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gconvert.patch
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gconvert.patch
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Only in gconvert: Gconvert
diff -ur gconvert_clean/Gconvert.cpp gconvert/Gconvert.cpp
--- gconvert_clean/Gconvert.cpp 2005-11-30 17:48:52.000000000 +0100
+++ gconvert/Gconvert.cpp 2009-12-03 16:31:25.000000000 +0100
@@ -79,7 +79,7 @@
bool quiet = false;
char* output_file = 0;
char* input_file = 0;
- char* delimiters = " \t";
+ const char* delimiters = " \t";
Format input_format = ADJACENCY_EDGE_LIST;
Format output_format = ADJACENCY_EDGE_LIST;
Multi_edge_policy multi_edge_policy = ADD;
diff -ur gconvert_clean/graph.cpp gconvert/graph.cpp
--- gconvert_clean/graph.cpp 2005-11-30 16:40:58.000000000 +0100
+++ gconvert/graph.cpp 2009-12-03 16:33:28.000000000 +0100
@@ -1,626 +1,627 @@
-// File: graph.cpp
-//-----------------------------------------------------------------------------
-// Gconvert v0.2 -- A simple tool to convert different graph formats.
-// Copyright (C) 2004-2005 Pascal Pons.
-//
-// This program 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 2 of the License, or
-// (at your option) any later version.
-//
-// This program 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 this program; if not, write to the Free Software
-// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-//-----------------------------------------------------------------------------
-// Author : Pascal Pons
-// Email : [email protected]
-// Web page : http://liafa.jussieu.fr/~pons/
-// Location : Paris, France
-// Time : December 2005
-//-----------------------------------------------------------------------------
-// see readme.txt for more details
-
-#include "graph.h"
-#include <cmath>
-#include <vector>
-#include <map>
-
-using namespace std;
-
-Graph::Graph(Format _input_format, Format _output_format, bool _output_real_name, Multi_edge_policy _multi_edge_policy, float _output_time, float _caracteristic_time, const char* _delimiters, bool _quiet):
- input_format(_input_format),
- output_format(_output_format),
- output_real_name(_output_real_name),
- multi_edge_policy(_multi_edge_policy),
- output_time(_output_time),
- caracteristic_time(_caracteristic_time),
- delimiters(_delimiters),
- quiet(_quiet),
- components(0),
- nb_vertices(0) {
-
- Vertices_name::G = this;
- size_t pos = 0;
- while(pos != string::npos) {
- pos = delimiters.find("\\t", 0);
- if(pos != string::npos) {
- delimiters.erase(pos, 2);
- delimiters.insert(pos, "\t");
- }
- }
- Vertex::policy = multi_edge_policy;
- Vertex::output_time = output_time;
- Vertex::caracteristic_time = caracteristic_time;
-
- if((output_format == EDGE_LIST || output_format == WEIGHTED_EDGE_LIST || output_format == ADJACENCY_EDGE_LIST || output_format == DYNAMIC_EDGE_LIST || output_format == DYNAMIC_WEIGHTED_EDGE_LIST)) {
- if (input_format == ARC_LIST) input_format = EDGE_LIST;
- if (input_format == DYNAMIC_ARC_LIST) input_format = DYNAMIC_EDGE_LIST;
- if (input_format == WEIGHTED_ARC_LIST) input_format = WEIGHTED_EDGE_LIST;
- if (input_format == DYNAMIC_WEIGHTED_ARC_LIST) input_format = DYNAMIC_WEIGHTED_EDGE_LIST;
- if (input_format == ADJACENCY_ARC_LIST) input_format = ADJACENCY_EDGE_LIST;
- }
-}
-
-Graph::~Graph() {
- if(components) delete[] components;
-}
-
-void Graph::add_arc(unsigned int v1, unsigned int v2, float w, float t) {
- switch(multi_edge_policy) {
- case ADD:
- if (t <= output_time && t >= output_time - caracteristic_time) {
- neighbor& n = vertices[v1][v2];
- n.w += w;
- n.t = t;
- }
- break;
- case MULTI:
- if (t <= output_time && t >= output_time - caracteristic_time) {
- neighbor& n = vertices[v1][v2];
- n.w = w;
- n.t = t;
- }
- break;
- case ADD_EXP:
- if (t <= output_time) {
- neighbor& n = vertices[v1][v2];
- n.w += w*exp(-log(2.)*(output_time-t)/caracteristic_time);
- n.t = t;
- }
- break;
- case ADD_LIN:
- if (t <= output_time && t >= output_time - caracteristic_time) {
- neighbor& n = vertices[v1][v2];
- n.w += w*(1.-(output_time-t)/caracteristic_time);
- n.t = t;
- }
- }
-}
-
-void Graph::add_edge(unsigned int v1, unsigned int v2, float w, float t) {
- add_arc(v1,v2,w,t);
- if(v1 != v2) add_arc(v2,v1,w,t);
-}
-
-ostream& operator<<(ostream& stream, Graph& G) {
-
- int* new_number = 0;
- if(G.components && !G.output_real_name) {
- new_number = new int[G.nb_vertices];
- int n = 0;
- for(unsigned int i = 0; i < G.nb_vertices; i++)
- if(G.components[i] == 0) new_number[i] = n++;
- else new_number[i] = -1;
- }
-
- if(G.output_format == EDGE_LIST || G.output_format == WEIGHTED_EDGE_LIST || G.output_format == ARC_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
- for(unsigned int i = 0; i < G.nb_vertices; ++i)
- if(!G.components || !G.components[i]) {
- neighbor* l = G.vertices[i].list();
- for(unsigned int j = 0; j < G.vertices[i].degree; ++j)
- if(G.output_format == ARC_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST || l[j].v >= i) {
-
- if(G.output_real_name)
- stream << G.names.name(i) << G.delimiters[0] << G.names.name(l[j].v);
- else {
- if(new_number) stream << new_number[i] << G.delimiters[0] << new_number[l[j].v];
- else stream << i << G.delimiters[0] << l[j].v;
- }
-
- if(G.output_format == DYNAMIC_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
- stream << G.delimiters[0] << l[j].t;
-
- if(G.output_format == WEIGHTED_EDGE_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
- stream << G.delimiters[0] << l[j].w;
-
- stream << endl;
- }
- delete[] l;
- }
-
- if(G.output_format == ADJACENCY_EDGE_LIST || G.output_format == ADJACENCY_ARC_LIST)
- for(unsigned int i = 0; i < G.nb_vertices; ++i)
- if(!G.components || !G.components[i]) {
- if(G.output_real_name)
- stream << G.names.name(i);
- else {
- if(new_number) stream << new_number[i];
- else stream << i;
- }
- neighbor* l = G.vertices[i].list();
- for(unsigned int j = 0; j < G.vertices[i].degree; ++j) {
- if(G.output_real_name)
- stream << G.delimiters[0] << G.names.name(l[j].v);
- else {
- if(new_number) stream << G.delimiters[0] << new_number[l[j].v];
- else stream << G.delimiters[0] << l[j].v;
- }
- }
- delete[] l;
- stream << endl;
- }
-
- if(new_number) delete[] new_number;
-
- return stream;
-}
-
-ostream& operator<<(ostream& stream, Vertices_name& names) {
-
- int* new_number = 0;
- if(names.G->components) {
- new_number = new int[names.G->nb_vertices];
- int n = 0;
- for(unsigned int i = 0; i < names.G->nb_vertices; i++)
- if(names.G->components[i] == 0) new_number[i] = n++;
- else new_number[i] = -1;
- }
-
- for(unsigned int i = 0; i < names.nb_vertices; ++i)
- if(!names.G->components || !names.G->components[i]) {
- if(new_number)
- stream << new_number[i] << " " << names.name(i) << endl;
- else
- stream << i << " " << names.name(i) << endl;
- }
-
- if(new_number) delete[] new_number;
- return stream;
-}
-
-istream& operator>>(istream& stream, Graph& G) {
-
- vector<unsigned int*> V;
- vector<float> W;
- vector<float> T;
-
- vector<string> line;
- unsigned long nb_line = 0;
-
- while (!stream.eof()) { // loop for each line of the file
- nb_line++;
- string str;
- getline(stream, str);
-// if(str == ".") break; // end of the graph
- if(str.length() == 0) continue; // an empty line
- if(str[0] == '#') continue; // a comment line
-
- line.clear();
- size_t pos = 0;
- while(pos < str.length()) {
- size_t next = str.find_first_of(G.delimiters, pos);
- if(next == string::npos) {
- line.push_back(str.substr(pos));
- pos = str.length();
- }
- else {
- if(next - pos > 0) line.push_back(str.substr(pos, next-pos));
- pos = next+1;
- }
- }
- if(line.size() == 0) continue;
-
-// verify the input format
- if(line.size() == 1) {
- if(!G.quiet) cerr << "Error -- line " << nb_line << " : only one vertex" << endl << str << endl;
- exit(0);
- }
-
- if(G.input_format == EDGE_LIST || G.input_format == ARC_LIST)
- if(line.size() > 2 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than two vertices (lasts vertices are ignored)" << endl << str << endl;
-
- if(G.input_format == WEIGHTED_EDGE_LIST || G.input_format == WEIGHTED_ARC_LIST) {
- if(line.size() > 3 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
-
- float w;
- if(line.size() == 2) {
- if(!G.quiet) cerr << "Warning -- line " << nb_line << " : no weight (default weight 1.0 is used)" << endl << str << endl;
- w = 1.;
- }
- else w = atof(line[2].c_str());
- if(w == 0.) {
- cerr << "Error -- line " << nb_line << " : invalid weight" << endl << str << endl;
- exit(0);
- }
- W.push_back(w);
- }
-
- if(G.input_format == DYNAMIC_EDGE_LIST || G.input_format == DYNAMIC_ARC_LIST) {
- if(line.size() > 3 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
-
- float t;
- if(line.size() == 2) {
- cerr << "Error -- line " << nb_line << " : no time" << endl << str << endl;
- exit(0);
- }
- t = atof(line[2].c_str());
- if(t <= 0.) {
- cerr << "Error -- line " << nb_line << " : invalid time" << endl << str << endl;
- exit(0);
- }
- T.push_back(t);
- }
-
- if(G.input_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.input_format == DYNAMIC_WEIGHTED_ARC_LIST) {
- if(line.size() > 4 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
-
- float w;
- float t;
- if(line.size() == 2) {
- cerr << "Error -- line " << nb_line << " : no time" << endl << str << endl;
- exit(0);
- }
- t = atof(line[2].c_str());
- if(line.size() == 3) {
- if(!G.quiet) cerr << "Warning -- line " << nb_line << " : no weight (default weight 1.0 is used)" << endl << str << endl;
- w = 1.;
- }
- else w = atof(line[3].c_str());
-
- if(w == 0.) {
- cerr << "Error -- line " << nb_line << " : invalid weight" << endl << str << endl;
- exit(0);
- }
- if(t <= 0.) {
- cerr << "Error -- line " << nb_line << " : invalid time" << endl << str << endl;
- exit(0);
- }
-
- T.push_back(t);
- W.push_back(w);
- }
-
- unsigned int* l;
- if(G.input_format == WEIGHTED_EDGE_LIST || G.input_format == EDGE_LIST || G.input_format == WEIGHTED_ARC_LIST || G.input_format == ARC_LIST || G.input_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.input_format == DYNAMIC_EDGE_LIST || G.input_format == DYNAMIC_WEIGHTED_ARC_LIST || G.input_format == DYNAMIC_ARC_LIST) {
- l = new unsigned int[2];
- l[0] = G.names.number(line[0].c_str());
- l[1] = G.names.number(line[1].c_str());
- }
- else {
- l = new unsigned int[line.size()+1];
- l[0] = line.size();
- for(unsigned int i = 0; i < line.size(); ++i)
- l[i+1] = G.names.number(line[i].c_str());
- }
- V.push_back(l);
- }
-
- if(G.output_time == 0.) {
- for(unsigned int i = 0; i < T.size(); i++)
- if(T[i] > G.output_time) G.output_time = T[i];
- }
- Vertex::output_time = G.output_time;
-
- if(G.caracteristic_time == 0.) {
- for(unsigned int i = 0; i < T.size(); i++)
- if(T[i] > G.caracteristic_time) G.caracteristic_time = T[i];
- }
- Vertex::caracteristic_time = G.caracteristic_time;
-
- G.nb_vertices = G.names.nb_vertices;
- G.vertices = new Vertex[G.nb_vertices];
-
- while(!V.empty()) {
- unsigned int* l = V.back();
- switch(G.input_format) {
- case ADJACENCY_EDGE_LIST:
- for(unsigned int i = 2; i <= l[0]; ++i)
- G.add_edge(l[1], l[i], 1., 0.);
- break;
- case ADJACENCY_ARC_LIST:
- for(unsigned int i = 2; i <= l[0]; ++i)
- G.add_arc(l[1], l[i], 1., 0.);
- break;
- case EDGE_LIST:
- G.add_edge(l[0], l[1], 1., 0.);
- break;
- case ARC_LIST:
- G.add_arc(l[0], l[1], 1., 0.);
- break;
- case WEIGHTED_EDGE_LIST:
- G.add_edge(l[0], l[1], W.back(), 0.);
- W.pop_back();
- break;
- case WEIGHTED_ARC_LIST:
- G.add_arc(l[0], l[1], W.back(), 0.);
- W.pop_back();
- break;
- case DYNAMIC_EDGE_LIST:
- G.add_edge(l[0], l[1], 1., T.back());
- T.pop_back();
- break;
- case DYNAMIC_ARC_LIST:
- G.add_arc(l[0], l[1], 1., T.back());
- T.pop_back();
- break;
- case DYNAMIC_WEIGHTED_EDGE_LIST:
- G.add_edge(l[0], l[1], W.back(), T.back());
- W.pop_back();
- T.pop_back();
- break;
- case DYNAMIC_WEIGHTED_ARC_LIST:
- G.add_arc(l[0], l[1], W.back(), T.back());
- W.pop_back();
- T.pop_back();
- break;
- case CLIQUE:
- for(unsigned int i = 1; i < l[0]; ++i)
- for(unsigned int j = i+1; j <= l[0]; ++j)
- G.add_edge(l[i], l[j], 1., 0.);
- break;
- case WEIGHTED_CLIQUE:
- for(unsigned int i = 1; i < l[0]; ++i)
- for(unsigned int j = i+1; j <= l[0]; ++j)
- G.add_edge(l[i], l[j], 2./float(l[0] - 1), 0.);
- }
-
- delete[] l;
- V.pop_back();
- }
-
- return stream;
-}
-
-struct inf : public binary_function<const Graph*, const Graph*, bool>{
- bool operator()(const Graph* G1, const Graph* G2) {return G1->nb_vertices > G2->nb_vertices;}
-};
-
-
-inline unsigned long Vertices_name::hash(const char* s, unsigned int index) {
- unsigned long h = index;
- for (; *s; ++s)
- h = 5*h + *s;
- return h;
-}
-
-
-const char* Vertices_name::name(unsigned int number) {
- if(number < nb_vertices)
- return name_of_number[number];
- else return "";
-}
-
-unsigned int Vertices_name::number(const char* name) {
- for(unsigned int i = 0; ; i++) {
- unsigned long h = hash(name, i);
- unsigned int &v = number_of_name[h % hash_table_size];
- if(v != static_cast<unsigned int>(-1)) {
- if(strcmp(name, name_of_number[v])) continue;
- else return v;
- }
- else { // add a new vertex name
- if(nb_vertices == name_of_number_size) increase_name_of_number_size();
- char* c = new char[strlen(name)+1];
- strcpy(c, name);
- name_of_number[nb_vertices] = c;
- v = nb_vertices;
- nb_vertices++;
- if(2*nb_vertices > hash_table_size) increase_hash_table_size();
- return (nb_vertices-1);
- }
- }
-}
-
-void Vertices_name::increase_hash_table_size() {
- delete[] number_of_name;
- hash_table_size *= 2;
- number_of_name = new unsigned int[hash_table_size];
- memset(number_of_name, -1, hash_table_size*sizeof(unsigned int));
-
- for(unsigned int v = 0; v < nb_vertices; ++v)
- for(unsigned int i = 0;; ++i) {
- unsigned long h = hash(name_of_number[v], i);
- if(number_of_name[h % hash_table_size] == static_cast<unsigned int>(-1)) {
- number_of_name[h % hash_table_size] = v;
- break;
- }
- }
-}
-
-void Vertices_name::increase_name_of_number_size() {
- char** tmp = new char*[2*name_of_number_size];
- memcpy(tmp, name_of_number, name_of_number_size*sizeof(char*));
- name_of_number_size *= 2;
- delete[] name_of_number;
- name_of_number = tmp;
-}
-
-Graph* Vertices_name::G = 0;
-
-Vertices_name::Vertices_name() {
- nb_vertices = 0;
- name_of_number_size = 2;
- name_of_number = new char*[name_of_number_size];
- hash_table_size = 2;
- number_of_name = new unsigned int[hash_table_size];
- memset(number_of_name, -1, hash_table_size*sizeof(unsigned int));
-}
-
-Vertices_name::~Vertices_name() {
- delete[] number_of_name;
- for(unsigned int i = 0; i < nb_vertices; ++i)
- delete[] name_of_number[i];
- delete[] name_of_number;
-}
-
-Multi_edge_policy Vertex::policy = ADD;
-float Vertex::output_time = 0.;
-float Vertex::caracteristic_time = 0.;
-
-
-void Vertex::increase_size() {
- unsigned int new_size = size + size/2;
- neighbor* tmp = new neighbor[new_size];
- for(unsigned int i = 0; i < new_size; ++i) {
- tmp[i].v = static_cast<unsigned int>(-1);
- tmp[i].w = 0.;
- tmp[i].t = 0.;
- }
-
- if(policy == MULTI)
- memcpy(tmp, H, degree*sizeof(neighbor));
- else {
- for(unsigned int i = 0; i < size; ++i)
- if(H[i].v != static_cast<unsigned int>(-1)) {
- unsigned long h = H[i].v;
- int j = 0;
- while(tmp[h % new_size].v != static_cast<unsigned int>(-1))
- h = h*5 + H[i].v + (++j);
- tmp[h % new_size].v = H[i].v;
- tmp[h % new_size].w = H[i].w;
- tmp[h % new_size].t = H[i].t;
- }
- }
- size = new_size;
- delete[] H;
- H = tmp;
-}
-
-neighbor& Vertex::operator[](unsigned int n) {
- if((degree + degree/2) > size) increase_size();
- if(policy == MULTI) {
- H[degree].v = n;
- return H[degree++];
- }
-
- unsigned long h = n;
- int i = 0;
- while(H[h % size].v != static_cast<unsigned int>(-1) && H[h % size].v != n)
- h = h*5 + n + (++i);
-
- if(H[h % size].v == static_cast<unsigned int>(-1)) {
- degree++;
- H[h % size].v = n;
- }
- return H[h % size];
-}
-
-neighbor* Vertex::list() {
- neighbor* l = new neighbor[degree];
- unsigned int c = 0;
- for(unsigned int i = 0; i < size; ++i)
- if(H[i].v != static_cast<unsigned int>(-1))
- l[c++] = H[i];
- return l;
-}
-
-Vertex::Vertex() {
- size = 2;
- degree = 0;
- H = new neighbor[2];
- for(unsigned int i = 0; i < size; ++i) {
- H[i].v = static_cast<unsigned int>(-1);
- H[i].w = 0.;
- H[i].t = 0.;
- }
-}
-
-Vertex::~Vertex() {
- delete[] H;
-}
-
-
-
-void Graph::merge_components(int v1, int v2) {
- int r1 = v1;
- while(components[r1] >= 0) r1 = components[r1];
-
- int r2 = v2;
- while(components[r2] >= 0) r2 = components[r2];
-
- if(r1 == r2) return;
-
- int r;
- if(components[r1] < components[r2]) {
- components[r1] += components[r2];
- components[r2] = r1;
- r = r1;
- }
- else {
- components[r2] += components[r1];
- components[r1] = r2;
- r = r2;
- }
-
- int tmp;
- while(v1 != r1) {
- tmp = components[v1];
- components[v1] = r;
- v1 = tmp;
- }
- while(v2 != r2) {
- tmp = components[v2];
- components[v2] = r;
- v2 = tmp;
- }
- return;
-}
-
-
-void Graph::compute_components() {
- if(nb_vertices > 0x7fffffff) {
- cerr << "unable to compute connected components when the number of vertices is greater than " << 0x7fffffff << endl;
- return;
- }
-
- if(components) delete[] components;
- components = new int[nb_vertices];
-
- for(unsigned int i = 0; i < nb_vertices; i++)
- components[i] = -1;
-
- for(unsigned int i = 0; i < nb_vertices; i++)
- if(vertices[i].degree > 0) {
- neighbor* l = vertices[i].list();
- for(unsigned int j = 0; j < vertices[i].degree; j++)
- merge_components(i,l[j].v);
- delete[] l;
- }
-
- map<int, int> M;
- for(unsigned int i = 0; i < nb_vertices; i++) {
- int r = i;
- while(components[r] >= 0 && components[r] != r) r = components[r];
- components[i] = r;
- M[r]++;
- }
-
- multimap<int, int> M2;
- for(map<int,int>::iterator it = M.begin(); it != M.end(); ++it)
- M2.insert(pair<int,int>(-it->second, it->first));
-
- int n = 0;
- for(multimap<int,int>::iterator it = M2.begin(); it != M2.end(); ++it)
- M[it->second] = n++;
-
-
- for(unsigned int i = 0; i < nb_vertices; i++)
- components[i] = M[components[i]];
-
- return;
-}
+// File: graph.cpp
+//-----------------------------------------------------------------------------
+// Gconvert v0.2 -- A simple tool to convert different graph formats.
+// Copyright (C) 2004-2005 Pascal Pons.
+//
+// This program 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 2 of the License, or
+// (at your option) any later version.
+//
+// This program 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 this program; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+//-----------------------------------------------------------------------------
+// Author : Pascal Pons
+// Email : [email protected]
+// Web page : http://liafa.jussieu.fr/~pons/
+// Location : Paris, France
+// Time : December 2005
+//-----------------------------------------------------------------------------
+// see readme.txt for more details
+
+#include "graph.h"
+#include <cmath>
+#include <vector>
+#include <map>
+#include <cstring>
+
+using namespace std;
+
+Graph::Graph(Format _input_format, Format _output_format, bool _output_real_name, Multi_edge_policy _multi_edge_policy, float _output_time, float _caracteristic_time, const char* _delimiters, bool _quiet):
+ input_format(_input_format),
+ output_format(_output_format),
+ output_real_name(_output_real_name),
+ multi_edge_policy(_multi_edge_policy),
+ output_time(_output_time),
+ caracteristic_time(_caracteristic_time),
+ delimiters(_delimiters),
+ quiet(_quiet),
+ components(0),
+ nb_vertices(0) {
+
+ Vertices_name::G = this;
+ size_t pos = 0;
+ while(pos != string::npos) {
+ pos = delimiters.find("\\t", 0);
+ if(pos != string::npos) {
+ delimiters.erase(pos, 2);
+ delimiters.insert(pos, "\t");
+ }
+ }
+ Vertex::policy = multi_edge_policy;
+ Vertex::output_time = output_time;
+ Vertex::caracteristic_time = caracteristic_time;
+
+ if((output_format == EDGE_LIST || output_format == WEIGHTED_EDGE_LIST || output_format == ADJACENCY_EDGE_LIST || output_format == DYNAMIC_EDGE_LIST || output_format == DYNAMIC_WEIGHTED_EDGE_LIST)) {
+ if (input_format == ARC_LIST) input_format = EDGE_LIST;
+ if (input_format == DYNAMIC_ARC_LIST) input_format = DYNAMIC_EDGE_LIST;
+ if (input_format == WEIGHTED_ARC_LIST) input_format = WEIGHTED_EDGE_LIST;
+ if (input_format == DYNAMIC_WEIGHTED_ARC_LIST) input_format = DYNAMIC_WEIGHTED_EDGE_LIST;
+ if (input_format == ADJACENCY_ARC_LIST) input_format = ADJACENCY_EDGE_LIST;
+ }
+}
+
+Graph::~Graph() {
+ if(components) delete[] components;
+}
+
+void Graph::add_arc(unsigned int v1, unsigned int v2, float w, float t) {
+ switch(multi_edge_policy) {
+ case ADD:
+ if (t <= output_time && t >= output_time - caracteristic_time) {
+ neighbor& n = vertices[v1][v2];
+ n.w += w;
+ n.t = t;
+ }
+ break;
+ case MULTI:
+ if (t <= output_time && t >= output_time - caracteristic_time) {
+ neighbor& n = vertices[v1][v2];
+ n.w = w;
+ n.t = t;
+ }
+ break;
+ case ADD_EXP:
+ if (t <= output_time) {
+ neighbor& n = vertices[v1][v2];
+ n.w += w*exp(-log(2.)*(output_time-t)/caracteristic_time);
+ n.t = t;
+ }
+ break;
+ case ADD_LIN:
+ if (t <= output_time && t >= output_time - caracteristic_time) {
+ neighbor& n = vertices[v1][v2];
+ n.w += w*(1.-(output_time-t)/caracteristic_time);
+ n.t = t;
+ }
+ }
+}
+
+void Graph::add_edge(unsigned int v1, unsigned int v2, float w, float t) {
+ add_arc(v1,v2,w,t);
+ if(v1 != v2) add_arc(v2,v1,w,t);
+}
+
+ostream& operator<<(ostream& stream, Graph& G) {
+
+ int* new_number = 0;
+ if(G.components && !G.output_real_name) {
+ new_number = new int[G.nb_vertices];
+ int n = 0;
+ for(unsigned int i = 0; i < G.nb_vertices; i++)
+ if(G.components[i] == 0) new_number[i] = n++;
+ else new_number[i] = -1;
+ }
+
+ if(G.output_format == EDGE_LIST || G.output_format == WEIGHTED_EDGE_LIST || G.output_format == ARC_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
+ for(unsigned int i = 0; i < G.nb_vertices; ++i)
+ if(!G.components || !G.components[i]) {
+ neighbor* l = G.vertices[i].list();
+ for(unsigned int j = 0; j < G.vertices[i].degree; ++j)
+ if(G.output_format == ARC_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST || l[j].v >= i) {
+
+ if(G.output_real_name)
+ stream << G.names.name(i) << G.delimiters[0] << G.names.name(l[j].v);
+ else {
+ if(new_number) stream << new_number[i] << G.delimiters[0] << new_number[l[j].v];
+ else stream << i << G.delimiters[0] << l[j].v;
+ }
+
+ if(G.output_format == DYNAMIC_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
+ stream << G.delimiters[0] << l[j].t;
+
+ if(G.output_format == WEIGHTED_EDGE_LIST || G.output_format == WEIGHTED_ARC_LIST || G.output_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.output_format == DYNAMIC_WEIGHTED_ARC_LIST)
+ stream << G.delimiters[0] << l[j].w;
+
+ stream << endl;
+ }
+ delete[] l;
+ }
+
+ if(G.output_format == ADJACENCY_EDGE_LIST || G.output_format == ADJACENCY_ARC_LIST)
+ for(unsigned int i = 0; i < G.nb_vertices; ++i)
+ if(!G.components || !G.components[i]) {
+ if(G.output_real_name)
+ stream << G.names.name(i);
+ else {
+ if(new_number) stream << new_number[i];
+ else stream << i;
+ }
+ neighbor* l = G.vertices[i].list();
+ for(unsigned int j = 0; j < G.vertices[i].degree; ++j) {
+ if(G.output_real_name)
+ stream << G.delimiters[0] << G.names.name(l[j].v);
+ else {
+ if(new_number) stream << G.delimiters[0] << new_number[l[j].v];
+ else stream << G.delimiters[0] << l[j].v;
+ }
+ }
+ delete[] l;
+ stream << endl;
+ }
+
+ if(new_number) delete[] new_number;
+
+ return stream;
+}
+
+ostream& operator<<(ostream& stream, Vertices_name& names) {
+
+ int* new_number = 0;
+ if(names.G->components) {
+ new_number = new int[names.G->nb_vertices];
+ int n = 0;
+ for(unsigned int i = 0; i < names.G->nb_vertices; i++)
+ if(names.G->components[i] == 0) new_number[i] = n++;
+ else new_number[i] = -1;
+ }
+
+ for(unsigned int i = 0; i < names.nb_vertices; ++i)
+ if(!names.G->components || !names.G->components[i]) {
+ if(new_number)
+ stream << new_number[i] << " " << names.name(i) << endl;
+ else
+ stream << i << " " << names.name(i) << endl;
+ }
+
+ if(new_number) delete[] new_number;
+ return stream;
+}
+
+istream& operator>>(istream& stream, Graph& G) {
+
+ vector<unsigned int*> V;
+ vector<float> W;
+ vector<float> T;
+
+ vector<string> line;
+ unsigned long nb_line = 0;
+
+ while (!stream.eof()) { // loop for each line of the file
+ nb_line++;
+ string str;
+ getline(stream, str);
+// if(str == ".") break; // end of the graph
+ if(str.length() == 0) continue; // an empty line
+ if(str[0] == '#') continue; // a comment line
+
+ line.clear();
+ size_t pos = 0;
+ while(pos < str.length()) {
+ size_t next = str.find_first_of(G.delimiters, pos);
+ if(next == string::npos) {
+ line.push_back(str.substr(pos));
+ pos = str.length();
+ }
+ else {
+ if(next - pos > 0) line.push_back(str.substr(pos, next-pos));
+ pos = next+1;
+ }
+ }
+ if(line.size() == 0) continue;
+
+// verify the input format
+ if(line.size() == 1) {
+ if(!G.quiet) cerr << "Error -- line " << nb_line << " : only one vertex" << endl << str << endl;
+ exit(0);
+ }
+
+ if(G.input_format == EDGE_LIST || G.input_format == ARC_LIST)
+ if(line.size() > 2 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than two vertices (lasts vertices are ignored)" << endl << str << endl;
+
+ if(G.input_format == WEIGHTED_EDGE_LIST || G.input_format == WEIGHTED_ARC_LIST) {
+ if(line.size() > 3 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
+
+ float w;
+ if(line.size() == 2) {
+ if(!G.quiet) cerr << "Warning -- line " << nb_line << " : no weight (default weight 1.0 is used)" << endl << str << endl;
+ w = 1.;
+ }
+ else w = atof(line[2].c_str());
+ if(w == 0.) {
+ cerr << "Error -- line " << nb_line << " : invalid weight" << endl << str << endl;
+ exit(0);
+ }
+ W.push_back(w);
+ }
+
+ if(G.input_format == DYNAMIC_EDGE_LIST || G.input_format == DYNAMIC_ARC_LIST) {
+ if(line.size() > 3 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
+
+ float t;
+ if(line.size() == 2) {
+ cerr << "Error -- line " << nb_line << " : no time" << endl << str << endl;
+ exit(0);
+ }
+ t = atof(line[2].c_str());
+ if(t <= 0.) {
+ cerr << "Error -- line " << nb_line << " : invalid time" << endl << str << endl;
+ exit(0);
+ }
+ T.push_back(t);
+ }
+
+ if(G.input_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.input_format == DYNAMIC_WEIGHTED_ARC_LIST) {
+ if(line.size() > 4 && !G.quiet) cerr << "Warning -- line " << nb_line << " : more than three items" << endl << str << endl;
+
+ float w;
+ float t;
+ if(line.size() == 2) {
+ cerr << "Error -- line " << nb_line << " : no time" << endl << str << endl;
+ exit(0);
+ }
+ t = atof(line[2].c_str());
+ if(line.size() == 3) {
+ if(!G.quiet) cerr << "Warning -- line " << nb_line << " : no weight (default weight 1.0 is used)" << endl << str << endl;
+ w = 1.;
+ }
+ else w = atof(line[3].c_str());
+
+ if(w == 0.) {
+ cerr << "Error -- line " << nb_line << " : invalid weight" << endl << str << endl;
+ exit(0);
+ }
+ if(t <= 0.) {
+ cerr << "Error -- line " << nb_line << " : invalid time" << endl << str << endl;
+ exit(0);
+ }
+
+ T.push_back(t);
+ W.push_back(w);
+ }
+
+ unsigned int* l;
+ if(G.input_format == WEIGHTED_EDGE_LIST || G.input_format == EDGE_LIST || G.input_format == WEIGHTED_ARC_LIST || G.input_format == ARC_LIST || G.input_format == DYNAMIC_WEIGHTED_EDGE_LIST || G.input_format == DYNAMIC_EDGE_LIST || G.input_format == DYNAMIC_WEIGHTED_ARC_LIST || G.input_format == DYNAMIC_ARC_LIST) {
+ l = new unsigned int[2];
+ l[0] = G.names.number(line[0].c_str());
+ l[1] = G.names.number(line[1].c_str());
+ }
+ else {
+ l = new unsigned int[line.size()+1];
+ l[0] = line.size();
+ for(unsigned int i = 0; i < line.size(); ++i)
+ l[i+1] = G.names.number(line[i].c_str());
+ }
+ V.push_back(l);
+ }
+
+ if(G.output_time == 0.) {
+ for(unsigned int i = 0; i < T.size(); i++)
+ if(T[i] > G.output_time) G.output_time = T[i];
+ }
+ Vertex::output_time = G.output_time;
+
+ if(G.caracteristic_time == 0.) {
+ for(unsigned int i = 0; i < T.size(); i++)
+ if(T[i] > G.caracteristic_time) G.caracteristic_time = T[i];
+ }
+ Vertex::caracteristic_time = G.caracteristic_time;
+
+ G.nb_vertices = G.names.nb_vertices;
+ G.vertices = new Vertex[G.nb_vertices];
+
+ while(!V.empty()) {
+ unsigned int* l = V.back();
+ switch(G.input_format) {
+ case ADJACENCY_EDGE_LIST:
+ for(unsigned int i = 2; i <= l[0]; ++i)
+ G.add_edge(l[1], l[i], 1., 0.);
+ break;
+ case ADJACENCY_ARC_LIST:
+ for(unsigned int i = 2; i <= l[0]; ++i)
+ G.add_arc(l[1], l[i], 1., 0.);
+ break;
+ case EDGE_LIST:
+ G.add_edge(l[0], l[1], 1., 0.);
+ break;
+ case ARC_LIST:
+ G.add_arc(l[0], l[1], 1., 0.);
+ break;
+ case WEIGHTED_EDGE_LIST:
+ G.add_edge(l[0], l[1], W.back(), 0.);
+ W.pop_back();
+ break;
+ case WEIGHTED_ARC_LIST:
+ G.add_arc(l[0], l[1], W.back(), 0.);
+ W.pop_back();
+ break;
+ case DYNAMIC_EDGE_LIST:
+ G.add_edge(l[0], l[1], 1., T.back());
+ T.pop_back();
+ break;