat) {
cat_ = cat;
}
/**
* Transfer the guts of another EList into this one without using
* operator=, etc. We have to set EList o's list_ field to NULL to
* avoid o's destructor from deleting list_ out from under us.
*/
void xfer(ESet<T>& o) {
// What does it mean to transfer to a different-category list?
assert_eq(cat_, o.cat());
// Can only transfer into an empty object
free();
list_ = o.list_;
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = NULL;
o.sz_ = o.cur_ = 0;
}
/**
* Return a pointer to the beginning of the buffer.
*/
T *ptr() { return list_; }
/**
* Return a const pointer to the beginning of the buffer.
*/
const T *ptr() const { return list_; }
private:
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
T *alloc(size_t sz) {
assert_gt(sz, 0);
T *tmp = new T[sz];
gMemTally.add(cat_, sz);
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
}
}
/**
* Simple linear scan that returns the index of the first element
* of list_ that is not less than el, or cur_ if all elements are
* less than el.
*/
size_t scanLoBound(const T& el) const {
for(size_t i = 0; i < cur_; i++) {
if(!(list_[i] < el)) {
// Shouldn't be equal
return i;
}
}
return cur_;
}
/**
* Perform a binary search for the first element that is not less
* than 'el'. Return cur_ if all elements are less than el.
*/
size_t bsearchLoBound(const T& el) const {
size_t hi = cur_;
size_t lo = 0;
while(true) {
if(lo == hi) {
#ifndef NDEBUG
if((rand() % 10) == 0) {
assert_eq(lo, scanLoBound(el));
}
#endif
return lo;
}
size_t mid = lo + ((hi-lo)>>1);
assert_neq(mid, hi);
if(list_[mid] < el) {
if(lo == mid) {
#ifndef NDEBUG
if((rand() % 10) == 0) {
assert_eq(hi, scanLoBound(el));
}
#endif
return hi;
}
lo = mid;
} else {
hi = mid;
}
}
}
/**
* Return true if sorted, assert otherwise.
*/
bool sorted() const {
if(cur_ <= 1) return true;
#ifndef NDEBUG
if((rand() % 20) == 0) {
for(size_t i = 0; i < cur_-1; i++) {
assert(list_[i] < list_[i+1]);
}
}
#endif
return true;
}
/**
* Insert value 'el' at offset 'idx'. It's OK to insert at cur_,
* which is equivalent to appending.
*/
void insert(const T& el, size_t idx) {
assert_leq(idx, cur_);
if(cur_ == sz_) {
expandCopy(sz_+1);
assert(sorted());
}
for(size_t i = cur_; i > idx; i--) {
list_[i] = list_[i-1];
}
list_[idx] = el;
cur_++;
assert(sorted());
}
/**
* Erase element at offset idx.
*/
void erase(size_t idx) {
assert_lt(idx, cur_);
for(size_t i = idx; i < cur_-1; i++) {
list_[i] = list_[i+1];
}
cur_--;
assert(sorted());
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic.
*/
void expandCopy(size_t thresh) {
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) {
newsz *= 2;
}
T* tmp = alloc(newsz);
for(size_t i = 0; i < cur_; i++) {
tmp[i] = list_[i];
}
free();
list_ = tmp;
sz_ = newsz;
}
int cat_; // memory category, for accounting purposes
T *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
template <typename T, int S = 128>
class ELSet {
public:
/**
* Allocate initial default of 128 elements.
*/
explicit ELSet(int cat = 0) :
cat_(cat), list_(NULL), sz_(S), cur_(0)
{
assert_geq(cat, 0);
}
/**
* Initially allocate given number of elements; should be > 0.
*/
explicit ELSet(size_t isz, int cat = 0) :
cat_(cat), list_(NULL), sz_(isz), cur_(0)
{
assert_gt(isz, 0);
assert_geq(cat, 0);
}
/**
* Copy from another ELList using operator=.
*/
ELSet(const ELSet<T, S>& o) :
cat_(0), list_(NULL), sz_(0), cur_(0)
{
*this = o;
}
/**
* Copy from another ELList using operator=.
*/
explicit ELSet(const ELSet<T, S>& o, int cat) :
cat_(cat), list_(NULL), sz_(0), cur_(0)
{
*this = o;
assert_geq(cat, 0);
}
/**
* Destructor.
*/
~ELSet() { free(); }
/**
* Make this object into a copy of o by allocating enough memory to
* fit the number of elements in o (note: the number of elements
* may be substantially less than the memory allocated in o) and
* using operator= to copy them over.
*/
ELSet<T, S>& operator=(const ELSet<T, S>& o) {
assert_eq(cat_, o.cat());
if(list_ == NULL) {
lazyInit();
}
if(o.cur_ == 0) {
cur_ = 0;
return *this;
}
if(sz_ < o.cur_) expandNoCopy(o.cur_ + 1);
assert_geq(sz_, o.cur_);
cur_ = o.cur_;
for(size_t i = 0; i < cur_; i++) {
// Note: using operator=, not xfer
assert_eq(list_[i].cat(), o.list_[i].cat());
list_[i] = o.list_[i];
}
return *this;
}
/**
* Transfer the guts of another ESet into this one without using
* operator=, etc. We have to set ESet o's list_ field to NULL to
* avoid o's destructor from deleting list_ out from under us.
*/
void xfer(ELSet<T, S>& o) {
assert_eq(cat_, o.cat());
list_ = o.list_; // list_ is an array of ESet<T>s
sz_ = o.sz_;
cur_ = o.cur_;
o.list_ = NULL;
o.sz_ = o.cur_ = 0;
}
/**
* Return number of elements.
*/
inline size_t size() const { return cur_; }
/**
* Return true iff there are no elements.
*/
inline bool empty() const { return cur_ == 0; }
/**
* Return true iff list hasn't been initialized yet.
*/
inline bool null() const { return list_ == NULL; }
/**
* Add an element to the back. No intialization is done.
*/
void expand() {
if(list_ == NULL) lazyInit();
if(cur_ == sz_) expandCopy(sz_+1);
cur_++;
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz > 0 && list_ == NULL) lazyInit();
if(sz <= cur_) {
cur_ = sz;
return;
}
if(sz_ < sz) {
expandCopy(sz);
}
cur_ = sz;
}
/**
* Make the stack empty.
*/
void clear() {
cur_ = 0; // re-use stack memory
// Don't clear heap; re-use it
}
/**
* Get the element on the top of the stack.
*/
inline ESet<T>& back() {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the element on the top of the stack, const version.
*/
inline const ESet<T>& back() const {
assert_gt(cur_, 0);
return list_[cur_-1];
}
/**
* Get the frontmost element (bottom of stack).
*/
inline ESet<T>& front() {
assert_gt(cur_, 0);
return list_[0];
}
/**
* Get the element on the bottom of the stack, const version.
*/
inline const ESet<T>& front() const { return front(); }
/**
* Return a reference to the ith element.
*/
inline ESet<T>& operator[](size_t i) {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline const ESet<T>& operator[](size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* Return a reference to the ith element.
*/
inline ESet<T>& get(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element.
*/
inline const ESet<T>& get(size_t i) const {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
ESet<T>& getSlow(size_t i) {
return operator[](i);
}
/**
* Return a reference to the ith element. This version is not
* inlined, which guarantees we can use it from the debugger.
*/
const ESet<T>& getSlow(size_t i) const {
return operator[](i);
}
/**
* Return a pointer to the beginning of the buffer.
*/
ESet<T> *ptr() { return list_; }
/**
* Return a const pointer to the beginning of the buffer.
*/
const ESet<T> *ptr() const { return list_; }
/**
* Set the memory category for this object and all children.
*/
void setCat(int cat) {
assert_gt(cat, 0);
cat_ = cat;
if(cat_ != 0) {
for(size_t i = 0; i < sz_; i++) {
assert(list_[i].null());
list_[i].setCat(cat_);
}
}
}
/**
* Return memory category.
*/
int cat() const { return cat_; }
protected:
/**
* Initialize memory for ELSet.
*/
void lazyInit() {
assert(list_ == NULL);
list_ = alloc(sz_);
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
ESet<T> *alloc(size_t sz) {
assert_gt(sz, 0);
ESet<T> *tmp = new ESet<T>[sz];
gMemTally.add(cat_, sz);
if(cat_ != 0) {
for(size_t i = 0; i < sz; i++) {
assert(tmp[i].ptr() == NULL);
tmp[i].setCat(cat_);
}
}
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
}
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Copy old contents into new buffer
* using operator=.
*/
void expandCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
ESet<T>* tmp = alloc(newsz);
if(list_ != NULL) {
for(size_t i = 0; i < cur_; i++) {
assert_eq(cat_, tmp[i].cat());
tmp[i].xfer(list_[i]);
assert_eq(cat_, tmp[i].cat());
}
free();
}
list_ = tmp;
sz_ = newsz;
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic. Don't copy old contents over.
*/
void expandNoCopy(size_t thresh) {
assert(list_ != NULL);
if(thresh <= sz_) return;
free();
size_t newsz = (sz_ * 2)+1;
while(newsz < thresh) newsz *= 2;
ESet<T>* tmp = alloc(newsz);
list_ = tmp;
sz_ = newsz;
assert_gt(sz_, 0);
}
int cat_; // memory category, for accounting purposes
ESet<T> *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
/**
* Expandable map using a heap-allocated sorted array.
*
* Note that the copy constructor and operator= routines perform
* shallow copies (w/ memcpy).
*/
template <typename K, typename V>
class EMap {
public:
/**
* Allocate initial default of 128 elements.
*/
EMap(int cat = 0) :
cat_(cat),
list_(NULL),
sz_(128),
cur_(0)
{
list_ = alloc(sz_);
}
/**
* Initially allocate given number of elements; should be > 0.
*/
EMap(size_t isz, int cat = 0) :
cat_(cat),
list_(NULL),
sz_(isz),
cur_(0)
{
assert_gt(isz, 0);
list_ = alloc(sz_);
}
/**
* Copy from another ESet.
*/
EMap(const EMap<K, V>& o) : list_(NULL) {
*this = o;
}
/**
* Destructor.
*/
~EMap() { free(); }
/**
* Copy contents of given ESet into this ESet.
*/
EMap& operator=(const EMap<K, V>& o) {
sz_ = o.sz_;
cur_ = o.cur_;
free();
list_ = alloc(sz_);
memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
return *this;
}
/**
* Return number of elements.
*/
size_t size() const { return cur_; }
/**
* Return the total size in bytes occupied by this map.
*/
size_t totalSizeBytes() const {
return sizeof(int) +
2 * sizeof(size_t) +
cur_ * sizeof(std::pair<K, V>);
}
/**
* Return the total capacity in bytes occupied by this map.
*/
size_t totalCapacityBytes() const {
return sizeof(int) +
2 * sizeof(size_t) +
sz_ * sizeof(std::pair<K, V>);
}
/**
* Return true iff there are no elements.
*/
bool empty() const { return cur_ == 0; }
/**
* Insert a new element into the set in sorted order.
*/
bool insert(const std::pair<K, V>& el) {
size_t i = 0;
if(cur_ == 0) {
insert(el, 0);
return true;
}
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el.first);
} else {
// Binary search
i = bsearchLoBound(el.first);
}
if(list_[i] == el) return false; // already there
insert(el, i);
return true; // not already there
}
/**
* Return true iff this set contains 'el'.
*/
bool contains(const K& el) const {
if(cur_ == 0) return false;
else if(cur_ == 1) return el == list_[0].first;
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
return i != cur_ && list_[i].first == el;
}
/**
* Return true iff this set contains 'el'.
*/
bool containsEx(const K& el, size_t& i) const {
if(cur_ == 0) return false;
else if(cur_ == 1) {
i = 0;
return el == list_[0].first;
}
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
return i != cur_ && list_[i].first == el;
}
/**
* Remove element from set.
*/
void remove(const K& el) {
size_t i;
if(cur_ < 16) {
// Linear scan
i = scanLoBound(el);
} else {
// Binary search
i = bsearchLoBound(el);
}
assert(i != cur_ && list_[i].first == el);
erase(i);
}
/**
* If size is less than requested size, resize up to at least sz
* and set cur_ to requested sz.
*/
void resize(size_t sz) {
if(sz <= cur_) return;
if(sz_ < sz) expandCopy(sz);
}
/**
* Get the ith key, value pair in the map.
*/
const std::pair<K, V>& get(size_t i) const {
assert_lt(i, cur_);
return list_[i];
}
/**
* Get the ith key, value pair in the map.
*/
const std::pair<K, V>& operator[](size_t i) const {
return get(i);
}
/**
* Clear set without deallocating (or setting) anything.
*/
void clear() { cur_ = 0; }
private:
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
std::pair<K, V> *alloc(size_t sz) {
assert_gt(sz, 0);
std::pair<K, V> *tmp = new std::pair<K, V>[sz];
gMemTally.add(cat_, sz);
return tmp;
}
/**
* Allocate a T array of length sz_ and store in list_. Also,
* tally into the global memory tally.
*/
void free() {
if(list_ != NULL) {
delete[] list_;
gMemTally.del(cat_, sz_);
list_ = NULL;
}
}
/**
* Simple linear scan that returns the index of the first element
* of list_ that is not less than el, or cur_ if all elements are
* less than el.
*/
size_t scanLoBound(const K& el) const {
for(size_t i = 0; i < cur_; i++) {
if(!(list_[i].first < el)) {
// Shouldn't be equal
return i;
}
}
return cur_;
}
/**
* Perform a binary search for the first element that is not less
* than 'el'. Return cur_ if all elements are less than el.
*/
size_t bsearchLoBound(const K& el) const {
size_t hi = cur_;
size_t lo = 0;
while(true) {
if(lo == hi) {
#ifndef NDEBUG
if((rand() % 10) == 0) {
assert_eq(lo, scanLoBound(el));
}
#endif
return lo;
}
size_t mid = lo + ((hi-lo)>>1);
assert_neq(mid, hi);
if(list_[mid].first < el) {
if(lo == mid) {
#ifndef NDEBUG
if((rand() % 10) == 0) {
assert_eq(hi, scanLoBound(el));
}
#endif
return hi;
}
lo = mid;
} else {
hi = mid;
}
}
}
/**
* Return true if sorted, assert otherwise.
*/
bool sorted() const {
if(cur_ <= 1) return true;
#ifndef NDEBUG
for(size_t i = 0; i < cur_-1; i++) {
assert(!(list_[i] == list_[i+1]));
assert(list_[i] < list_[i+1]);
}
#endif
return true;
}
/**
* Insert value 'el' at offset 'idx'. It's OK to insert at cur_,
* which is equivalent to appending.
*/
void insert(const std::pair<K, V>& el, size_t idx) {
assert_leq(idx, cur_);
if(cur_ == sz_) {
expandCopy(sz_+1);
}
for(size_t i = cur_; i > idx; i--) {
list_[i] = list_[i-1];
}
list_[idx] = el;
assert(idx == cur_ || list_[idx] < list_[idx+1]);
cur_++;
assert(sorted());
}
/**
* Erase element at offset idx.
*/
void erase(size_t idx) {
assert_lt(idx, cur_);
for(size_t i = idx; i < cur_-1; i++) {
list_[i] = list_[i+1];
}
cur_--;
assert(sorted());
}
/**
* Expand the list_ buffer until it has at least 'thresh' elements.
* Expansions are quadratic.
*/
void expandCopy(size_t thresh) {
if(thresh <= sz_) return;
size_t newsz = sz_ * 2;
while(newsz < thresh) newsz *= 2;
std::pair<K, V>* tmp = alloc(newsz);
for(size_t i = 0; i < cur_; i++) {
tmp[i] = list_[i];
}
free();
list_ = tmp;
sz_ = newsz;
}
int cat_; // memory category, for accounting purposes
std::pair<K, V> *list_; // list pointer, returned from new[]
size_t sz_; // capacity
size_t cur_; // occupancy (AKA size)
};
/**
* A class that allows callers to create objects that are referred to by ID.
* Objects should not be referred to via pointers or references, since they
* are stored in an expandable buffer that might be resized and thereby moved
* to another address.
*/
template <typename T, int S = 128>
class EFactory {
public:
explicit EFactory(size_t isz, int cat = 0) : l_(isz, cat) { }
explicit EFactory(int cat = 0) : l_(cat) { }
/**
* Clear the list.
*/
void clear() {
l_.clear();
}
/**
* Add one additional item to the list and return its ID.
*/
size_t alloc() {
l_.expand();
return l_.size()-1;
}
/**
* Return the number of items in the list.
*/
size_t size() const {
return l_.size();
}
/**
* Return the number of items in the factory.
*/
size_t totalSizeBytes() const {
return l_.totalSizeBytes();
}
/**
* Return the total capacity in bytes occupied by this factory.
*/
size_t totalCapacityBytes() const {
return l_.totalCapacityBytes();
}
/**
* Resize the list.
*/
void resize(size_t sz) {
l_.resize(sz);
}
/**
* Return true iff the list is empty.
*/
bool empty() const {
return size() == 0;
}
/**
* Shrink the list such that the topmost (most recently allocated) element
* is removed.
*/
void pop() {
l_.resize(l_.size()-1);
}
/**
* Return mutable list item at offset 'off'
*/
T& operator[](size_t off) {
return l_[off];
}
/**
* Return immutable list item at offset 'off'
*/
const T& operator[](size_t off) const {
return l_[off];
}
protected:
EList<T, S> l_;
};
/**
* An expandable bit vector based on EList
*/
template <int S = 128>
class EBitList {
public:
explicit EBitList(size_t isz, int cat = 0) : l_(isz, cat) { reset(); }
explicit EBitList(int cat = 0) : l_(cat) { reset(); }
/**
* Reset to empty state.
*/
void clear() {
reset();
}
/**
* Reset to empty state.
*/
void reset() {
l_.clear();
max_ = std::numeric_limits<size_t>::max();
}
/**
* Set a bit.
*/
void set(size_t off) {
resize(off);
l_[off >> 3] |= (1 << (off & 7));
if(off > max_ || max_ == std::numeric_limits<size_t>::max()) {
max_ = off;
}
}
/**
* Return mutable list item at offset 'off'
*/
bool test(size_t off) const {
if((size_t)(off >> 3) >= l_.size()) {
return false;
}
return (l_[off >> 3] & (1 << (off & 7))) != 0;
}
/**
* Return size of the underlying byte array.
*/
size_t size() const {
return l_.size();
}
/**
* Resize to accomodate at least the given number of bits.
*/
void resize(size_t off) {
if((size_t)(off >> 3) >= l_.size()) {
size_t oldsz = l_.size();
l_.resize((off >> 3) + 1);
for(size_t i = oldsz; i < l_.size(); i++) {
l_[i] = 0;
}
}
}
/**
* Return max set bit.
*/
size_t max() const {
return max_;
}
protected:
EList<uint8_t, S> l_;
size_t max_;
};
/**
* Implements a min-heap.
*/
template <typename T, int S = 128>
class EHeap {
public:
/**
* Add the element to the next available leaf position and percolate up.
*/
void insert(T o) {
size_t pos = l_.size();
l_.push_back(o);
while(pos > 0) {
size_t parent = (pos-1) >> 1;
if(l_[pos] < l_[parent]) {
T tmp(l_[pos]);
l_[pos] = l_[parent];
l_[parent] = tmp;
pos = parent;
} else break;
}
assert(repOk());
}
/**
* Return the topmost element.
*/
T top() {
assert_gt(l_.size(), 0);
return l_[0];
}
/**
* Remove the topmost element.
*/
T pop() {
assert_gt(l_.size(), 0);
T ret = l_[0];
l_[0] = l_[l_.size()-1];
l_.resize(l_.size()-1);
size_t cur = 0;
while(true) {
size_t c1 = ((cur+1) << 1) - 1;
size_t c2 = c1 + 1;
if(c2 < l_.size()) {
if(l_[c1] < l_[cur] && l_[c1] <= l_[c2]) {
T tmp(l_[c1]);
l_[c1] = l_[cur];
l_[cur] = tmp;
cur = c1;
} else if(l_[c2] < l_[cur]) {
T tmp(l_[c2]);
l_[c2] = l_[cur];
l_[cur] = tmp;
cur = c2;
} else {
break;
}
} else if(c1 < l_.size()) {
if(l_[c1] < l_[cur]) {
T tmp(l_[c1]);
l_[c1] = l_[cur];
l_[cur] = tmp;
cur = c1;
} else {
break;
}
} else {
break;
}
}
assert(repOk());
return ret;
}
/**
* Return number of elements in the heap.
*/
size_t size() const {
return l_.size();
}
/**
* Return the total size in bytes occupied by this heap.
*/
size_t totalSizeBytes() const {
return l_.totalSizeBytes();
}
/**
* Return the total capacity in bytes occupied by this heap.
*/
size_t totalCapacityBytes() const {
return l_.totalCapacityBytes();
}
/**
* Return true when heap is empty.
*/
bool empty() const {
return l_.empty();
}
/**
* Return element at offset i.
*/
const T& operator[](size_t i) const {
return l_[i];
}
#ifndef NDEBUG
/**
* Check that heap property holds.
*/
bool repOk() const {
if(empty()) return true;
return repOkNode(0);
}
/**
* Check that heap property holds at and below this node.
*/
bool repOkNode(size_t cur) const {
size_t c1 = ((cur+1) << 1) - 1;
size_t c2 = c1 + 1;
if(c1 < l_.size()) {
assert_leq(l_[cur], l_[c1]);
}
if(c2 < l_.size()) {
assert_leq(l_[cur], l_[c2]);
}
if(c2 < l_.size()) {
return repOkNode(c1) && repOkNode(c2);
} else if(c1 < l_.size()) {
return repOkNode(c1);
}
return true;
}
#endif
/**
* Clear the heap so that it's empty.
*/
void clear() {
l_.clear();
}
protected:
EList<T, S> l_;
};
/**
* Dispenses pages of memory for all the lists in the cache, including
* the sequence-to-range map, the range list, the edits list, and the
* offsets list. All lists contend for the same pool of memory.
*/
class Pool {
public:
Pool(
uint64_t bytes,
uint32_t pagesz,
int cat = 0) :
cat_(cat),
cur_(0),
bytes_(bytes),
pagesz_(pagesz),
pages_(cat)
{
for(size_t i = 0; i < ((bytes+pagesz-1)/pagesz); i++) {
pages_.push_back(new uint8_t[pagesz]);
gMemTally.add(cat, pagesz);
assert(pages_.back() != NULL);
}
assert(repOk());
}
/**
* Free each page.
*/
~Pool() {
for(size_t i = 0; i < pages_.size(); i++) {
assert(pages_[i] != NULL);
delete[] pages_[i];
gMemTally.del(cat_, pagesz_);
}
}
/**
* Allocate one page, or return NULL if no pages are left.
*/
uint8_t * alloc() {
assert(repOk());
if(cur_ == pages_.size()) return NULL;
return pages_[cur_++];
}
bool full() { return cur_ == pages_.size(); }
/**
* Clear the pool so that no pages are considered allocated.
*/
void clear() {
cur_ = 0;
assert(repOk());
}
/**
* Reset the Pool to be as though
*/
void free() {
// Currently a no-op because the only freeing method supported
// now is to clear the entire pool
}
#ifndef NDEBUG
/**
* Check that pool is internally consistent.
*/
bool repOk() const {
assert_leq(cur_, pages_.size());
assert(!pages_.empty());
assert_gt(bytes_, 0);
assert_gt(pagesz_, 0);
return true;
}
#endif
public:
int cat_; // memory category, for accounting purposes
uint32_t cur_; // next page to hand out
const uint64_t bytes_; // total bytes in the pool
const uint32_t pagesz_; // size of a single page
EList<uint8_t*> pages_; // the pages themselves
};
/**
* An expandable list backed by a pool.
*/
template<typename T, int S>
class PList {
#define PLIST_PER_PAGE (S / sizeof(T))
public:
/**
* Initialize the current-edit pointer to 0 and set the number of
* edits per memory page.
*/
PList(int cat = 0) :
cur_(0),
curPage_(0),
pages_(cat) { }
/**
* Add 1 object to the list.
*/
bool add(Pool& p, const T& o) {
assert(repOk());
if(!ensure(p, 1)) return false;
if(cur_ == PLIST_PER_PAGE) {
cur_ = 0;
curPage_++;
}
assert_lt(curPage_, pages_.size());
assert(repOk());
assert_lt(cur_, PLIST_PER_PAGE);
pages_[curPage_][cur_++] = o;
return true;
}
/**
* Add a list of objects to the list.
*/
bool add(Pool& p, const EList<T>& os) {
if(!ensure(p, os.size())) return false;
for(size_t i = 0; i < os.size(); i++) {
if(cur_ == PLIST_PER_PAGE) {
cur_ = 0;
curPage_++;
}
assert_lt(curPage_, pages_.size());
assert(repOk());
assert_lt(cur_, PLIST_PER_PAGE);
pages_[curPage_][cur_++] = os[i];
}
return true;
}
/**
* Add a list of objects to the list.
*/
bool copy(
Pool& p,
const PList<T, S>& src,
size_t i,
size_t len)
{
if(!ensure(p, src.size())) return false;
for(size_t i = 0; i < src.size(); i++) {
if(cur_ == PLIST_PER_PAGE) {
cur_ = 0;
curPage_++;
}
assert_lt(curPage_, pages_.size());
assert(repOk());
assert_lt(cur_, PLIST_PER_PAGE);
pages_[curPage_][cur_++] = src[i];
}
return true;
}
/**
* Add 'num' objects, all equal to 'o' to the list.
*/
bool addFill(Pool& p, size_t num, const T& o) {
if(!ensure(p, num)) return false;
for(size_t i = 0; i < num; i++) {
if(cur_ == PLIST_PER_PAGE) {
cur_ = 0;
curPage_++;
}
assert_lt(curPage_, pages_.size());
assert(repOk());
assert_lt(cur_, PLIST_PER_PAGE);
pages_[curPage_][cur_++] = o;
}
return true;
}
/**
* Free all pages associated with the list.
*/
void clear() {
pages_.clear();
cur_ = curPage_ = 0;
}
#ifndef NDEBUG
/**
* Check that list is internally consistent.
*/
bool repOk() const {
assert(pages_.size() == 0 || curPage_ < pages_.size());
assert_leq(cur_, PLIST_PER_PAGE);
return true;
}
#endif
/**
* Return the number of elements in the list.
*/
size_t size() const {
return curPage_ * PLIST_PER_PAGE + cur_;
}
/**
* Return true iff the PList has no elements.
*/
bool empty() const {
return size() == 0;
}
/**
* Get the ith element added to the list.
*/
inline const T& getConst(size_t i) const {
assert_lt(i, size());
size_t page = i / PLIST_PER_PAGE;
size_t elt = i % PLIST_PER_PAGE;
return pages_[page][elt];
}
/**
* Get the ith element added to the list.
*/
inline T& get(size_t i) {
assert_lt(i, size());
size_t page = i / PLIST_PER_PAGE;
size_t elt = i % PLIST_PER_PAGE;
assert_lt(page, pages_.size());
assert(page < pages_.size()-1 || elt < cur_);
return pages_[page][elt];
}
/**
* Get the most recently added element.
*/
inline T& back() {
size_t page = (size()-1) / PLIST_PER_PAGE;
size_t elt = (size()-1) % PLIST_PER_PAGE;
assert_lt(page, pages_.size());
assert(page < pages_.size()-1 || elt < cur_);
return pages_[page][elt];
}
/**
* Get const version of the most recently added element.
*/
inline const T& back() const {
size_t page = (size()-1) / PLIST_PER_PAGE;
size_t elt = (size()-1) % PLIST_PER_PAGE;
assert_lt(page, pages_.size());
assert(page < pages_.size()-1 || elt < cur_);
return pages_[page][elt];
}
/**
* Get the element most recently added to the list.
*/
T& last() {
assert(!pages_.empty());
assert_gt(PLIST_PER_PAGE, 0);
if(cur_ == 0) {
assert_gt(pages_.size(), 1);
return pages_[pages_.size()-2][PLIST_PER_PAGE-1];
} else {
return pages_.back()[cur_-1];
}
}
/**
* Return true iff 'num' additional objects will fit in the pages
* allocated to the list. If more pages are needed, they are
* added if possible.
*/
bool ensure(Pool& p, size_t num) {
assert(repOk());
if(num == 0) return true;
// Allocation of the first page
if(pages_.size() == 0) {
if(expand(p) == NULL) {
return false;
}
assert_eq(1, pages_.size());
}
size_t cur = cur_;
size_t curPage = curPage_;
while(cur + num > PLIST_PER_PAGE) {
assert_lt(curPage, pages_.size());
if(curPage == pages_.size()-1 && expand(p) == NULL) {
return false;
}
num -= (PLIST_PER_PAGE - cur);
cur = 0;
curPage++;
}
return true;
}
protected:
/**
* Expand our page supply by 1
*/
T* expand(Pool& p) {
T* newpage = (T*)p.alloc();
if(newpage == NULL) {
return NULL;
}
pages_.push_back(newpage);
return pages_.back();
}
size_t cur_; // current elt within page
size_t curPage_; // current page
EList<T*> pages_; // the pages
};
/**
* A slice of an EList.
*/
template<typename T, int S>
class EListSlice {
public:
EListSlice() :
i_(0),
len_(0),
list_()
{ }
EListSlice(
EList<T, S>& list,
size_t i,
size_t len) :
i_(i),
len_(len),
list_(&list)
{ }
/**
* Initialize from a piece of another PListSlice.
*/
void init(const EListSlice<T, S>& sl, size_t first, size_t last) {
assert_gt(last, first);
assert_leq(last - first, sl.len_);
i_ = sl.i_ + first;
len_ = last - first;
list_ = sl.list_;
}
/**
* Reset state to be empty.
*/
void reset() {
i_ = len_ = 0;
list_ = NULL;
}
/**
* Get the ith element of the slice.
*/
inline const T& get(size_t i) const {
assert(valid());
assert_lt(i, len_);
return list_->get(i + i_);
}
/**
* Get the ith element of the slice.
*/
inline T& get(size_t i) {
assert(valid());
assert_lt(i, len_);
return list_->get(i + i_);
}
/**
* Return a reference to the ith element.
*/
inline T& operator[](size_t i) {
assert(valid());
assert_lt(i, len_);
return list_->get(i + i_);
}
/**
* Return a reference to the ith element.
*/
inline const T& operator[](size_t i) const {
assert(valid());
assert_lt(i, len_);
return list_->get(i + i_);
}
/**
* Return true iff this slice is initialized.
*/
bool valid() const {
return len_ != 0;
}
/**
* Return number of elements in the slice.
*/
size_t size() const {
return len_;
}
#ifndef NDEBUG
/**
* Ensure that the PListSlice is internally consistent and
* consistent with the backing PList.
*/
bool repOk() const {
assert_leq(i_ + len_, list_->size());
return true;
}
#endif
/**
* Return true iff this slice refers to the same slice of the same
* list as the given slice.
*/
bool operator==(const EListSlice& sl) const {
return i_ == sl.i_ && len_ == sl.len_ && list_ == sl.list_;
}
/**
* Return false iff this slice refers to the same slice of the same
* list as the given slice.
*/
bool operator!=(const EListSlice& sl) const {
return !(*this == sl);
}
/**
* Set the length. This could leave things inconsistent (e.g. could
* include elements that fall off the end of list_).
*/
void setLength(size_t nlen) {
len_ = (uint32_t)nlen;
}
protected:
size_t i_;
size_t len_;
EList<T, S>* list_;
};
/**
* A slice of a PList.
*/
template<typename T, int S>
class PListSlice {
public:
PListSlice() :
i_(0),
len_(0),
list_()
{ }
PListSlice(
PList<T, S>& list,
TIndexOffU i,
TIndexOffU len) :
i_(i),
len_(len),
list_(&list)
{ }
/**
* Initialize from a piece of another PListSlice.
*/
void init(const PListSlice<T, S>& sl, size_t first, size_t last) {
assert_gt(last, first);
assert_leq(last - first, sl.len_);
i_ = (uint32_t)(sl.i_ + first);
len_ = (uint32_t)(last - first);
list_ = sl.list_;
}
/**
* Reset state to be empty.
*/
void reset() {
i_ = len_ = 0;
list_ = NULL;
}
/**
* Get the ith element of the slice.
*/
inline const T& get(size_t i) const {
assert(valid());
assert_lt(i, len_);
return list_->get(i+i_);
}
/**
* Get the ith element of the slice.
*/
inline T& get(size_t i) {
assert(valid());
assert_lt(i, len_);
return list_->get(i+i_);
}
/**
* Return a reference to the ith element.
*/
inline T& operator[](size_t i) {
assert(valid());
assert_lt(i, len_);
return list_->get(i+i_);
}
/**
* Return a reference to the ith element.
*/
inline const T& operator[](size_t i) const {
assert(valid());
assert_lt(i, len_);
return list_->get(i+i_);
}
/**
* Return true iff this slice is initialized.
*/
bool valid() const {
return len_ != 0;
}
/**
* Return number of elements in the slice.
*/
size_t size() const {
return len_;
}
#ifndef NDEBUG
/**
* Ensure that the PListSlice is internally consistent and
* consistent with the backing PList.
*/
bool repOk() const {
assert_leq(i_ + len_, list_->size());
return true;
}
#endif
/**
* Return true iff this slice refers to the same slice of the same
* list as the given slice.
*/
bool operator==(const PListSlice& sl) const {
return i_ == sl.i_ && len_ == sl.len_ && list_ == sl.list_;
}
/**
* Return false iff this slice refers to the same slice of the same
* list as the given slice.
*/
bool operator!=(const PListSlice& sl) const {
return !(*this == sl);
}
/**
* Set the length. This could leave things inconsistent (e.g. could
* include elements that fall off the end of list_).
*/
void setLength(size_t nlen) {
len_ = (uint32_t)nlen;
}
protected:
uint32_t i_;
uint32_t len_;
PList<T, S>* list_;
};
/**
* A Red-Black tree node. Links to parent & left and right children.
* Key and Payload are of types K and P. Node total ordering is based
* on K's total ordering. K must implement <, == and > operators.
*/
template<typename K, typename P> // K=key, P=payload
class RedBlackNode {
typedef RedBlackNode<K,P> TNode;
public:
TNode *parent; // parent
TNode *left; // left child
TNode *right; // right child
bool red; // true -> red, false -> black
K key; // key, for ordering
P payload; // payload (i.e. value)
/**
* Return the parent of this node's parent, or NULL if none exists.
*/
RedBlackNode *grandparent() {
return parent != NULL ? parent->parent : NULL;
}
/**
* Return the sibling of this node's parent, or NULL if none exists.
*/
RedBlackNode *uncle() {
if(parent == NULL) return NULL; // no parent
if(parent->parent == NULL) return NULL; // parent has no siblings
return (parent->parent->left == parent) ? parent->parent->right : parent->parent->left;
}
/**
* Return true iff this node is its parent's left child.
*/
bool isLeftChild() const { assert(parent != NULL); return parent->left == this; }
/**
* Return true iff this node is its parent's right child.
*/
bool isRightChild() const { assert(parent != NULL); return parent->right == this; }
/**
* Return true iff this node is its parent's right child.
*/
void replaceChild(RedBlackNode* ol, RedBlackNode* nw) {
if(left == ol) {
left = nw;
} else {
assert(right == ol);
right = nw;
}
}
/**
* Return the number of non-null children this node has.
*/
int numChildren() const {
return ((left != NULL) ? 1 : 0) + ((right != NULL) ? 1 : 0);
}
#ifndef NDEBUG
/**
* Check that node is internally consistent.
*/
bool repOk() const {
if(parent != NULL) {
assert(parent->left == this || parent->right == this);
}
return true;
}
#endif
/**
* True -> my key is less than than the given node's key.
*/
bool operator<(const TNode& o) const { return key < o.key; }
/**
* True -> my key is greater than the given node's key.
*/
bool operator>(const TNode& o) const { return key > o.key; }
/**
* True -> my key equals the given node's key.
*/
bool operator==(const TNode& o) const { return key == o.key; }
/**
* True -> my key is less than the given key.
*/
bool operator<(const K& okey) const { return key < okey; }
/**
* True -> my key is greater than the given key.
*/
bool operator>(const K& okey) const { return key > okey; }
/**
* True -> my key is equal to the given key.
*/
bool operator==(const K& okey) const { return key == okey; }
};
/**
* A Red-Black tree that associates keys (of type K) with payloads (of
* type P). Red-Black trees are self-balancing and guarantee that the
* tree as always "balanced" to a factor of 2, i.e., the longest
* root-to-leaf path is never more than twice as long as the shortest
* root-to-leaf path.
*/
template<typename K, typename P> // K=key, P=payload
class RedBlack {
typedef RedBlackNode<K,P> TNode;
public:
/**
* Initialize the current-edit pointer to 0 and set the number of
* edits per memory page.
*/
RedBlack(uint32_t pageSz, int cat = 0) :
perPage_(pageSz/sizeof(TNode)), pages_(cat) { clear(); }
/**
* Given a DNA string, find the red-black node corresponding to it,
* if one exists.
*/
inline TNode* lookup(const K& key) const {
TNode* cur = root_;
while(cur != NULL) {
if((*cur) == key) return cur;
if((*cur) < key) {
cur = cur->right;
} else {
cur = cur->left;
}
}
return NULL;
}
/**
* Add a new key as a node in the red-black tree.
*/
TNode* add(
Pool& p, // in: pool for memory pages
const K& key, // in: key to insert
bool* added) // if true, assert is thrown if key exists
{
// Look for key; if it's not there, get its parent
TNode* cur = root_;
assert(root_ == NULL || !root_->red);
TNode* parent = NULL;
bool leftChild = true;
while(cur != NULL) {
if((*cur) == key) {
// Found it; break out of loop with cur != NULL
break;
}
parent = cur;
if((*cur) < key) {
if((cur = cur->right) == NULL) {
// Fell off the bottom of the tree as the right
// child of parent 'lastCur'
leftChild = false;
}
} else {
if((cur = cur->left) == NULL) {
// Fell off the bottom of the tree as the left
// child of parent 'lastCur'
leftChild = true;
}
}
}
if(cur != NULL) {
// Found an entry; assert if we weren't supposed to
if(added != NULL) *added = false;
} else {
assert(root_ == NULL || !root_->red);
if(!addNode(p, cur)) {
// Exhausted memory
return NULL;
}
assert(cur != NULL);
assert(cur != root_);
assert(cur != parent);
// Initialize new node
cur->key = key;
cur->left = cur->right = NULL;
cur->red = true; // red until proven black
keys_++;
if(added != NULL) *added = true;
// Put it where we know it should go
addNode(cur, parent, leftChild);
}
return cur; // return the added or found node
}
#ifndef NDEBUG
/**
* Check that list is internally consistent.
*/
bool repOk() const {
assert(curPage_ == 0 || curPage_ < pages_.size());
assert_leq(cur_, perPage_);
assert(root_ == NULL || !root_->red);
return true;
}
#endif
/**
* Clear all state.
*/
void clear() {
cur_ = curPage_ = 0;
root_ = NULL;
keys_ = 0;
intenseRepOkCnt_ = 0;
pages_.clear();
}
/**
* Return number of keys added.
*/
size_t size() const {
return keys_;
}
/**
* Return true iff there are no keys in the map.
*/
bool empty() const {
return keys_ == 0;
}
/**
* Add another node and return a pointer to it in 'node'. A new
* page is allocated if necessary. If the allocation fails, false
* is returned.
*/
bool addNode(Pool& p, TNode*& node) {
assert_leq(cur_, perPage_);
assert(repOk());
assert(this != NULL);
// Allocation of the first page
if(pages_.size() == 0) {
if(addPage(p) == NULL) {
node = NULL;
return false;
}
assert_eq(1, pages_.size());
}
if(cur_ == perPage_) {
assert_lt(curPage_, pages_.size());
if(curPage_ == pages_.size()-1 && addPage(p) == NULL) {
return false;
}
cur_ = 0;
curPage_++;
}
assert_lt(cur_, perPage_);
assert_lt(curPage_, pages_.size());
node = &pages_[curPage_][cur_];
assert(node != NULL);
cur_++;
return true;
}
const TNode* root() const { return root_; }
protected:
#ifndef NDEBUG
/**
* Check specifically that the red-black invariants are satistfied.
*/
bool redBlackRepOk(TNode* n) {
if(n == NULL) return true;
if(++intenseRepOkCnt_ < 500) return true;
intenseRepOkCnt_ = 0;
int minNodes = -1; // min # nodes along any n->leaf path
int maxNodes = -1; // max # nodes along any n->leaf path
// The number of black nodes along paths from n to leaf
// (must be same for all paths)
int blackConst = -1;
size_t nodesTot = 0;
redBlackRepOk(
n,
1, /* 1 node so far */
n->red ? 0 : 1, /* black nodes so far */
blackConst,
minNodes,
maxNodes,
nodesTot);
if(n == root_) {
assert_eq(nodesTot, keys_);
}
assert_gt(minNodes, 0);
assert_gt(maxNodes, 0);
assert_leq(maxNodes, 2*minNodes);
return true;
}
/**
* Check specifically that the red-black invariants are satistfied.
*/
bool redBlackRepOk(
TNode* n,
int nodes,
int black,
int& blackConst,
int& minNodes,
int& maxNodes,
size_t& nodesTot) const
{
assert_gt(black, 0);
nodesTot++; // account for leaf node
if(n->left == NULL) {
if(blackConst == -1) blackConst = black;
assert_eq(black, blackConst);
if(nodes+1 > maxNodes) maxNodes = nodes+1;
if(nodes+1 < minNodes || minNodes == -1) minNodes = nodes+1;
} else {
if(n->red) assert(!n->left->red); // Red can't be child of a red
redBlackRepOk(
n->left, // next node
nodes + 1, // # nodes so far on path
black + (n->left->red ? 0 : 1), // # black so far on path
blackConst, // invariant # black nodes on root->leaf path
minNodes, // min root->leaf len so far
maxNodes, // max root->leaf len so far
nodesTot); // tot nodes so far
}
if(n->right == NULL) {
if(blackConst == -1) blackConst = black;
assert_eq(black, blackConst);
if(nodes+1 > maxNodes) maxNodes = nodes+1;
if(nodes+1 < minNodes || minNodes == -1) minNodes = nodes+1;
} else {
if(n->red) assert(!n->right->red); // Red can't be child of a red
redBlackRepOk(
n->right, // next node
nodes + 1, // # nodes so far on path
black + (n->right->red ? 0 : 1), // # black so far on path
blackConst, // invariant # black nodes on root->leaf path
minNodes, // min root->leaf len so far
maxNodes, // max root->leaf len so far
nodesTot); // tot nodes so far
}
return true;
}
#endif
/**
* Rotate to the left such that n is replaced by its right child
* w/r/t n's current parent.
*/
void leftRotate(TNode* n) {
TNode* r = n->right;
assert(n->repOk());
assert(r->repOk());
n->right = r->left;
if(n->right != NULL) {
n->right->parent = n;
assert(n->right->repOk());
}
r->parent = n->parent;
n->parent = r;
r->left = n;
if(r->parent != NULL) {
r->parent->replaceChild(n, r);
}
if(root_ == n) root_ = r;
assert(!root_->red);
assert(n->repOk());
assert(r->repOk());
}
/**
* Rotate to the right such that n is replaced by its left child
* w/r/t n's current parent. n moves down to the right and loses
* its left child, while its former left child moves up and gains a
* right child.
*/
void rightRotate(TNode* n) {
TNode* r = n->left;
assert(n->repOk());
assert(r->repOk());
n->left = r->right;
if(n->left != NULL) {
n->left->parent = n;
assert(n->left->repOk());
}
r->parent = n->parent;
n->parent = r;
r->right = n;
if(r->parent != NULL) {
r->parent->replaceChild(n, r);
}
if(root_ == n) root_ = r;
assert(!root_->red);
assert(n->repOk());
assert(r->repOk());
}
/**
* Add a node to the red-black tree, maintaining the red-black
* invariants.
*/
void addNode(TNode* n, TNode* parent, bool leftChild) {
assert(n != NULL);
if(parent == NULL) {
// Case 1: inserted at root
root_ = n;
root_->red = false; // root must be black
n->parent = NULL;
assert(redBlackRepOk(root_));
assert(n->repOk());
} else {
assert(!root_->red);
// Add new node to tree
if(leftChild) {
assert(parent->left == NULL);
parent->left = n;
} else {
assert(parent->right == NULL);
parent->right = n;
}
n->parent = parent;
int thru = 0;
while(true) {
thru++;
parent = n->parent;
if(parent != NULL) assert(parent->repOk());
if(parent == NULL && n->red) {
n->red = false;
}
if(parent == NULL || !parent->red) {
assert(redBlackRepOk(root_));
break;
}
TNode* uncle = n->uncle();
TNode* gparent = n->grandparent();
assert(gparent != NULL); // if parent is red, grandparent must exist
bool uncleRed = (uncle != NULL ? uncle->red : false);
if(uncleRed) {
// Parent is red, uncle is red; recursive case
assert(uncle != NULL);
parent->red = uncle->red = false;
gparent->red = true;
n = gparent;
continue;
} else {
if(parent->isLeftChild()) {
// Parent is red, uncle is black, parent is
// left child
if(!n->isLeftChild()) {
n = parent;
leftRotate(n);
}
n = n->parent;
n->red = false;
n->parent->red = true;
rightRotate(n->parent);
assert(redBlackRepOk(n));
assert(redBlackRepOk(root_));
} else {
// Parent is red, uncle is black, parent is
// right child.
if(!n->isRightChild()) {
n = parent;
rightRotate(n);
}
n = n->parent;
n->red = false;
n->parent->red = true;
leftRotate(n->parent);
assert(redBlackRepOk(n));
assert(redBlackRepOk(root_));
}
}
break;
}
}
assert(redBlackRepOk(root_));
}
/**
* Expand our page supply by 1
*/
TNode* addPage(Pool& p) {
TNode *n = (TNode *)p.alloc();
if(n != NULL) {
pages_.push_back(n);
}
return n;
}
size_t keys_; // number of keys so far
size_t cur_; // current elt within page
size_t curPage_; // current page
const size_t perPage_; // # edits fitting in a page
TNode* root_; // root node
EList<TNode*> pages_; // the pages
int intenseRepOkCnt_; // counter for the computationally intensive repOk function
};
/**
* For assembling doubly-linked lists of Edits.
*/
template <typename T>
struct DoublyLinkedList {
DoublyLinkedList() : payload(), prev(NULL), next(NULL) { }
/**
* Add all elements in the doubly-linked list to the provided EList.
*/
void toList(EList<T>& l) {
// Add this and all subsequent elements
DoublyLinkedList<T> *cur = this;
while(cur != NULL) {
l.push_back(cur->payload);
cur = cur->next;
}
// Add all previous elements
cur = prev;
while(cur != NULL) {
l.push_back(cur->payload);
cur = cur->prev;
}
}
T payload;
DoublyLinkedList<T> *prev;
DoublyLinkedList<T> *next;
};
template <typename T1, typename T2>
struct Pair {
T1 a;
T2 b;
Pair() : a(), b() { }
Pair(
const T1& a_,
const T2& b_) { a = a_; b = b_; }
bool operator==(const Pair& o) const {
return a == o.a && b == o.b;
}
bool operator<(const Pair& o) const {
if(a < o.a) return true;
if(a > o.a) return false;
if(b < o.b) return true;
return false;
}
};
template <typename T1, typename T2, typename T3>
struct Triple {
T1 a;
T2 b;
T3 c;
Triple() : a(), b(), c() { }
Triple(
const T1& a_,
const T2& b_,
const T3& c_) { a = a_; b = b_; c = c_; }
bool operator==(const Triple& o) const {
return a == o.a && b == o.b && c == o.c;
}
bool operator<(const Triple& o) const {
if(a < o.a) return true;
if(a > o.a) return false;
if(b < o.b) return true;
if(b > o.b) return false;
if(c < o.c) return true;
return false;
}
};
template <typename T1, typename T2, typename T3, typename T4>
struct Quad {
Quad() : a(), b(), c(), d() { }
Quad(
const T1& a_,
const T2& b_,
const T3& c_,
const T4& d_) { a = a_; b = b_; c = c_; d = d_; }
Quad(
const T1& a_,
const T1& b_,
const T1& c_,
const T1& d_)
{
init(a_, b_, c_, d_);
}
void init(
const T1& a_,
const T1& b_,
const T1& c_,
const T1& d_)
{
a = a_; b = b_; c = c_; d = d_;
}
bool operator==(const Quad& o) const {
return a == o.a && b == o.b && c == o.c && d == o.d;
}
bool operator<(const Quad& o) const {
if(a < o.a) return true;
if(a > o.a) return false;
if(b < o.b) return true;
if(b > o.b) return false;
if(c < o.c) return true;
if(c > o.c) return false;
if(d < o.d) return true;
return false;
}
T1 a;
T2 b;
T3 c;
T4 d;
};
/**
* For assembling doubly-linked lists of EList.
*/
template <typename T>
struct LinkedEListNode {
LinkedEListNode() : payload(), next(NULL) { }
T payload;
LinkedEListNode<T> *next;
};
/**
* For assembling doubly-linked lists of EList.
*/
template <typename T>
struct LinkedEList {
LinkedEList() : head(NULL) {
ASSERT_ONLY(num_allocated = 0);
ASSERT_ONLY(num_new_node = 0);
ASSERT_ONLY(num_delete_node = 0);
}
~LinkedEList() {
ASSERT_ONLY(size_t num_deallocated = 0);
while(head != NULL) {
LinkedEListNode<T>* next = head->next;
delete head;
ASSERT_ONLY(num_deallocated++);
head = next;
}
// daehwan - for debugging purposes
// assert_eq(num_allocated, num_deallocated);
}
LinkedEListNode<T>* new_node() {
ASSERT_ONLY(num_new_node++);
LinkedEListNode<T> *result = NULL;
if(head == NULL) {
head = new LinkedEListNode<T>();
head-> next = NULL;
ASSERT_ONLY(num_allocated++);
}
assert(head != NULL);
result = head;
head = head->next;
assert(result != NULL);
return result;
}
void delete_node(LinkedEListNode<T> *node) {
ASSERT_ONLY(num_delete_node++);
assert(node != NULL);
// check if this is already deleted.
#ifndef NDEBUG
LinkedEListNode<T> *temp = head;
while(temp != NULL) {
assert(temp != node);
temp = temp->next;
}
#endif
node->next = head;
head = node;
}
LinkedEListNode<T> *head;
ASSERT_ONLY(size_t num_allocated);
ASSERT_ONLY(size_t num_new_node);
ASSERT_ONLY(size_t num_delete_node);
};
#endif /* DS_H_ */
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