Added half nibble code.

This commit is contained in:
Davi de Castro Reis 2010-10-27 17:17:09 -07:00
parent 724e716d67
commit 385ce27a10
8 changed files with 213 additions and 142 deletions

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@ -1,4 +1,4 @@
bin_PROGRAMS = cmph_hash_map_test mphtable_test
bin_PROGRAMS = cmph_hash_map_test mphtable_test trigraph_test
lib_LTLIBRARIES = libcxxmph.la
libcxxmph_la_SOURCES = stringpiece.h MurmurHash2.h randomly_seeded_hash.h trigragh.h trigraph.cc mphtable.h mphtable.cc
@ -9,3 +9,6 @@ cmph_hash_map_test_SOURCES = cmph_hash_map_test.cc
mphtable_test_LDADD = libcxxmph.la
mphtable_test_SOURCES = mphtable_test.cc
trigraph_test_LDADD = libcxxmph.la
trigraph_test_SOURCES = trigraph_test.cc

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@ -1,3 +1,6 @@
#ifndef __CXXMPH_MURMUR_HASH2__
#define __CXXMPH_MURMUR_HASH2__
//-----------------------------------------------------------------------------
// MurmurHash2, by Austin Appleby
@ -12,6 +15,8 @@
// 2. It will not produce the same results on little-endian and big-endian
// machines.
namespace {
unsigned int MurmurHash2 ( const void * key, int len, unsigned int seed )
{
// 'm' and 'r' are mixing constants generated offline.
@ -62,3 +67,7 @@ unsigned int MurmurHash2 ( const void * key, int len, unsigned int seed )
return h;
}
}
#endif // __CXXMPH_MURMUR_HASH2__

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@ -1,49 +1,58 @@
#include <limits>
#include <iostream>
using std::cerr;
using std::endl;
#include "mphtable.h"
using std::vector;
namespace {
static const cmph_uint8 kUnassigned = 3;
// table used for looking up the number of assigned vertices to a 8-bit integer
static cmph_uint8 kBdzLookupTable[] =
{
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 0
};
static const cmph_uint8 valuemask[] = { 0xfc, 0xf3, 0xcf, 0x3f};
void set_2bit_value(vector<cmph_uint8> *d, cmph_uint8 i, cmph_uint8 v) {
(*d)[(i >> 2)] &= (v << ((i & 3) << 1)) | valuemask[i & 3];
}
cmph_uint8 get_2bit_value(const vector<cmph_uint8>& d, cmph_uint8 i) {
return (d[(i >> 2)] >> ((i & 3) << 1)) & 3;
}
} // anonymous namespace
namespace cxxmph {
template <class Key, class HashFcn>
template <class ForwardIterator>
bool MPHTable<Key, HashFcn>::Reset(ForwardIterator begin, ForwardIterator end) {
TableBuilderState<ForwardIterator> st;
m_ = end - begin;
r_ = static_cast<cmph_uint32>(ceil((c_*m_)/3));
if (r_ % 2) == 0) r_ += 1;
n_ = 3*r_;
k_ = 1U << b_;
int iterations = 1000;
while (1) {
for (int i = 0; i < 3; ++i) hash_function_[i] = hasher();
vector<Edge> edges;
vector<cmph_uint32> queue;
if (Mapping(begin, end, &edges, &queue)) break;
else --iterations;
if (iterations == 0) break;
}
if (iterations == 0) return false;
vector<Edge>& edges;
graph->ExtractEdgesAndClear(&edges);
Assigning(queue, edges);
vector<cmph_uint32>().swap(edges);
Ranking();
}
template <class Key, class HashFcn>
bool MPHTable<Key, HashFcn>::GenerateQueue(
bool MPHTable::GenerateQueue(
TriGraph* graph, vector<cmph_uint32>* queue_output) {
cmph_uint32 queue_head = 0, queue_tail = 0;
cmph_uint32 nedges = n_;
cmph_uint32 nvertices = m_;
cmph_uint32 nedges = m_;
cmph_uint32 nvertices = n_;
// Relies on vector<bool> using 1 bit per element
vector<bool> marked_edge((nedges >> 3) + 1, false);
Queue queue(nvertices, 0);
for (int i = 0; i < nedges; ++i) {
vector<cmph_uint32> queue(nvertices, 0);
for (cmph_uint32 i = 0; i < nedges; ++i) {
const TriGraph::Edge& e = graph->edges()[i];
if (graph->vertex_degree()[e[0]] == 1 ||
graph->vertex_degree()[e[1]] == 1 ||
@ -74,102 +83,56 @@ bool MPHTable<Key, HashFcn>::GenerateQueue(
return cycles == 0;
}
template <class Key, class HashFcn>
template <class ForwardIterator>
bool MPHTable<Key, HashFcn>::Mapping(
ForwardIterator begin, ForwardIterator end,
vector<Edge>* edges, vector<cmph_uint32> queue) {
int cycles = 0;
TriGraph graph(m, n);
for (ForwardIterator it = begin; it != end; ++it) {
cmph_uint32 h[3];
for (int i = 0; i < 3; ++i) h[i] = hash_function_[i](*it);
cmph_uint32 v0 = h[0] % r_;
cmph_uint32 v1 = h[1] % r_ + r_;
cmph_uint32 v2 = h[2] % r_ + (r_ << 1);
graph.AddEdge(Edge(v0, v1, v2));
}
if (GenerateQueue(&graph, queue)) {
graph.ExtractEdgesAndClear(edges);
return true;
}
return false;
}
template <class Key, class HashFcn>
void MPHTable<Key, HashFcn>::Assigning(
const vector<Edge>& edges, const vector<cmph_uint32>& queue) {
void MPHTable::Assigning(
const vector<TriGraph::Edge>& edges, const vector<cmph_uint32>& queue) {
cmph_uint32 nedges = n_;
cmph_uint32 current_edge = 0;
vector<bool> marked_vertices(nedges + 1);
// TODO(davi) use half nibbles instead
// vector<cmph_uint8> g(static_cast<cmph_uint32>(ceil(nedges / 4.0)),
// std::numerical_limits<cmph_uint8>::max());
static const cmph_uint8 kUnassigned = 3;
vector<cmph_uint8>(nedges, kUnassigned).swap(g_);
// Initialize vector of half nibbles with all bits set.
vector<cmph_uint8>(nedges, std::numeric_limits<cmph_uint8>::max()).swap(g_);
for (int i = nedges - 1; i + 1 >= 1; --i) {
current_edge = queue[i];
const TriGraph::Edge& e = edges[current_edge];
if (!marked_vertices[e[0]]) {
if (!marked_vertices[e[1]]) {
g_[e[1]] = kUnassigned;
set_2bit_value(&g_, e[1], kUnassigned);
marked_vertices[e[1]] = true;
}
if (!marked_vertices[e[2]]) {
g_[e[2]] = kUnassigned;
set_2bit_value(&g_, e[2], kUnassigned);
marked_vertices[e[2]] = true;
}
g_[e[0]] = (6 - g_[e[1]] + g_[e2]) % 3;
set_2bit_value(&g_, e[0], (6 - (get_2bit_value(g_, e[1]) + get_2bit_value(g_, e[2]))) % 3);
marked_vertices[e[0]] = true;
} else if (!marked_vertices[e[1]])) {
if (!marked_vertices[e[2]])) {
g_[e[2]] = kUnassigned;
} else if (!marked_vertices[e[1]]) {
if (!marked_vertices[e[2]]) {
set_2bit_value(&g_, e[2], kUnassigned);
marked_vertices[e[2]] = true;
}
g_[e[1]] = 7 - (g_[e[0]] + g_[e[2]]) % 3;
set_2bit_value(&g_, e[1], (7 - (get_2bit_value(g_, e[0]) + get_2bit_value(g_, e[2]))) % 3);
marked_vertices[e[1]] = true;
} else {
g_[e[2]] = (8 - g_[e[0]] + g_[e[1]]) % 3;
set_2bit_value(&g_, e[2], (8 - (get_2bit_value(g_, e[0]) + get_2bit_value(g_, e[1]))) % 3);
marked_vertices[e[2]] = true;
}
}
}
// table used for looking up the number of assigned vertices to a 8-bit integer
static cmph_uint8 kBdzLookupTable[] =
{
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
4, 4, 4, 3, 4, 4, 4, 3, 4, 4, 4, 3, 3, 3, 3, 2,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
3, 3, 3, 2, 3, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1,
2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 0
};
template <class Key, class HashFcn>
void MPHTable<Key, HashFcn>::Ranking() {
cmph_uint32 nbytes_total = static_cast<cmph_uint32>(ceil(st->n / 4.0));
void MPHTable::Ranking() {
cmph_uint32 nbytes_total = static_cast<cmph_uint32>(ceil(n_ / 4.0));
cmph_uint32 size = k_ >> 2U;
ranktablesize = static_cast<cmph_uint32>(ceil(n_ / static_cast<double>(k_)));
// TODO(davi) Change swap of member classes for resize + memset to avoid fragmentation
cmph_uint32 ranktablesize = static_cast<cmph_uint32>(
ceil(n_ / static_cast<double>(k_)));
// TODO(davi) Change swap of member classes for resize + memset to avoid
// fragmentation
vector<cmph_uint32> (ranktablesize).swap(ranktable_);;
cmph_uint32 offset = 0;
cmph_uint32 count = 0;
cmph_uint32 i = 0;
while (1) {
if (i == ranktable.size()) break;
if (i == ranktable_.size()) break;
cmph_uint32 nbytes = size < nbytes_total ? size : nbytes_total;
for (j = 0; j < nbytes; ++j) count += kBdzLookupTable[g_[offset + j]];
for (cmph_uint32 j = 0; j < nbytes; ++j) count += kBdzLookupTable[g_[offset + j]];
ranktable_[i] = count;
offset += nbytes;
nbytes_total -= size;
@ -177,36 +140,32 @@ void MPHTable<Key, HashFcn>::Ranking() {
}
}
template <class Key, class HashFcn>
cmph_uint32 MPHTable<Key, HashFcn>::Search(const key_type& key) const {
cmph_uint32 vertex;
cmph_uint32 MPHTable::Search(const key_type& key) const {
cmph_uint32 h[3];
for (int i = 0; i < 3; ++i) h[i] = hash_function_[i](key);
h[0] = h[0] % st->r;
h[1] = h[1] % st->r + st->r;
h[2] = h[2] % st->r + (st->r << 1);
cmph_uint32 vertex = h[(h[g_[h[0]] + g_[h[1]] + g_[h[2]]) % 3];
return Rank(st->b, st->ranktable, vertex);
h[0] = h[0] % r_;
h[1] = h[1] % r_ + r_;
h[2] = h[2] % r_ + (r_ << 1);
cmph_uint32 vertex = h[(g_[h[0]] + g_[h[1]] + g_[h[2]]) % 3];
return Rank(vertex);
}
template <class Key, class HashFcn>
cmph_uint32 MPHTable<Key, HashFcn>::Rank(cmph_uint32 vertex) const {
cmph_uint32 MPHTable::Rank(cmph_uint32 vertex) const {
cmph_uint32 index = vertex >> b_;
cmph_uint32 base_rank = ranktable_[index];
cmph_uint32 beg_idx_v = index << b;
cmph_uint32 beg_idx_b = index >> 2
cmph_uint32 end_idx_b = index >> 2
cmph_uint32 beg_idx_v = index << b_;
cmph_uint32 beg_idx_b = index >> 2;
cmph_uint32 end_idx_b = index >> 2;
while (beg_idx_b < end_idx_b) base_rank += kBdzLookupTable[g_[beg_idx_b++]];
beg_idx_v = beg_idx_b << 2;
while (beg_idx_v < vertex) {
if (g_[beg_idx_v) != kUnassigned) ++base_rank;
if (g_[beg_idx_v] != kUnassigned) ++base_rank;
++beg_idx_v;
}
return base_rank;
}
template <class Key, class HashFcn>
cmph_uint32 MPHTable<Key, HashFcn>::index(const key_type& key) const {
cmph_uint32 MPHTable::index(const key_type& key) const {
return Search(key);
}

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@ -3,21 +3,29 @@
// Minimal perfect hash abstraction implementing the BDZ algorithm
#include <cmath>
#include <vector>
#include <iostream>
using std::cerr;
using std::endl;
#include "randomly_seeded_hash.h"
#include "stringpiece.h"
#include "trigraph.h"
namespace cxxmph {
template <class Key, class NewRandomlySeededHashFcn = RandomlySeededMurmur2>
class MPHTable {
public:
typedef Key key_type;
typedef NewRandomlySeededHashFcn hasher;
// This class could be a template for both key type and hash function, but we
// chose to go with simplicity.
typedef StringPiece key_type;
typedef RandomlySeededHashFunction<Murmur2StringPiece> hasher_type;
MPHTable(double c = 1.23, cmph_uint8 b = 7) : c_(c), b_(b) { }
~MPHTable();
~MPHTable() {}
template <class ForwardIterator>
bool Reset(ForwardIterator begin, ForwardIterator end);
@ -26,21 +34,23 @@ class MPHTable {
private:
template <class ForwardIterator>
bool Mapping(ForwardIterator begin, ForwardIterator end,
vector<Edge>* edges, vector<cmph_uint32> queue);
bool GenerateQueue(TriGraph* graph, vector<cmph_uint32>* queue);
void Assigning(TriGraph* graph_builder, Queue* queue);
void Ranking(TriGraph* graph_builder, Queue* queue);
cmph_uint32 Search(const StringPiece& key);
cmph_uint32 Rank(const StringPiece& key);
std::vector<TriGraph::Edge>* edges,
std::vector<cmph_uint32>* queue);
bool GenerateQueue(TriGraph* graph, std::vector<cmph_uint32>* queue);
void Assigning(const std::vector<TriGraph::Edge>& edges,
const std::vector<cmph_uint32>& queue);
void Ranking();
cmph_uint32 Search(const key_type& key) const;
cmph_uint32 Rank(cmph_uint32 vertex) const;
// Algorithm parameters
cmph_uint8 b_; // Number of bits of the kth index in the ranktable
double c_; // Number of bits per key (? is it right)
cmph_uint8 b_; // Number of bits of the kth index in the ranktable
// Values used during generation
cmph_uint32 m_; // edges count
cmph_uint32 n_; // vertex count
cmph_uint32 k_ // kth index in ranktable, $k = log_2(n=3r)\varepsilon$
cmph_uint32 k_; // kth index in ranktable, $k = log_2(n=3r)\varepsilon$
// Values used during search
@ -52,10 +62,59 @@ class MPHTable {
std::vector<cmph_uint32> ranktable_;
// The selected hash function triplet for finding the edges in the minimal
// perfect hash function graph.
hasher hash_function_[3];
hasher_type hash_function_[3];
};
// Template method needs to go in the header file.
template <class ForwardIterator>
bool MPHTable::Reset(ForwardIterator begin, ForwardIterator end) {
m_ = end - begin;
r_ = static_cast<cmph_uint32>(ceil((c_*m_)/3));
if ((r_ % 2) == 0) r_ += 1;
n_ = 3*r_;
k_ = 1U << b_;
cerr << "m " << m_ << " n " << n_ << " r " << r_ << endl;
int iterations = 1000;
std::vector<TriGraph::Edge> edges;
std::vector<cmph_uint32> queue;
while (1) {
cerr << "Iterations missing: " << iterations << endl;
for (int i = 0; i < 3; ++i) hash_function_[i] = hasher_type();
if (Mapping(begin, end, &edges, &queue)) break;
else --iterations;
if (iterations == 0) break;
}
if (iterations == 0) return false;
Assigning(edges, queue);
std::vector<TriGraph::Edge>().swap(edges);
Ranking();
return true;
}
template <class ForwardIterator>
bool MPHTable::Mapping(
ForwardIterator begin, ForwardIterator end,
std::vector<TriGraph::Edge>* edges, std::vector<cmph_uint32>* queue) {
TriGraph graph(n_, m_);
for (ForwardIterator it = begin; it != end; ++it) {
cmph_uint32 h[3];
for (int i = 0; i < 3; ++i) h[i] = hash_function_[i](*it);
cmph_uint32 v0 = h[0] % r_;
cmph_uint32 v1 = h[1] % r_ + r_;
cmph_uint32 v2 = h[2] % r_ + (r_ << 1);
cerr << "Key: " << *it << " vertex " << it - begin << " (" << v0 << "," << v1 << "," << v2 << ")" << endl;
graph.AddEdge(TriGraph::Edge(v0, v1, v2));
}
if (GenerateQueue(&graph, queue)) {
graph.ExtractEdgesAndClear(edges);
return true;
}
return false;
}
} // namespace cxxmph
#define // __CXXMPH_MPHTABLE_H__
#endif // __CXXMPH_MPHTABLE_H__

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@ -1,22 +1,30 @@
#include <cassert>
#include <string>
#include <vector>
#include "mphtable.h"
using std::string;
using std::vector;
using cxxmph::MPHTable;
int main(int argc, char** argv) {
vector<int> keys;
keys.push_back(10);
keys.push_back(4);
keys.push_back(3);
vector<string> keys;
keys.push_back("davi");
keys.push_back("paulo");
keys.push_back("joao");
keys.push_back("maria");
keys.push_back("bruno");
MPHTable<int> mphtable;
MPHTable mphtable;
assert(mphtable.Reset(keys.begin(), keys.end()));
vector<int> ids;
for (int i = 0; i < keys.size(); ++i) ids.push_back(mphtable.index(keys[i]));
for (vector<int>::size_type i = 0; i < keys.size(); ++i) {
ids.push_back(mphtable.index(keys[i]));
cerr << " " << *(ids.end() - 1);
}
cerr << endl;
sort(ids.begin(), ids.end());
for (int i = 0; i < ids.size(); ++i) assert(ids[i] == i);
for (vector<int>::size_type i = 0; i < ids.size(); ++i) assert(ids[i] == static_cast<vector<int>::value_type>(i));
}

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@ -8,17 +8,35 @@
#include "../src/cmph_types.h"
#include "MurmurHash2.h"
#include "stringpiece.h"
namespace cxxmph {
struct RandomlySeededMurmur2 {
template <class HashFun>
struct RandomlySeededHashFunction { };
class Murmur2StringPiece { };
class Murmur2Pod { };
template <>
struct RandomlySeededHashFunction<Murmur2StringPiece> {
RandomlySeededHashFunction() : seed(random()) { }
cmph_uint32 operator()(const StringPiece& key) {
cmph_uint32 operator()(const StringPiece& key) const {
return MurmurHash2(key.data(), key.length(), seed);
}
cmph_uint32 seed;
};
template<>
struct RandomlySeededHashFunction<Murmur2Pod> {
RandomlySeededHashFunction() : seed(random()) { }
template<class Key>
cmph_uint32 operator()(const Key& key) const {
return MurmurHash2(&key, sizeof(key), seed);
}
cmph_uint32 seed;
};
} // namespace cxxmph
#endif // __CXXMPH_RANDOMLY_SEEDED_HASH__

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@ -1,8 +1,11 @@
#include <cassert>
#include <limits>
#include <iostream>
#include "trigraph.h"
using std::cerr;
using std::endl;
using std::vector;
namespace {
@ -11,9 +14,10 @@ static const cmph_uint8 kInvalidEdge = std::numeric_limits<cmph_uint8>::max();
namespace cxxmph {
TriGraph::TriGraph(cmph_uint32 nedges, cmph_uint32 nvertices)
TriGraph::TriGraph(cmph_uint32 nvertices, cmph_uint32 nedges)
: nedges_(0),
edges_(nedges),
next_edge_(nedges),
first_edge_(nvertices, kInvalidEdge),
vertex_degree_(nvertices, 0) { }
@ -26,6 +30,12 @@ void TriGraph::ExtractEdgesAndClear(vector<Edge>* edges) {
}
void TriGraph::AddEdge(const Edge& edge) {
edges_[nedges_] = edge;
assert(first_edge_.size() > edge[0]);
assert(first_edge_.size() > edge[1]);
assert(first_edge_.size() > edge[0]);
assert(first_edge_.size() > edge[1]);
assert(first_edge_.size() > edge[2]);
assert(next_edge_.size() > nedges_);
next_edge_[nedges_] = Edge(
first_edge_[edge[0]], first_edge_[edge[1]], first_edge_[edge[2]]);
first_edge_[edge[0]] = first_edge_[edge[1]] = first_edge_[edge[2]] = nedges_;
@ -36,7 +46,7 @@ void TriGraph::AddEdge(const Edge& edge) {
}
void TriGraph::RemoveEdge(cmph_uint32 current_edge) {
cmph_uint32 vertex, edge1, edge2;
cerr << "Removing edge " << current_edge << " from " << nedges_ << " existing edges " << endl;
for (int i = 0; i < 3; ++i) {
cmph_uint32 vertex = edges_[current_edge][i];
cmph_uint32 edge1 = first_edge_[vertex];

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@ -14,9 +14,14 @@
namespace cxxmph {
class TriGraph {
public:
struct Edge {
Edge() { }
Edge(cmph_uint32 v0, cmph_uint32 v1, cmph_uint32 v2);
Edge(cmph_uint32 v0, cmph_uint32 v1, cmph_uint32 v2) {
vertices[0] = v0;
vertices[1] = v1;
vertices[2] = v2;
}
cmph_uint32& operator[](cmph_uint8 v) { return vertices[v]; }
const cmph_uint32& operator[](cmph_uint8 v) const { return vertices[v]; }
cmph_uint32 vertices[3];