int initIgraph(int *m){
igraph_t g;
igraph_matrix_t mat;
long int i, j;
igraph_matrix_init(&mat, numNodos, numNodos);
for (i=0; i<numNodos; i++) for (j=0; j<numNodos; j++) MATRIX(mat, i, j) = m[i+numNodos*j];
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_UPPER, 0, /*loops=*/ 1);
//print(&g);
FILE *stp;
stp = fopen("/home/john/git/primAlgorithm/grafo2.gml", "w");
if (stp==0) {
printf("Problema abriendo archivo de grafo\n");
return EXIT_FAILURE;
}
igraph_write_graph_gml(&g, stp, 0, "gml Test");
fclose(stp);
igraph_destroy(&g);
return EXIT_SUCCESS;
}
int main() {
igraph_t graph;
FILE *ifile = fopen("cattr_bool_bug.graphml", "r");
if (!ifile) {
printf("Cannot open input file");
return 1;
}
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_read_graph_graphml(&graph, ifile, 0);
fclose(ifile);
check_attr(&graph, 10);
igraph_to_directed(&graph, IGRAPH_TO_DIRECTED_ARBITRARY);
check_attr(&graph, 20);
if (GAB(&graph, "loops")) { return 2; }
igraph_destroy(&graph);
return 0;
}
int main() {
igraph_t g;
igraph_vector_t y;
/* turn on attribute handling */
igraph_i_set_attribute_table(&igraph_cattribute_table);
/* Create a graph, add some attributes and save it as a GraphML file */
igraph_famous(&g, "Petersen");
SETGAS(&g, "name", "Petersen's graph");
SETGAN(&g, "vertices", igraph_vcount(&g));
SETGAN(&g, "edges", igraph_ecount(&g));
igraph_vector_init_seq(&y, 1, igraph_vcount(&g));
SETVANV(&g, "id", &y);
igraph_vector_destroy(&y);
SETVAS(&g, "name", 0, "foo");
SETVAS(&g, "name", 1, "foobar");
igraph_vector_init_seq(&y, 1, igraph_ecount(&g));
SETEANV(&g, "id", &y);
igraph_vector_destroy(&y);
SETEAS(&g, "name", 0, "FOO");
SETEAS(&g, "name", 1, "FOOBAR");
igraph_write_graph_gml(&g, stdout, 0, "");
igraph_write_graph_graphml(&g, stdout);
igraph_destroy(&g);
return 0;
}
TEgraphMF::TEgraphMF() {
igraph_i_set_attribute_table(&igraph_cattribute_table);
cacheValid=false;
e=0.1;
recalculationDelay=60;
defaultBW=1;
te_thread= NULL;
}
int main() {
igraph_i_set_attribute_table(&igraph_cattribute_table);
if (test_graph_from_leda_tutorial())
return 1;
if (!IGRAPH_FINALLY_STACK_EMPTY) {
printf("Finally stack still has %d elements.\n", IGRAPH_FINALLY_STACK_SIZE());
return 4;
}
return 0;
}
int main(int argc, char* argv[]) {
if(argc != 2) {
printf("USAGE: %s path/to/file.graphml.xml\n", argv[0]);
return -1;
}
char* fileName = argv[1];
igraph_attribute_table_t* oldHandler = igraph_i_set_attribute_table(&igraph_cattribute_table);
FILE* graphFile = fopen(fileName, "r");
if(!graphFile) {
printf("error opening graph file at %s\n", fileName);
return -2;
}
igraph_t graph;
time_t start = time(NULL);
int r = igraph_read_graph_graphml(&graph, graphFile, 0);
time_t end = time(NULL);
fclose(graphFile);
if(r != IGRAPH_SUCCESS) {
printf("error loading graph file at %s\n", fileName);
r = -3;
} else {
printf("successfully loaded graph file at %s in %li seconds\n", fileName, (long int)(end-start));
r = 0;
}
printf("graph has %li vertices and %li edges\n", (long int)igraph_vcount(&graph), (long int)igraph_ecount(&graph));
igraph_integer_t largestCliqueSize = 0;
start = time(NULL);
r = igraph_clique_number(&graph, &largestCliqueSize);
end = time(NULL);
if(r != IGRAPH_SUCCESS) {
printf("error computing igraph_clique_number\n");
r = -4;
} else {
printf("igraph_clique_number = %i in %li seconds\n", (int) largestCliqueSize, (long int)(end-start));
r = 0;
}
start = time(NULL);
igraph_destroy(&graph);
end = time(NULL);
printf("igraph_destroy finished in %li seconds\n", (long int)end-start);
return r;
}
int main() {
igraph_t g;
igraph_strvector_t names;
igraph_i_set_attribute_table(&igraph_cattribute_table);
/* save a simple ring graph */
igraph_ring(&g, 10, IGRAPH_DIRECTED, 0 /* mutual */, 1 /* circular */);
igraph_write_graph_pajek(&g, stdout);
/* add some vertex attributes */
igraph_strvector_init(&names, 0);
igraph_strvector_add(&names, "A");
igraph_strvector_add(&names, "B");
igraph_strvector_add(&names, "C");
igraph_strvector_add(&names, "D");
igraph_strvector_add(&names, "E");
igraph_strvector_add(&names, "F");
igraph_strvector_add(&names, "G");
igraph_strvector_add(&names, "H");
igraph_strvector_add(&names, "I");
igraph_strvector_add(&names, "J");
SETVASV(&g, "id", &names);
igraph_strvector_destroy(&names);
/* save the graph with vertex names */
igraph_write_graph_pajek(&g, stdout);
igraph_strvector_init(&names, 0);
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "escaping spaces");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "escaping \\backslashes\\");
igraph_strvector_add(&names, "square");
igraph_strvector_add(&names, "escaping \"quotes\"");
SETVASV(&g, "shape", &names);
igraph_strvector_destroy(&names);
/* save the graph with escaped shapes */
igraph_write_graph_pajek(&g, stdout);
/* destroy the graph */
igraph_destroy(&g);
return 0;
}
int main()
{
igraph_t g;
/* init the attributes in igraph */
igraph_i_set_attribute_table(&igraph_cattribute_table);
/* read a graph on stdin */
assert(ggen_read_graph(&g,stdin) == 0);
/* output it to stdout */
assert(ggen_write_graph(&g,stdout) == 0);
return 0;
}
int GraphRepresentation::buildIGraphTopology() {
int source_vertex_id, destination_vertex_id;
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_empty(&igraph, 0, true);
//cout << "iGraph: number of nodes: " << dm->number_of_nodes << endl;
//cout << "iGraph: number number_of_connections nodes: " << dm->number_of_connections << endl;
for (int i = 0; i < dm->network_nodes.size(); i++) {
NetworkNode *nn = dm->network_nodes[i];
for (int j = 0; j < nn->connections.size(); j++) {
NetworkConnection *nc = nn->connections[j];
map <string, int>::iterator index_it;
/*find that node - if exists*/
index_it = reverse_node_index.find(nc->src_label);
/*check if the source node exists in the reverse index*/
if (index_it == reverse_node_index.end()) {
/*it does not exist...add it*/
source_vertex_id = igraph_vcount(&igraph);
igraph_add_vertices(&igraph, 1, 0);
reverse_node_index.insert(pair<string, int>(nc->src_label, source_vertex_id));
igraph_cattribute_VAS_set(&igraph, "NODEID", source_vertex_id, nc->src_label.c_str());
//cout << "added node " << nc->src_label << " in the igraph" << endl;
} else {
source_vertex_id = (*index_it).second;
}
index_it = reverse_node_index.find(nc->dst_label);
/*check if the destination node exists in the reverse index*/
if (index_it == reverse_node_index.end()) {
/*it does not exist...add it*/
destination_vertex_id = igraph_vcount(&igraph);
igraph_add_vertices(&igraph, 1, 0);
reverse_node_index.insert(pair<string, int>(nc->dst_label, destination_vertex_id));
igraph_cattribute_VAS_set(&igraph, "NODEID", destination_vertex_id, nc->dst_label.c_str());
//cout << "added node " << nc->dst_label << " in the igraph" << endl;
} else {
destination_vertex_id = (*index_it).second;
}
/*add an edge in the graph*/
igraph_add_edge(&igraph, source_vertex_id, destination_vertex_id);
igraph_cattribute_EAS_set(&igraph, "LID", igraph_ecount(&igraph) - 1, nc->LID.to_string().c_str());
reverse_edge_index.insert(pair<string, int>(nc->LID.to_string(), igraph_ecount(&igraph) - 1));
}
}
for (int i = 0; i < dm->network_nodes.size(); i++) {
NetworkNode *nn = dm->network_nodes[i];
igraph_cattribute_VAS_set(&igraph, "iLID", i, nn->iLid.to_string().c_str());
}
}
int main() {
igraph_t graph;
igraph_t full, tree;
igraph_hrg_t hrg;
igraph_t dendrogram;
// int i, j;
// igraph_vector_t neis;
igraph_rng_seed(igraph_rng_default(), 42);
// We need attributes
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_full(&full, 10, /*directed=*/ 0, /*loops=*/ 0);
igraph_tree(&tree, 15, /*children=*/ 2, /*type=*/ IGRAPH_TREE_UNDIRECTED);
igraph_disjoint_union(&graph, &full, &tree);
igraph_add_edge(&graph, 0, 10);
igraph_destroy(&full);
igraph_destroy(&tree);
// Fit
igraph_hrg_init(&hrg, igraph_vcount(&graph));
igraph_hrg_fit(&graph, &hrg, /*start=*/ 0, /*steps=*/ 0);
// Create a graph from it
igraph_hrg_dendrogram(&dendrogram, &hrg);
// Print the tree, with labels
// igraph_vector_init(&neis, 0);
// for (i=0; i<igraph_vcount(&graph)-1; i++) {
// printf("Vertex # %2i, ", (int) (i+igraph_vcount(&graph)));
// igraph_neighbors(&dendrogram, &neis, i+igraph_vcount(&graph), IGRAPH_OUT);
// printf("left: # %2i, right: # %2i, ", (int) VECTOR(neis)[0],
// (int) VECTOR(neis)[1]);
// printf("prob: %6.2g\n",
// VAN(&dendrogram, "probability", i+igraph_vcount(&graph)));
// }
// igraph_vector_destroy(&neis);
igraph_destroy(&dendrogram);
igraph_hrg_destroy(&hrg);
igraph_destroy(&graph);
return 0;
}
int* readGrafo(){
int *grafo;
igraph_matrix_t gMatrix;
igraph_t g;
igraph_i_set_attribute_table(&igraph_cattribute_table);
FILE *ifile;
ifile=fopen("/home/john/git/primAlgorithm/celegansneural.gml"/*"/home/john/git/primAlgorithm/grafo.gml"*/, "r");
if (ifile==0) {
printf("Problema abriendo archivo de grafo\n");
return NULL;
}
igraph_read_graph_gml(&g, ifile);
fclose(ifile);
numNodos = igraph_vcount(&g);
grafo = malloc(numNodos*numNodos*sizeof(int));
igraph_matrix_init(&gMatrix,numNodos,numNodos);
igraph_get_adjacency(&g,&gMatrix,IGRAPH_GET_ADJACENCY_BOTH,1);
igraph_vector_t el;
int ii, jj, n;
igraph_vector_init(&el, 0);
igraph_get_edgelist(&g, &el, 0);
n = igraph_ecount(&g);
memset(grafo,INT_MAX2,numNodos*numNodos*sizeof(int));
for (ii=0, jj=0; ii<n; ii++, jj+=2) {
grafo[((long)VECTOR(el)[jj])+numNodos*((long)VECTOR(el)[jj+1])] = (int)EAN(&g, "weight", ii);
grafo[((long)VECTOR(el)[jj+1])+numNodos*((long)VECTOR(el)[jj])] = (int)EAN(&g, "weight", ii);
}
printf("\nNumero de nodos %d",numNodos);
igraph_vector_destroy(&el);
igraph_destroy(&g);
return grafo;
}
int main() {
igraph_t g;
FILE *ifile;
int i, n;
/* turn on attribute handling */
igraph_i_set_attribute_table(&igraph_cattribute_table);
ifile=fopen("bipartite.net", "r");
if (!ifile) { return 5; }
igraph_read_graph_pajek(&g, ifile);
fclose(ifile);
if (igraph_vcount(&g) != 13 || igraph_ecount(&g) != 11 ||
igraph_is_directed(&g)) { return 6; }
for (i=0, n=igraph_vcount(&g); i<n; i++) {
printf("%i ", (int) VAN(&g, "type", i));
}
igraph_destroy(&g);
return 0;
}
static void
fit_rvine_trees(igraph_t **trees,
const gsl_matrix *data,
const dml_vine_weight_t weight,
const dml_vine_trunc_t trunc,
const dml_copula_indeptest_t indeptest,
const double indeptest_level,
const dml_copula_type_t *types,
const size_t types_size,
const dml_copula_select_t select,
const gsl_rng *rng)
{
size_t m, n;
igraph_t *graph;
igraph_vector_t *graph_weight;
dml_copula_t *copula;
gsl_vector *x;
igraph_integer_t e; // Edge id.
igraph_integer_t a, aa, ab, b, ba, bb; // Vertex id.
gsl_vector *u = NULL, *v = NULL;
igraph_integer_t Cea, Ceb;
gsl_vector_short *Ue, *Ua, *Ub;
size_t k;
dml_measure_t *measure;
double tree_aic, copula_aic;
gsl_permutation *perm, *rank, *u_rank = NULL, *v_rank = NULL;
igraph_i_set_attribute_table(&igraph_cattribute_table);
m = data->size1;
n = data->size2;
graph = g_malloc(sizeof(igraph_t));
graph_weight = g_malloc(sizeof(igraph_vector_t));
perm = gsl_permutation_alloc(m);
for (k = 0; k < n - 1; k++) { // Tree index.
if (k == 0) {
igraph_full(graph, n, IGRAPH_UNDIRECTED, IGRAPH_NO_LOOPS);
// Assign the observations to the nodes.
for (size_t i = 0; i < n; i++) { // Variable and node index.
x = gsl_vector_alloc(m);
gsl_matrix_get_col(x, data, i);
// Results of the h-function of the copula assigned to the
// edge that corresponds to this vertex in the previous tree.
// h for the h-function with its arguments in order and
// hrev for the h-function with its arguments reversed. In the
// first tree both are equal to the observations of the
// corresponding variable, in the rest of the trees they differ.
SETVAP(graph, "h", i, x);
SETVAP(graph, "hrev", i, x);
gsl_sort_vector_index(perm, x);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
// Ranks of the h and hrev vectors.
SETVAP(graph, "hrank", i, rank);
SETVAP(graph, "hrevrank", i, rank);
}
for (e = 0; e < igraph_ecount(graph); e++) {
igraph_edge(graph, e, &a, &b);
// Variables "connected" by this edge.
Ue = gsl_vector_short_calloc(n);
gsl_vector_short_set(Ue, a, 1);
gsl_vector_short_set(Ue, b, 1);
SETEAP(graph, "Ue", e, Ue);
// Conditioned set.
SETEAN(graph, "Cea", e, a + 1);
SETEAN(graph, "Ceb", e, b + 1);
Cea = EAN(graph, "Cea", e);
Ceb = EAN(graph, "Ceb", e);
// Calculate the weight of the edge.
u = VAP(graph, "h", a);
v = VAP(graph, "h", b);
u_rank = VAP(graph, "hrank", a);
v_rank = VAP(graph, "hrank", b);
// The conditioned set is ordered to make the order of the
// arguments in the bivariate copulas unique as suggested in
// Czado, C. (2010) Pair-Copula Constructions of Multivariate
// Copulas. In Jaworski, P. and Durante, F. and Hardle, W. K.
// and Rychlik, T. (eds.) Copula Theory and Its Applications,
// Springer-Verlag, 93-109.
if (Cea < Ceb) {
rvine_set_weight(graph, weight, e, u, v, u_rank, v_rank);
} else {
rvine_set_weight(graph, weight, e, v, u, v_rank, u_rank);
}
}
} else {
igraph_empty(graph, n - k, IGRAPH_UNDIRECTED);
// Adding all "possible" edges.
for (a = 0; a < igraph_vcount(graph) - 1; a++) {
for (b = a + 1; b < igraph_vcount(graph); b++) {
igraph_edge(trees[k - 1], a, &aa, &ab);
igraph_edge(trees[k - 1], b, &ba, &bb);
// Checking the proximity condition.
if (aa == ba || aa == bb || ab == ba || ab == bb) {
igraph_add_edge(graph, a, b);
igraph_get_eid(graph, &e, a, b, IGRAPH_UNDIRECTED, 1);
// Variables "connected" by this edge and conditioned set.
Ua = EAP(trees[k - 1], "Ue", a);
Ub = EAP(trees[k - 1], "Ue", b);
Ue = gsl_vector_short_calloc(n);
for (size_t i = 0; i < n; i++) {
gsl_vector_short_set(Ue, i,
gsl_vector_short_get(Ua, i)
| gsl_vector_short_get(Ub, i));
if (gsl_vector_short_get(Ua, i)
&& !gsl_vector_short_get(Ub, i)) {
SETEAN(graph, "Cea", e, i + 1);
}
if (gsl_vector_short_get(Ub, i)
&& !gsl_vector_short_get(Ua, i)) {
SETEAN(graph, "Ceb", e, i + 1);
}
}
SETEAP(graph, "Ue", e, Ue);
}
}
}
// Compute pseudo-observations and edge weights.
for (a = 0; a < igraph_vcount(graph); a++) {
// See the comment in the code for the first tree.
SETVAP(graph, "h", a, NULL);
SETVAP(graph, "hrev", a, NULL);
SETVAP(graph, "hrank", a, NULL);
SETVAP(graph, "hrevrank", a, NULL);
}
for (e = 0; e < igraph_ecount(graph); e++) {
igraph_edge(graph, e, &a, &b);
Cea = EAN(graph, "Cea", e);
Ceb = EAN(graph, "Ceb", e);
// Assign u and u_rank.
if ((Cea == EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
< EAN(trees[k - 1], "Ceb", a)))
|| (Cea != EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
> EAN(trees[k - 1], "Ceb", a)))) {
u = VAP(graph, "h", a);
if (u == NULL) {
copula = EAP(trees[k - 1], "copula", a);
measure = EAP(trees[k - 1], "measure", a);
u = gsl_vector_alloc(m);
dml_copula_h(copula, measure->x, measure->y, u);
SETVAP(graph, "h", a, u);
gsl_sort_vector_index(perm, u);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrank", a, rank);
}
u_rank = VAP(graph, "hrank", a);
}
if ((Cea == EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
> EAN(trees[k - 1], "Ceb", a)))
|| (Cea != EAN(trees[k - 1], "Cea", a)
&& (EAN(trees[k - 1], "Cea", a)
< EAN(trees[k - 1], "Ceb", a)))) {
u = VAP(graph, "hrev", a);
if (u == NULL) {
copula = EAP(trees[k - 1], "copula", a);
measure = EAP(trees[k - 1], "measure", a);
u = gsl_vector_alloc(m);
dml_copula_h(copula, measure->y, measure->x, u);
SETVAP(graph, "hrev", a, u);
gsl_sort_vector_index(perm, u);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrevrank", a, rank);
}
u_rank = VAP(graph, "hrevrank", a);
}
// Assign v and v_rank.
if ((Ceb == EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
< EAN(trees[k - 1], "Ceb", b)))
|| (Ceb != EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
> EAN(trees[k - 1], "Ceb", b)))) {
v = VAP(graph, "h", b);
if (v == NULL) {
copula = EAP(trees[k - 1], "copula", b);
measure = EAP(trees[k - 1], "measure", b);
v = gsl_vector_alloc(m);
dml_copula_h(copula, measure->x, measure->y, v);
SETVAP(graph, "h", b, v);
gsl_sort_vector_index(perm, v);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrank", b, rank);
}
v_rank = VAP(graph, "hrank", b);
}
if ((Ceb == EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
> EAN(trees[k - 1], "Ceb", b)))
|| (Ceb != EAN(trees[k - 1], "Cea", b)
&& (EAN(trees[k - 1], "Cea", b)
< EAN(trees[k - 1], "Ceb", b)))) {
v = VAP(graph, "hrev", b);
if (v == NULL) {
copula = EAP(trees[k - 1], "copula", b);
measure = EAP(trees[k - 1], "measure", b);
v = gsl_vector_alloc(m);
dml_copula_h(copula, measure->y, measure->x, v);
SETVAP(graph, "hrev", b, v);
gsl_sort_vector_index(perm, v);
rank = gsl_permutation_alloc(m);
gsl_permutation_inverse(rank, perm);
SETVAP(graph, "hrevrank", b, rank);
}
v_rank = VAP(graph, "hrevrank", b);
}
// Set the weight of the edge. The arguments are ordered here.
// The order determines the x and y fields of measure.
if (Cea < Ceb) {
rvine_set_weight(graph, weight, e, u, v, u_rank, v_rank);
} else {
rvine_set_weight(graph, weight, e, v, u, v_rank, u_rank);
}
}
}
// Compute the minimum weight spanning tree.
trees[k] = g_malloc(sizeof(igraph_t));
igraph_vector_init(graph_weight, igraph_ecount(graph));
EANV(graph, "weight", graph_weight);
igraph_minimum_spanning_tree_prim(graph, trees[k], graph_weight);
igraph_vector_destroy(graph_weight);
tree_aic = 0;
for (e = 0; e < igraph_ecount(trees[k]); e++) {
igraph_edge(trees[k], e, &a, &b);
Cea = EAN(trees[k], "Cea", e);
Ceb = EAN(trees[k], "Ceb", e);
measure = EAP(trees[k], "measure", e);
// Assign a bivariate copula to the edge.
if (Cea < Ceb) {
copula = dml_copula_select(measure->x, measure->y, measure,
indeptest, indeptest_level, types,
types_size, select, rng);
// Get information for the truncation of the vine.
if (trunc == DML_VINE_TRUNC_AIC) {
dml_copula_aic(copula, measure->x, measure->y, &copula_aic);
tree_aic += copula_aic;
}
} else {
copula = dml_copula_select(measure->y, measure->x, measure,
indeptest, indeptest_level, types,
types_size, select, rng);
// Get information for the truncation of the vine.
if (trunc == DML_VINE_TRUNC_AIC) {
dml_copula_aic(copula, measure->y, measure->x, &copula_aic);
tree_aic += copula_aic;
}
}
SETEAP(trees[k], "copula", e, copula);
}
igraph_destroy(graph);
// Check if the vine should be truncated.
if (trunc == DML_VINE_TRUNC_AIC && tree_aic >= 0) {
// Free the memory used for the last tree.
rvine_tree_cleanup(trees[k]);
for (e = 0; e < igraph_ecount(trees[k]); e++) {
copula = EAP(trees[k], "copula", e);
dml_copula_free(copula);
}
igraph_destroy(trees[k]);
g_free(trees[k]);
trees[k] = NULL;
break;
}
if (k > 0) rvine_tree_cleanup(trees[k - 1]);
}
// Cleanup the last tree if the vine was completely estimated.
// If the vine was truncated, the last tree will be freed in
// the function vine_fit_rvine, because the rvine_trees_to_vine
// function needs some attributes of its edges.
if (k == n - 1) {
rvine_tree_cleanup(trees[n - 2]);
}
g_free(graph_weight);
g_free(graph);
gsl_permutation_free(perm);
}
static void
rvine_trees_to_vine(dml_vine_t *vine, igraph_t **trees)
{
size_t n = vine->dim;
size_t *order_inv;
gsl_vector_short *B;
igraph_integer_t Cea, Ceb;
size_t x = 0, x_hat = 0, x_hat_hat = 0; // Initialized to avoid GCC warnings.
dml_copula_t *copula = NULL; // Initialized to avoid GCC warnings.
igraph_integer_t e; // Edge id.
igraph_integer_t a, b, aa, ab, ba, bb; // Vertex id.
igraph_t **last_trees = NULL;
igraph_t *graph = NULL;
gsl_vector_short *Ue, *Ua, *Ub;
// Set the number of trees of the vines.
vine->trees = n - 1;
while (trees[vine->trees - 1] == NULL) vine->trees--;
// Nothing to do for vines without trees.
if (vine->trees == 0) return;
// Selecting a structure for the trees that were truncated.
// Is this really necessary? Think a better solution.
if (vine->trees != n - 1) {
igraph_i_set_attribute_table(&igraph_cattribute_table);
last_trees = g_malloc_n(n - 1 - vine->trees, sizeof(igraph_t *));
graph = g_malloc(sizeof(igraph_t));
for (size_t k = vine->trees; k < n - 1; k++) { // Tree index.
igraph_empty(graph, n - k, IGRAPH_UNDIRECTED);
// Adding all "possible" edges.
for (a = 0; a < igraph_vcount(graph) - 1; a++) {
for (b = a + 1; b < igraph_vcount(graph); b++) {
// Checking the proximity condition.
igraph_edge(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], a, &aa, &ab);
igraph_edge(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], b, &ba, &bb);
if (aa == ba || aa == bb || ab == ba || ab == bb) {
igraph_add_edge(graph, a, b);
igraph_get_eid(graph, &e, a, b, IGRAPH_UNDIRECTED, 1);
// Variables "connected" by this edge and conditioned set.
Ua = EAP(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], "Ue", a);
Ub = EAP(k <= vine->trees ? trees[k - 1] : last_trees[k - 1 - vine->trees], "Ue", b);
Ue = gsl_vector_short_calloc(n);
for (size_t i = 0; i < n; i++) {
gsl_vector_short_set(Ue, i,
gsl_vector_short_get(Ua, i)
| gsl_vector_short_get(Ub, i));
if (gsl_vector_short_get(Ua, i)
&& !gsl_vector_short_get(Ub, i)) {
SETEAN(graph, "Cea", e, i + 1);
}
if (gsl_vector_short_get(Ub, i)
&& !gsl_vector_short_get(Ua, i)) {
SETEAN(graph, "Ceb", e, i + 1);
}
}
SETEAP(graph, "Ue", e, Ue);
}
}
}
// Compute the minimum weight spanning tree.
last_trees[k - vine->trees] = g_malloc(sizeof(igraph_t));
igraph_minimum_spanning_tree_unweighted(graph, last_trees[k - vine->trees]);
igraph_destroy(graph);
}
}
order_inv = g_malloc0_n(n, sizeof(size_t));
B = gsl_vector_short_calloc(n);
// for loop in line 2.
for (size_t i = 0; i < n - 1; i++) {
if (trees[n - i - 2] == NULL) {
for (e = 0; e < igraph_ecount(last_trees[n - i - 2 - vine->trees]); e++) {
x = EAN(last_trees[n - i - 2 - vine->trees], "Cea", e);
x_hat = EAN(last_trees[n - i - 2 - vine->trees], "Ceb", e);
if (!gsl_vector_short_get(B, x - 1)
&& !gsl_vector_short_get(B, x_hat - 1)) {
x_hat = 0;
copula = NULL;
break;
}
}
} else {
for (e = 0; e < igraph_ecount(trees[n - i - 2]); e++) {
x = EAN(trees[n - i - 2], "Cea", e);
x_hat = EAN(trees[n - i - 2], "Ceb", e);
if (!gsl_vector_short_get(B, x - 1)
&& !gsl_vector_short_get(B, x_hat - 1)) {
copula = EAP(trees[n - i - 2], "copula", e);
break;
}
}
}
// Line 4.
gsl_vector_short_set(B, x - 1, 1);
vine->order[n - i - 1] = x - 1;
order_inv[x - 1] = n - i;
vine->matrix[i][i] = x;
vine->matrix[i + 1][i] = x_hat;
vine->copulas[i + 1][i] = copula;
// for loop in line 5.
for (size_t k = i + 2; k < n; k++) {
if (trees[n - k - 1] != NULL) {
for (e = 0; e < igraph_ecount(trees[n - k - 1]); e++) {
Cea = EAN(trees[n - k - 1], "Cea", e);
Ceb = EAN(trees[n - k - 1], "Ceb", e);
if (x == Cea) {
x_hat_hat = Ceb;
if (!gsl_vector_short_get(B, x_hat_hat - 1)) {
// The pseudocode of the algorithm does not included
// this check. Invalid matrices were generated when
// x_hat_hat is set to an index already assigned
// to a diagonal entry.
copula = EAP(trees[n - k - 1], "copula", e);
break;
}
} else if (x == Ceb) {
x_hat_hat = Cea;
if (!gsl_vector_short_get(B, x_hat_hat - 1)) {
// Ibdem to the previous comment.
copula = EAP(trees[n - k - 1], "copula", e);
break;
}
}
}
vine->matrix[k][i] = x_hat_hat;
vine->copulas[k][i] = copula;
}
}
}
for (size_t i = 0; i < n; i++) {
if (!gsl_vector_short_get(B, i)) {
vine->matrix[n - 1][n - 1] = i + 1;
vine->order[0] = i;
order_inv[i] = 1;
break;
}
}
// Reorder the variables. The simulation algorithm assumes that the
// diagonal entries of the R-vine matrix are ordered from n to 1.
for (size_t i = 0; i < n; i++) {
for (size_t j = 0; j <= i; j++) {
if (vine->matrix[i][j] > 0) {
vine->matrix[i][j] = order_inv[vine->matrix[i][j] - 1];
}
}
}
if (vine->trees != n - 1) {
for (size_t i = 0; i < n - 1 - vine->trees; i++) {
for (e = 0; e < igraph_ecount(last_trees[i]); e++) {
Ue = EAP(last_trees[i], "Ue", e);
gsl_vector_short_free(Ue);
}
DELEA(last_trees[i], "Ue");
igraph_destroy(last_trees[i]);
g_free(last_trees[i]);
}
g_free(last_trees);
g_free(graph);
}
g_free(order_inv);
gsl_vector_short_free(B);
}
int main(int argc, char* argv[])
{
igraph_i_set_attribute_table(&igraph_cattribute_table);
char * in_graph_fn;
char * out_graph_fn;
if (argc < 3) {
printf("[ERROR] usage: mm-writer in_graph_fn out_graph_fn\n");
exit(-1);
}
else {
in_graph_fn = &argv[1][0];
out_graph_fn = &argv[2][0];
}
igraph_t g;
FILE *ifile, *ofile;
ifile = fopen(in_graph_fn, "r");
if (ifile == 0) {
return 10;
}
igraph_read_graph_graphml(&g, ifile, 0);
fclose(ifile);
igraph_to_directed(&g, IGRAPH_TO_DIRECTED_ARBITRARY);
printf("The graph stats:\n");
printf("Vertices: %li\n", (long int) igraph_vcount(&g));
printf("Edges: %li\n", (long int) igraph_ecount(&g));
printf("Directed: %i\n", (int) igraph_is_directed(&g));
ofile = fopen(out_graph_fn, "w");
if (ofile == 0) {
return 10;
}
// Write MM format
fprintf(ofile, "%li %li %li\n", (long int) igraph_vcount(&g),
(long int) igraph_vcount(&g), (long int) igraph_ecount(&g));
igraph_integer_t to;
igraph_integer_t from;
igraph_integer_t eid;
igraph_real_t weight;
for (eid = 0; eid < (long int) igraph_ecount(&g); eid++) {
igraph_edge(&g, eid, &from, &to);
weight = igraph_cattribute_EAN(&g, "weight",eid); // TODO: time
fprintf(ofile, "%i %i %f\n", from, to, weight);
//printf("Edge %i => %i --> %i\n", eid, from, to);
//printf("Edge %i has weight %f\n", eid, igraph_cattribute_EAN(&g, "weight",eid)); // TODO: time
}
// For all. TODO: time
#if 0
igraph_es_t eids;
igraph_es_all(&eids, IGRAPH_EDGEORDER_ID); // Order edges
igraph_vector_t result;
igraph_vector_init(&result, (int long) igraph_ecount(&g));
igraph_cattribute_EANV(&g, "weight", eids, &result);
igraph_integer_t i;
for (i = 0; i < (int long) igraph_ecount(&g); i++)
printf("Edge %i value: %f\n", i, VECTOR(result)[i]);
// Free memory
igraph_es_destroy(&eids);
igraph_vector_destroy(&result);
#endif
igraph_destroy(&g);
fclose(ofile);
return 0;
}
void LayoutBuilder::produce(AbstractPetriNetBuilder *builder){
if(!attrTableAttached){
igraph_i_set_attribute_table(&igraph_cattribute_table);
attrTableAttached = true;
}
size_t V = places.size() + transitions.size();
size_t E = inArcs.size() + outArcs.size();
igraph_t graph;
// Create a directed graph
igraph_empty(&graph, V, true);
// Create vector with all edges
igraph_vector_t edges;
igraph_vector_init(&edges, E * 2);
// Add edges to vector
int i = 0;
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++){
VECTOR(edges)[i++] = numberFromName(it->start);
VECTOR(edges)[i++] = numberFromName(it->end);
}
// Add the edges to graph
igraph_add_edges(&graph, &edges, 0);
// Delete the vector with edges
igraph_vector_destroy(&edges);
// Arrays to store result in
double posx[V];
double posy[V];
// Provide current positions, if they're used at all
if(startFromCurrentPositions){
int i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
posx[i] = it->x;
posy[i] = it->y;
igraph_cattribute_VAN_set(&graph, "id", i, i);
i++;
}
}
// Decompose the graph, and layout subgraphs induvidually
igraph_vector_ptr_t subgraphs;
igraph_vector_ptr_init(&subgraphs, 0);
igraph_decompose(&graph, &subgraphs, IGRAPH_WEAK, -1, 0);
// Offset for places subgraphs
double offsetx = 0;
double offsety = 0;
// Layout, translate and extract results for each subgraph
for(int i = 0; i < igraph_vector_ptr_size(&subgraphs); i++){
//Get the subgraph
igraph_t* subgraph = (igraph_t*)VECTOR(subgraphs)[i];
// Allocate result matrix
igraph_matrix_t sublayout;
igraph_matrix_init(&sublayout, 0, 0);
// Vertex selector and iterator
igraph_vs_t vs;
igraph_vit_t vit;
// Select all and create iterator
igraph_vs_all(&vs);
igraph_vit_create(subgraph, vs, &vit);
// Initialize sublayout, using original positions
if(startFromCurrentPositions){
// Count vertices
int vertices = 0;
// Iterator over vertices to count them, hacked but it works
while(!IGRAPH_VIT_END(vit)){
vertices++;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Resize sublayout
igraph_matrix_resize(&sublayout, vertices, 2);
// Iterator over vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
MATRIX(sublayout, subindex, 0) = posx[index];
MATRIX(sublayout, subindex, 1) = posy[index];
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
}
igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
// Other layout algorithms with reasonable parameters
//igraph_layout_kamada_kawai(subgraph, &sublayout, 1000, ((double)V)/4.0, 10, 0.99, V*V, startFromCurrentPositions);
//igraph_layout_grid_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, V*V/4, startFromCurrentPositions);
//igraph_layout_fruchterman_reingold(subgraph, &sublayout, 500, V, V*V, 1.5, V*V*V, startFromCurrentPositions, NULL);
//igraph_layout_lgl(subgraph, &sublayout, 150, V, V*V, 1.5, V*V*V, sqrt(V), -1);
//Find min and max values:
double minx = DBL_MAX,
miny = DBL_MAX,
maxx = -DBL_MAX,
maxy = -DBL_MAX;
//Iterator over all vertices
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
minx = minx < x ? minx : x;
miny = miny < y ? miny : y;
maxx = maxx > x ? maxx : x;
maxy = maxy > y ? maxy : y;
IGRAPH_VIT_NEXT(vit);
}
//Reset vertex iterator
IGRAPH_VIT_RESET(vit);
// Compute translation
double tx = margin - minx;
double ty = margin - miny;
// Decide whether to put it below or left of current content
if(maxx - minx + offsetx < maxy - miny + offsety){
tx += offsetx;
offsetx += maxx - minx + margin;
if(offsety < maxy - miny + margin)
offsety = maxy - miny + margin;
}else{
ty += offsety;
offsety += maxy - miny + margin;
if(offsetx < maxx - minx + margin)
offsetx = maxx - minx + margin;
}
// Translate and extract results
while(!IGRAPH_VIT_END(vit)){
int subindex = (int)IGRAPH_VIT_GET(vit);
int index = (int)igraph_cattribute_VAN(subgraph, "id", subindex);
double x = MATRIX(sublayout, subindex, 0) * factor;
double y = MATRIX(sublayout, subindex, 1) * factor;
posx[index] = x + tx;
posy[index] = y + ty;
IGRAPH_VIT_NEXT(vit);
}
// Destroy iterator and selector
igraph_vit_destroy(&vit);
igraph_vs_destroy(&vs);
// Destroy the sublayout
igraph_matrix_destroy(&sublayout);
// Destroy subgraph
igraph_destroy(subgraph);
free(VECTOR(subgraphs)[i]);
}
// Remove the attributes
igraph_cattribute_remove_v(&graph, "id");
// Destroy the graph
igraph_destroy(&graph);
// Insert results
i = 0;
for(PlaceIter it = places.begin(); it != places.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++){
it->x = posx[i];
it->y = posy[i];
i++;
}
// Produce variables
for(VarIter it = vars.begin(); it != vars.end(); it++)
builder->addVariable(it->name, it->initialValue, it->range);
for(BoolVarIter it = boolVars.begin(); it != boolVars.end(); it++)
builder->addBoolVariable(it->name, it->initialValue);
for(PlaceIter it = places.begin(); it != places.end(); it++)
builder->addPlace(it->name, it->tokens, it->x, it->y);
for(TransitionIter it = transitions.begin(); it != transitions.end(); it++)
builder->addTransition(it->name, it->conditions, it->assignments, it->x, it->y);
for(ArcIter it = inArcs.begin(); it != inArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
for(ArcIter it = outArcs.begin(); it != outArcs.end(); it++)
builder->addInputArc(it->start, it->end, it->weight);
//Reset builder state (just in case some idoit decides to reuse it!
vars.clear();
boolVars.clear();
places.clear();
transitions.clear();
inArcs.clear();
outArcs.clear();
}
int main(int argc, char** argv) {
int response;
igraph_t graph;
igraph_vector_ptr_t complist;
iclust_collection * collection = NULL;
time_t time_start, time_end;
/* turn on attribute handling */
igraph_i_set_attribute_table(&igraph_cattribute_table);
double minimal_weight;
unsigned int maximal_steps_delimieter;
char graphncol[1024], logconfig[1024];
Config *cfg = ConfigNew();
const char * configuration = getopt_configfile(argc, argv, "./graphtocluster.conf");
massert((ConfigReadFile(configuration, &cfg) == CONFIG_OK), "Configuration file is not readable");
ConfigReadString(cfg, "sources", "graphncol", graphncol, sizeof(graphncol), 0);
ConfigReadString(cfg, "sources", "logconfig", logconfig, sizeof(logconfig), 0);
ConfigReadDouble(cfg, "limits", "minimal_weight", &minimal_weight, 0);
ConfigReadUnsignedInt(cfg, "limits", "maximal_steps_delimieter", &maximal_steps_delimieter, 1);
massert((maximal_steps_delimieter > 0), "Delimiter can not be equal to zero");
ConfigFree(cfg);
logger_init(logconfig, "graphtocluster");
logger_info("File:\t configuration %s", configuration);
logger_info("File:\t configuration logger %s", logconfig);
logger_info("File:\t ncol graph source %s", graphncol);
logger_info("Min:\t edge weight %f", minimal_weight);
logger_info("Max:\t step delimeter %u", maximal_steps_delimieter);
FILE *graph_source = fopen(graphncol, "r");
response = igraph_read_graph_ncol(&graph, graph_source, NULL, true, IGRAPH_ADD_WEIGHTS_YES, 0);
massert((response == IGRAPH_SUCCESS), "Can not read a graph");
logger_info("Count:\t edges at start: %d", igraph_ecount(&graph));
fclose(graph_source);
time(&time_start);
igraph_edges_remove_by(&graph, "weight", minimal_weight, double_lt);
time(&time_end);
logger_info("Time:\t remove edges: %f", difftime(time_end, time_start));
logger_info("Count:\t edges after remove: %d", igraph_ecount(&graph));
response = igraph_vector_ptr_init(&complist, 0);
massert((response == IGRAPH_SUCCESS), "Can not initialize vector pointer");
response = igraph_decompose(&graph, &complist, IGRAPH_WEAK, -1, 0);
massert((response == IGRAPH_SUCCESS), "Can not decompose graph");
unsigned int n = igraph_vector_ptr_size(&complist);
collection = iclust_collection_new();
massert((collection != NULL), "Cluster collection object can not be empty");
time(&time_start);
for (unsigned int i = 0; i < n; i++) {
igraph_t *subgraph = VECTOR(complist)[i];
massert((subgraph != NULL), "Subgraph object can not be empty");
iclust_collection_fill_leading_eigenvector(collection, subgraph, (i + 1), maximal_steps_delimieter);
igraph_destroy(subgraph);
}
time(&time_end);
logger_info("Time:\t cluster: %f", difftime(time_end, time_start));
/* Sort collection by cluster id to be
* able to build a second column correct*/
time(&time_start);
iclust_collection_sort(collection);
time(&time_end);
logger_info("Time:\t cluster sorting: %f", difftime(time_end, time_start));
unsigned long cluster_index = 1, cluster = 0;
for (unsigned long i = 0; i < collection->length; i++) {
iclust_collection_element * element = collection->collection[i];
massert((element != NULL), "Cluster collection element object can not be empty");
if (element->cluster != cluster) {
cluster = element->cluster;
cluster_index = 0;
}
printf("%lu\t%lu\t%s\n", cluster, ++cluster_index, element->name);
}
iclust_collection_destroy(collection);
igraph_vector_ptr_destroy(&complist);
igraph_destroy(&graph);
logger_destroy();
return EXIT_SUCCESS;
}
void Init_igraph(){
//Modules
VALUE cIGraph_generate;
VALUE cIGraph_genrandom;
VALUE cIGraph_connectivity;
VALUE cIGraph_mincuts;
VALUE cIGraph_layout;
VALUE cIGraph_clique;
VALUE cIGraph_indyver;
VALUE cIGraph_isomor;
VALUE cIGraph_motifs;
VALUE cIGraph_sorting;
VALUE cIGraph_filewrite;
VALUE cIGraph_fileread;
VALUE cIGraph_community;
VALUE cIGraph_shortestpaths;
VALUE cIGraph_neighborhoodm;
VALUE cIGraph_components;
VALUE cIGraph_closenessm;
VALUE cIGraph_spanning;
VALUE cIGraph_transitivitym;
VALUE cIGraph_spectral;
VALUE cIGraph_kcore;
VALUE cIGraph_otherop;
VALUE cIGraph_randomise;
igraph_i_set_attribute_table(&cIGraph_attribute_table);
igraph_set_error_handler(cIGraph_error_handler);
igraph_set_warning_handler(cIGraph_warning_handler);
cIGraph = rb_define_class("IGraph", rb_cObject);
cIGraphError = rb_define_class("IGraphError", rb_eRuntimeError);
rb_define_alloc_func(cIGraph, cIGraph_alloc);
rb_define_method(cIGraph, "initialize", cIGraph_initialize, -1);
rb_define_method(cIGraph, "initialize_copy", cIGraph_init_copy, 1);
rb_include_module(cIGraph, rb_mEnumerable);
/* Functions for deterministically generating graphs. */
cIGraph_generate = rb_define_module_under(cIGraph, "Generate");
rb_include_module(cIGraph, cIGraph_generate);
rb_define_singleton_method(cIGraph_generate, "adjacency", cIGraph_adjacency, 2); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "star", cIGraph_star, 3); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "lattice", cIGraph_lattice, 4); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "ring", cIGraph_ring, 4); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "tree", cIGraph_tree, 3); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "full", cIGraph_full, 3); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "atlas", cIGraph_atlas, 1); /* in cIGraph_generators_deterministic.c */
rb_define_singleton_method(cIGraph_generate, "extended_chordal_ring", cIGraph_extended_chordal_ring, 2); /* in cIGraph_generators_deterministic.c */
/* Functions for randomly generating graphs. */
cIGraph_genrandom = rb_define_module_under(cIGraph, "GenerateRandom");
rb_include_module(cIGraph, cIGraph_genrandom);
rb_define_singleton_method(cIGraph_genrandom, "grg_game", cIGraph_grg_game, 3); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "barabasi_game", cIGraph_barabasi_game, 4); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "nonlinear_barabasi_game", cIGraph_nonlinear_barabasi_game, 6); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "erdos_renyi_game", cIGraph_erdos_renyi_game, 5); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "watts_strogatz_game", cIGraph_watts_strogatz_game, 4); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "degree_sequence_game", cIGraph_degree_sequence_game, 2); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "growing_random_game", cIGraph_growing_random_game, 4); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "callaway_traits_game", cIGraph_callaway_traits_game, 6); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "establishment_game", cIGraph_establishment_game, 6); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "preference_game", cIGraph_preference_game, 6); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "asymmetric_preference_game", cIGraph_asymmetric_preference_game, 5); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "recent_degree_game", cIGraph_recent_degree_game, 7); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "barabasi_aging_game", cIGraph_barabasi_aging_game, 11); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "recent_degree_aging_game", cIGraph_recent_degree_aging_game, 9); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "cited_type_game", cIGraph_cited_type_game, 5); /* in cIGraph_generators_random.c */
rb_define_singleton_method(cIGraph_genrandom, "citing_cited_type_game", cIGraph_citing_cited_type_game, 5); /* in cIGraph_generators_random.c */
rb_define_method(cIGraph, "[]", cIGraph_get_edge_attr, 2); /* in cIGraph_attribute_handler.c */
rb_define_method(cIGraph, "[]=", cIGraph_set_edge_attr, 3); /* in cIGraph_attribute_handler.c */
rb_define_alias (cIGraph, "get_edge_attr", "[]");
rb_define_alias (cIGraph, "set_edge_attr", "[]=");
rb_define_method(cIGraph, "attributes", cIGraph_graph_attributes, 0); /* in cIGraph_attribute_handler.c */
rb_define_method(cIGraph, "each_vertex", cIGraph_each_vertex, 0); /* in cIGraph_iterators.c */
rb_define_method(cIGraph, "each_edge", cIGraph_each_edge, 1); /* in cIGraph_iterators.c */
rb_define_method(cIGraph, "each_edge_eid", cIGraph_each_edge_eid,1); /* in cIGraph_iterators.c */
rb_define_alias (cIGraph, "each", "each_vertex");
rb_define_method(cIGraph, "vertices", cIGraph_all_v, 0); /* in cIGraph_selectors.c */
rb_define_method(cIGraph, "adjacent_vertices", cIGraph_adj_v, 2); /* in cIGraph_selectors.c */
rb_define_method(cIGraph, "nonadjacent_vertices", cIGraph_nonadj_v, 2); /* in cIGraph_selectors.c */
rb_define_alias (cIGraph, "all_vertices", "vertices");
rb_define_method(cIGraph, "edges", cIGraph_all_e, 1); /* in cIGraph_selectors.c */
rb_define_method(cIGraph, "adjacent_edges", cIGraph_adj_e, 2); /* in cIGraph_selectors.c */
rb_define_alias (cIGraph, "all_edges", "edges");
rb_define_method(cIGraph, "vcount", cIGraph_vcount, 0); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "ecount", cIGraph_ecount, 0); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "edge", cIGraph_edge, 1); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "get_eid", cIGraph_get_eid, 2); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "neighbours", cIGraph_neighbors, 2); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "adjacent", cIGraph_adjacent, 2); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "degree", cIGraph_degree, 3); /* in cIGraph_basic_query.c */
rb_define_method(cIGraph, "is_directed?", cIGraph_is_directed, 0); /* in cIGraph_basic_query.c */
rb_define_alias (cIGraph, "is_directed", "is_directed?");
rb_define_alias (cIGraph, "neighbors", "neighbours");
rb_define_method(cIGraph, "add_edges", cIGraph_add_edges, -1); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "add_vertices", cIGraph_add_vertices, 1); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "add_edge", cIGraph_add_edge, -1); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "add_vertex", cIGraph_add_vertex, 1); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "delete_edge", cIGraph_delete_edge, 2); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "delete_vertex", cIGraph_delete_vertex, 1); /* in cIGraph_add_delete.c */
rb_define_method(cIGraph, "are_connected", cIGraph_are_connected,2); /* in cIGraph_basic_properties.c */
rb_define_alias (cIGraph, "are_connected?", "are_connected");
rb_define_method(cIGraph, "to_directed", cIGraph_to_directed, 1); /* in cIGraph_direction.c */
rb_define_method(cIGraph, "to_undirected", cIGraph_to_undirected, 1); /* in cIGraph_direction.c */
/* These methods randomise a graph by rewiring the edges. */
cIGraph_randomise = rb_define_module_under(cIGraph, "Randomise");
rb_include_module(cIGraph, cIGraph_randomise);
rb_define_method(cIGraph_randomise, "rewire_edges", cIGraph_rewire_edges, 1); /* in cIGraph_randomisation.c */
rb_define_method(cIGraph_randomise, "rewire", cIGraph_rewire, 1); /* in cIGraph_randomisation.c */
/* Functions for calculating the shortest path through a graph */
cIGraph_shortestpaths = rb_define_module_under(cIGraph, "ShortestPaths");
rb_include_module(cIGraph, cIGraph_shortestpaths);
rb_define_method(cIGraph_shortestpaths, "shortest_paths", cIGraph_shortest_paths, 2); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "get_shortest_paths", cIGraph_get_shortest_paths, 3); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "get_all_shortest_paths", cIGraph_get_all_shortest_paths, 3); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "average_path_length", cIGraph_average_path_length, 2); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "diameter", cIGraph_diameter, 2); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "girth", cIGraph_girth, 0); /* in cIGraph_shortest_paths.c */
rb_define_method(cIGraph_shortestpaths, "dijkstra_shortest_paths", cIGraph_dijkstra_shortest_paths, 3); /* in cIGraph_dijkstra.c */
/* Functions for querying the neighborhood of vertices */
cIGraph_neighborhoodm = rb_define_module_under(cIGraph, "Neighborhood");
rb_include_module(cIGraph, cIGraph_neighborhoodm);
rb_define_method(cIGraph_neighborhoodm, "neighbourhood_size", cIGraph_neighborhood_size, 3); /* in cIGraph_vertex_neighbourhood.c */
rb_define_method(cIGraph_neighborhoodm, "neighbourhood", cIGraph_neighborhood, 3); /* in cIGraph_vertex_neighbourhood.c */
rb_define_method(cIGraph_neighborhoodm, "neighbourhood_graphs", cIGraph_neighborhood_graphs, 3); /* in cIGraph_vertex_neighbourhood.c */
rb_define_alias (cIGraph_neighborhoodm, "neighborhood_size", "neighbourhood_size");
rb_define_alias (cIGraph_neighborhoodm, "neighborhood", "neighbourhood");
rb_define_alias (cIGraph_neighborhoodm, "neighborhood_graphs", "neighbourhood_graphs");
rb_define_method(cIGraph_neighborhoodm, "connect_neighborhood", cIGraph_connect_neighborhood, 2); /* in cIGraph_generators_deterministic.c */
/* Functions for splitting the graph into components */
cIGraph_components = rb_define_module_under(cIGraph, "Components");
rb_include_module(cIGraph, cIGraph_components);
rb_define_method(cIGraph_components, "subcomponent", cIGraph_subcomponent, 2); /* in cIGraph_components.c */
rb_define_method(cIGraph_components, "subgraph", cIGraph_subgraph, 1); /* in cIGraph_components.c */
rb_define_method(cIGraph_components, "clusters", cIGraph_clusters, 1); /* in cIGraph_components.c */
rb_define_method(cIGraph_components, "decompose", cIGraph_decompose, -1); /* in cIGraph_components.c */
/* Graph centrality functions */
cIGraph_closenessm = rb_define_module_under(cIGraph, "Closeness");
rb_include_module(cIGraph, cIGraph_closenessm);
rb_define_method(cIGraph_closenessm, "closeness", cIGraph_closeness, 2); /* in cIGraph_centrality.c */
rb_define_method(cIGraph_closenessm, "betweenness", cIGraph_betweenness, 2); /* in cIGraph_centrality.c */
rb_define_method(cIGraph_closenessm, "edge_betweenness", cIGraph_edge_betweenness, 1); /* in cIGraph_centrality.c */
rb_define_method(cIGraph_closenessm, "pagerank", cIGraph_pagerank, 5); /* in cIGraph_centrality.c */
rb_define_method(cIGraph_closenessm, "constraint", cIGraph_constraint, -1); /* in cIGraph_centrality.c */
rb_define_method(cIGraph_closenessm, "maxdegree", cIGraph_maxdegree, 3); /* in cIGraph_centrality.c */
/* Minimum spanning tree functions */
cIGraph_spanning = rb_define_module_under(cIGraph, "Spanning");
rb_include_module(cIGraph, cIGraph_spanning);
rb_define_method(cIGraph_spanning, "minimum_spanning_tree_unweighted", cIGraph_minimum_spanning_tree_unweighted, 0); /* in cIGraph_spanning.c */
rb_define_method(cIGraph_spanning, "minimum_spanning_tree_prim", cIGraph_minimum_spanning_tree_prim, 1); /* in cIGraph_spanning.c */
/* Graph transitivity functions */
cIGraph_transitivitym = rb_define_module_under(cIGraph, "Transitivity");
rb_include_module(cIGraph, cIGraph_transitivitym);
rb_define_method(cIGraph_transitivitym, "transitivity", cIGraph_transitivity, 0); /* in cIGraph_transitivity.c */
rb_define_method(cIGraph_transitivitym, "transitivity_local", cIGraph_transitivity_local, 1); /* in cIGraph_transitivity.c */
rb_define_method(cIGraph_transitivitym, "transitivity_avglocal", cIGraph_transitivity_avglocal, 0); /* in cIGraph_transitivity.c */
/* Functions for the Laplacian matrix. */
cIGraph_spectral = rb_define_module_under(cIGraph, "Spectral");
rb_include_module(cIGraph, cIGraph_spectral);
rb_define_method(cIGraph_spectral, "laplacian", cIGraph_laplacian, 1); /* in cIGraph_spectral.c */
/* Functions for finding the coreness of a graph */
cIGraph_kcore = rb_define_module_under(cIGraph, "KCores");
rb_include_module(cIGraph, cIGraph_kcore);
rb_define_method(cIGraph_kcore, "coreness", cIGraph_coreness, 1); /* in cIGraph_kcores.c */
/* Other general graph operations */
cIGraph_otherop = rb_define_module_under(cIGraph, "OtherOperations");
rb_include_module(cIGraph, cIGraph_otherop);
rb_define_method(cIGraph_otherop, "density", cIGraph_density, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph_otherop, "simplify", cIGraph_simplify, 2); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph_otherop, "reciprocity", cIGraph_reciprocity, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph_otherop, "bibcoupling", cIGraph_bibcoupling, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph_otherop, "cocitation", cIGraph_cocitation, 1); /* in cIGraph_other_ops.c */
rb_define_method(cIGraph_otherop, "get_adjacency", cIGraph_get_adjacency, 1); /* in cIGraph_other_ops.c */
/* Clique finding functions */
cIGraph_clique = rb_define_module_under(cIGraph, "Cliques");
rb_include_module(cIGraph, cIGraph_clique);
rb_define_method(cIGraph_clique, "cliques", cIGraph_cliques, 2); /* in cIGraph_cliques.c */
rb_define_method(cIGraph_clique, "largest_cliques", cIGraph_largest_cliques, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph_clique, "maximal_cliques", cIGraph_maximal_cliques, 0); /* in cIGraph_cliques.c */
rb_define_method(cIGraph_clique, "clique_number", cIGraph_clique_number, 0); /* in cIGraph_cliques.c */
/* Independent vertex set finding functions */
cIGraph_indyver = rb_define_module_under(cIGraph, "IndependentVertexSets");
rb_include_module(cIGraph, cIGraph_indyver);
rb_define_method(cIGraph_indyver, "independent_vertex_sets", cIGraph_independent_vertex_sets, 2); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "largest_independent_vertex_sets", cIGraph_largest_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "maximal_independent_vertex_sets", cIGraph_maximal_independent_vertex_sets, 0); /* in cIGraph_independent_vertex_sets.c */
rb_define_method(cIGraph_indyver, "independence_number", cIGraph_independence_number, 0); /* in cIGraph_independent_vertex_sets.c */
/* Functions for isomorphism and isoclasses */
cIGraph_isomor = rb_define_module_under(cIGraph, "Isomorphism");
rb_include_module(cIGraph, cIGraph_isomor);
rb_define_method(cIGraph_isomor, "isomorphic", cIGraph_isomorphic, 1); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isomorphic_vf2", cIGraph_isomorphic_vf2, 1); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isoclass", cIGraph_isoclass, 0); /* in cIGraph_isomorphism.c */
rb_define_method(cIGraph_isomor, "isoclass_subgraph", cIGraph_isoclass_subgraph, 1); /* in cIGraph_isomorphism.c */
rb_define_singleton_method(cIGraph_generate, "isoclass_create", cIGraph_isoclass_create, 3); /* in cIGraph_isomorphism.c */
/* Motif finding functions */
cIGraph_motifs = rb_define_module_under(cIGraph, "Motifs");
rb_include_module(cIGraph, cIGraph_motifs);
rb_define_method(cIGraph_motifs, "motifs_randesu", cIGraph_motifs_randesu, 2); /* in cIGraph_motif.c */
rb_define_method(cIGraph_motifs, "motifs_randesu_no", cIGraph_motifs_randesu_no, 2); /* in cIGraph_motif.c */
rb_define_method(cIGraph_motifs, "motifs_randesu_estimate", cIGraph_motifs_randesu_estimate, 4); /* in cIGraph_motif.c */
/* Graph sorting functions. */
cIGraph_sorting = rb_define_module_under(cIGraph, "Sorting");
rb_include_module(cIGraph, cIGraph_sorting);
rb_define_method(cIGraph_sorting, "topological_sorting", cIGraph_topological_sorting, 1); /* in cIGraph_topological_sort.c */
/* Functions for reading graphs from files */
cIGraph_fileread = rb_define_module_under(cIGraph, "FileRead");
rb_include_module(cIGraph, cIGraph_fileread);
#ifdef __APPLE__
rb_define_singleton_method(cIGraph_fileread, "read_graph_edgelist", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_graphml", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_ncol", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_lgl", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_dimacs", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_graphdb", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_gml", cIGraph_unavailable_method, -1);
rb_define_singleton_method(cIGraph_fileread, "read_graph_pajek", cIGraph_unavailable_method, -1);
#else
rb_define_singleton_method(cIGraph_fileread, "read_graph_edgelist", cIGraph_read_graph_edgelist, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_graphml", cIGraph_read_graph_graphml, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_ncol", cIGraph_read_graph_ncol, 5); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_lgl", cIGraph_read_graph_lgl, 3); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_dimacs", cIGraph_read_graph_dimacs, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_graphdb", cIGraph_read_graph_graphdb, 2); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_gml", cIGraph_read_graph_gml, 1); /* in cIGraph_file.c */
rb_define_singleton_method(cIGraph_fileread, "read_graph_pajek", cIGraph_read_graph_pajek, 2); /* in cIGraph_file.c */
#endif
/* Functions for writing graphs to files */
cIGraph_filewrite = rb_define_module_under(cIGraph, "FileWrite");
rb_include_module(cIGraph, cIGraph_filewrite);
#ifdef __APPLE__
rb_define_method(cIGraph_filewrite, "write_graph_edgelist", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_graphml", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_gml", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_ncol", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_lgl", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_dimacs", cIGraph_unavailable_method, -1);
rb_define_method(cIGraph_filewrite, "write_graph_pajek", cIGraph_unavailable_method, -1);
#else
rb_define_method(cIGraph_filewrite, "write_graph_edgelist", cIGraph_write_graph_edgelist, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_graphml", cIGraph_write_graph_graphml, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_gml", cIGraph_write_graph_gml, 1); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_ncol", cIGraph_write_graph_ncol, 3); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_lgl", cIGraph_write_graph_lgl, 4); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_dimacs", cIGraph_write_graph_dimacs, 4); /* in cIGraph_file.c */
rb_define_method(cIGraph_filewrite, "write_graph_pajek", cIGraph_write_graph_pajek, 1); /* in cIGraph_file.c */
#endif
/* Graph layout functions */
cIGraph_layout = rb_define_module_under(cIGraph, "Layout");
rb_include_module(cIGraph, cIGraph_layout);
rb_define_method(cIGraph_layout, "layout_random", cIGraph_layout_random, 0); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_circle", cIGraph_layout_circle, 0); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_fruchterman_reingold", cIGraph_layout_fruchterman_reingold, 6); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_kamada_kawai", cIGraph_layout_kamada_kawai, 5); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_reingold_tilford", cIGraph_layout_reingold_tilford, 1); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_reingold_tilford_circular", cIGraph_layout_reingold_tilford_circular, 1); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_grid_fruchterman_reingold", cIGraph_layout_grid_fruchterman_reingold, 7); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_lgl", cIGraph_layout_lgl, 7); /* in cIGraph_layout.c */
rb_define_method(cIGraph_layout, "layout_random_3d", cIGraph_layout_random_3d, 0); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_sphere", cIGraph_layout_sphere, 0); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_fruchterman_reingold_3d", cIGraph_layout_fruchterman_reingold_3d, 5); /* in cIGraph_layout3d.c */
rb_define_method(cIGraph_layout, "layout_kamada_kawai_3d", cIGraph_layout_kamada_kawai_3d, 5); /* in cIGraph_layout3d.c */
rb_define_singleton_method(cIGraph_layout, "layout_merge_dla", cIGraph_layout_merge_dla, 2); /* in cIGraph_layout.c */
/* Minimum cuts related functions */
cIGraph_mincuts = rb_define_module_under(cIGraph, "MinimumCuts");
rb_include_module(cIGraph, cIGraph_mincuts);
rb_define_method(cIGraph_mincuts, "maxflow_value", cIGraph_maxflow_value, 3); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "st_mincut_value", cIGraph_st_mincut_value, 3); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "mincut_value", cIGraph_mincut_value, 1); /* in cIGraph_min_cuts.c */
rb_define_method(cIGraph_mincuts, "mincut", cIGraph_mincut, 1); /* in cIGraph_min_cuts.c */
/* Vertex and edge connectivity functions */
cIGraph_connectivity = rb_define_module_under(cIGraph, "Connectivity");
rb_include_module(cIGraph, cIGraph_connectivity);
rb_define_method(cIGraph_connectivity, "st_edge_connectivity", cIGraph_st_edge_connectivity, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "edge_connectivity", cIGraph_edge_connectivity, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "st_vertex_connectivity", cIGraph_st_vertex_connectivity, 3); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "vertex_connectivity", cIGraph_vertex_connectivity, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "edge_disjoint_paths", cIGraph_edge_disjoint_paths, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "vertex_disjoint_paths", cIGraph_vertex_disjoint_paths, 2); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "adhesion", cIGraph_adhesion, 0); /* in cIGraph_connectivity.c */
rb_define_method(cIGraph_connectivity, "cohesion", cIGraph_cohesion, 0); /* in cIGraph_connectivity.c */
/* Community and modularity related functions */
cIGraph_community = rb_define_module_under(cIGraph, "Community");
rb_include_module(cIGraph, cIGraph_community);
rb_define_method(cIGraph_community, "modularity", cIGraph_modularity, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_to_membership", cIGraph_community_to_membership, 3); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_spinglass", cIGraph_community_spinglass, 8); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_spinglass_single", cIGraph_community_spinglass_single, 5); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector", cIGraph_community_leading_eigenvector, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector_naive", cIGraph_community_leading_eigenvector_naive, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_leading_eigenvector_step", cIGraph_community_leading_eigenvector_step, 2); /* in cIGraph_community.c */ rb_define_method(cIGraph_community, "community_walktrap", cIGraph_community_walktrap, 2); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_edge_betweenness", cIGraph_community_edge_betweenness, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_eb_get_merges", cIGraph_community_eb_get_merges, 1); /* in cIGraph_community.c */
rb_define_method(cIGraph_community, "community_fastgreedy", cIGraph_community_fastgreedy, 0); /* in cIGraph_community.c */
rb_define_const(cIGraph, "VERSION", rb_str_new2("0.9.1"));
rb_define_const(cIGraph, "EDGEORDER_ID", INT2NUM(1));
rb_define_const(cIGraph, "EDGEORDER_FROM", INT2NUM(2));
rb_define_const(cIGraph, "EDGEORDER_TO", INT2NUM(3));
rb_define_const(cIGraph, "OUT", INT2NUM(1));
rb_define_const(cIGraph, "IN", INT2NUM(2));
rb_define_const(cIGraph, "ALL", INT2NUM(3));
rb_define_const(cIGraph, "TOTAL", INT2NUM(4));
rb_define_const(cIGraph_components, "WEAK", INT2NUM(1));
rb_define_const(cIGraph_components, "STRONG", INT2NUM(2));
rb_define_const(cIGraph, "ARBITRARY", INT2NUM(0));
rb_define_const(cIGraph, "MUTUAL", INT2NUM(1));
rb_define_const(cIGraph, "EACH", INT2NUM(0));
rb_define_const(cIGraph, "COLLAPSE", INT2NUM(1));
rb_define_const(cIGraph_otherop, "GET_ADJACENCY_UPPER", INT2NUM(0));
rb_define_const(cIGraph_otherop, "GET_ADJACENCY_LOWER", INT2NUM(1));
rb_define_const(cIGraph_otherop, "GET_ADJACENCY_BOTH", INT2NUM(2));
rb_define_const(cIGraph, "ERDOS_RENYI_GNP", INT2NUM(0));
rb_define_const(cIGraph, "ERDOS_RENYI_GNM", INT2NUM(1));
rb_define_const(cIGraph_generate, "ADJ_DIRECTED", INT2NUM(0));
rb_define_const(cIGraph_generate, "ADJ_UNDIRECTED", INT2NUM(1));
rb_define_const(cIGraph_generate, "ADJ_MAX", INT2NUM(2));
rb_define_const(cIGraph_generate, "ADJ_MIN", INT2NUM(3));
rb_define_const(cIGraph_generate, "ADJ_PLUS", INT2NUM(4));
rb_define_const(cIGraph_generate, "ADJ_UPPER", INT2NUM(5));
rb_define_const(cIGraph_generate, "ADJ_LOWER", INT2NUM(6));
rb_define_const(cIGraph_generate, "STAR_OUT", INT2NUM(0));
rb_define_const(cIGraph_generate, "STAR_IN", INT2NUM(1));
rb_define_const(cIGraph_generate, "STAR_UNDIRECTED", INT2NUM(2));
rb_define_const(cIGraph_generate, "TREE_OUT", INT2NUM(0));
rb_define_const(cIGraph_generate, "TREE_IN", INT2NUM(1));
rb_define_const(cIGraph_generate, "TREE_UNDIRECTED", INT2NUM(2));
rb_define_const(cIGraph_connectivity, "VCONN_NEI_ERROR", INT2NUM(0));
rb_define_const(cIGraph_connectivity, "VCONN_NEI_INFINITY", INT2NUM(1));
rb_define_const(cIGraph_connectivity, "VCONN_NEI_IGNORE", INT2NUM(2));
rb_define_const(cIGraph_community, "SPINCOMM_UPDATE_SIMPLE", INT2NUM(0));
rb_define_const(cIGraph_community, "SPINCOMM_UPDATE_CONFIG", INT2NUM(1));
/* This class wraps the igraph matrix type. It can be created from and
* converted to an Array of Ruby Arrays.
*/
cIGraphMatrix = rb_define_class("IGraphMatrix", rb_cObject);
rb_define_alloc_func(cIGraphMatrix, cIGraph_matrix_alloc);
rb_define_method(cIGraphMatrix, "initialize", cIGraph_matrix_initialize, -1); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "initialize_copy", cIGraph_matrix_init_copy, 1); /* in cIGraph_matrix.c */
//rb_define_singleton_method(cIGraphMatrix, "[]", cIGraph_matrix_initialize, -1);
rb_include_module(cIGraphMatrix, rb_mEnumerable);
rb_define_method (cIGraphMatrix, "each", cIGraph_matrix_each,0); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "[]", cIGraph_matrix_get, 2); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "[]=", cIGraph_matrix_set, 3); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "size", cIGraph_matrix_size, 0); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "nrow", cIGraph_matrix_nrow, 0); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "ncol", cIGraph_matrix_ncol, 0); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "max", cIGraph_matrix_max, 0); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "*", cIGraph_matrix_scale, 1); /* in cIGraph_matrix.c */
rb_define_method(cIGraphMatrix, "to_a", cIGraph_matrix_toa, 0); /* in cIGraph_matrix.c */
}
TMIgraph::TMIgraph() {
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_empty(&graph, 0, true);
}
int main(void) {
// This needs to be done *first*. See igraph doc for why.
igraph_i_set_attribute_table(&igraph_cattribute_table);
printf("sizeof(int)=%d sizeof(long)=%d sizeof(igraph_integer_t)=%d\n", (int) sizeof(int), (int) sizeof(long), (int) sizeof(igraph_integer_t));
pause();
printf("Loading graph from file...\n");
FILE* f = fopen("donnees/arretes.test", "r");
//FILE* f = fopen("graph_a.ncol", "r");
igraph_t gr;
igraph_read_graph_ncol(&gr, f, NULL, 1, 0, 0);
fclose(f);
f = NULL;
long vcount = igraph_vcount(&gr);
long ecount = igraph_ecount(&gr);
printf("Main graph: |V| = %ld, |E| = %ld\n", vcount, ecount);
pause();
// get connected components
printf("Computing connected components...\n");
igraph_vector_t membership;
igraph_vector_t csize;
igraph_integer_t cnum = 0;
igraph_vector_init(&membership, 1);
igraph_vector_init(&csize, 1);
igraph_clusters(&gr, &membership, &csize, &cnum, IGRAPH_STRONG);
printf("There are %ld connected components.\n", (long) cnum);
// work with connected components
{
printf("Writing connected components to file...\n");
// open file
FILE* filout = fopen("groupes", "w");
long membership_size = igraph_vector_size(&membership);
if (membership_size != vcount) {
fprintf(stderr, "FATAL ERROR: membership_size != vcount\n");
exit(1);
}
for (long i = 0; i < membership_size; i++) {
fprintf(filout,
"%ld\t%s\n",
// connected component id:
(long) igraph_vector_e(&membership , i),
// veretex name:
igraph_cattribute_VAS(&gr, "name", i));
}
fclose(filout);
filout = NULL;
printf("Connected components written.\n");
}
pause();
// free connected components
igraph_vector_destroy(&membership);
igraph_vector_destroy(&csize);
// free main graph
igraph_destroy(&gr);
printf("Program ends.\n");
pause();
return 0;
}
int main(int argc, char *argv[])
{
if (argc == 2)
{
char *inputFile = malloc(sizeof(char)*50);
inputFile = (char *) argv[1];
// Funzione che crea una tabella di attributi da assegnare agli argomenti del grafo.
// Concretamente, essa viene chiamata per una visualizzazione più immediata del risultato del SAT Solver.
igraph_i_set_attribute_table(&igraph_cattribute_table);
// Chiamata alla funzione presente nel file "file.c", che legge un file e crea un grafo orientato.
igraph_t g;
graph myGraph = {g, malloc(sizeof(int)*100000)};
myGraph = openFile_and_createGraph(inputFile);
cnf myCNF = {malloc(sizeof(char)*999999999), 0, 0, 0};
myCNF.expr[0] = '\0'; // Assegnazione necessaria per il corretto funzionamento di "strcat()".
cnf cnfdf = {malloc(sizeof(char)*999999999), 0, 0, 0};
// Chiamata alla funzione presente nel file "createCNF.c", la quale chiama altre funzioni e calcola la CNF.
myCNF = createCNF(myCNF, myGraph);
preferredExtension myPE = {malloc(sizeof(char)*999999999), 0};
myPE.ep[0] = '\0'; // Assegnazione necessaria per il corretto funzionamento di "strcat()".
int num_variables = 3*(igraph_vcount(&(myGraph.graph)));
int last_comp_found[num_variables];
int ret_value = 0, pref_cand;
// Enumerating the preferred extensions of an Argumentation Framework.
do
{
strcpy(cnfdf.expr, myCNF.expr);
cnfdf.num_clauses = myCNF.num_clauses;
pref_cand = 0;
do
{
cnfdf.undec_args = 0;
cnfdf.not_in_args = 0;
ret_value = glucoseSAT(cnfdf.expr, num_variables, cnfdf.num_clauses, last_comp_found);
if (ret_value == 10)
{
pref_cand = 1;
cnfdf = firstIf(cnfdf, ret_value, num_variables, last_comp_found, myGraph);
}
} while (ret_value == 10 && cnfdf.undec_args == 1);
if (pref_cand == 1)
{
myCNF = secondIf(myCNF, num_variables, last_comp_found, myGraph, myPE);
myPE.num_extensions++;
}
} while (pref_cand == 1);
if (strlen(myPE.ep) == 0)
strcat(myPE.ep, "{}");
printf("%s", myPE.ep);
igraph_destroy(&(myGraph.graph));
}
else
{
printf("Missing input file.\n");
printf("###Running\n");
printf("./IgraphSAT <inputfile>\n");
}
return 0;
}
TGenGraph* tgengraph_new(gchar* path) {
if(!path || !g_file_test(path, G_FILE_TEST_IS_REGULAR|G_FILE_TEST_EXISTS)) {
tgen_critical("path '%s' to tgen config graph is not valid or does not exist", path);
return NULL;
}
TGenGraph* g = g_new0(TGenGraph, 1);
g->magic = TGEN_MAGIC;
g->actions = g_hash_table_new_full(g_direct_hash, g_direct_equal, NULL, (GDestroyNotify)tgenaction_unref);
g->weights = g_hash_table_new_full(g_direct_hash, g_direct_equal, NULL, g_free);
g->graphPath = path ? _tgengraph_getHomePath(path) : NULL;
GError* error = NULL;
gboolean exists = g_file_test(g->graphPath, G_FILE_TEST_IS_REGULAR|G_FILE_TEST_EXISTS);
if(!exists) {
error = g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"graph file does not exist at path '%s'", g->graphPath);
}
if(!error && g->graphPath) {
tgen_lock();
/* use the built-in C attribute handler */
igraph_attribute_table_t* oldHandler = igraph_i_set_attribute_table(&igraph_cattribute_table);
g->graph = _tgengraph_loadNewGraph(g->graphPath);
if(!g->graph) {
error = g_error_new(G_MARKUP_ERROR, G_MARKUP_ERROR_PARSE,
"unable to read graph at path '%s'", g->graphPath);
}
/* parse edges first for choose, needs hash table of weights filled for error handling */
if(!error) {
error = _tgengraph_parseGraphProperties(g);
}
if(!error) {
error = _tgengraph_parseGraphEdges(g);
}
if(!error) {
error = _tgengraph_parseGraphVertices(g);
}
/* replace the old handler */
igraph_i_set_attribute_table(oldHandler);
tgen_unlock();
}
if(error) {
tgen_critical("error (%i) while loading graph: %s", error->code, error->message);
g_error_free(error);
tgengraph_free(g);
return NULL;
}
tgen_message("successfully loaded graphml file '%s' and validated actions: "
"graph is %s with %u %s, %u %s, and %u %s", g->graphPath,
g->isConnected ? "weakly connected" : "disconnected",
(guint)g->clusterCount, g->clusterCount == 1 ? "cluster" : "clusters",
(guint)g->vertexCount, g->vertexCount == 1 ? "vertex" : "vertices",
(guint)g->edgeCount, g->edgeCount == 1 ? "edge" : "edges");
return g;
}
int main() {
igraph_t g, g2;
igraph_attribute_combination_t comb;
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_small(&g, 4, IGRAPH_DIRECTED,
0, 1, 0, 1, 0, 1,
1, 2, 2, 3,
-1);
SETEAB(&g, "type", 0, 1);
SETEAB(&g, "type", 1, 1);
SETEAB(&g, "type", 2, 0);
SETEAB(&g, "type", 3, 0);
SETEAB(&g, "type", 4, 1);
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_SUM,
"type", IGRAPH_ATTRIBUTE_COMBINE_FIRST,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_LAST,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_LAST,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_SUM,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_PROD,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_MIN,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_MAX,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_MEAN,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
"type", IGRAPH_ATTRIBUTE_COMBINE_MEDIAN,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout, /*prefixattr=*/ 1);
igraph_destroy(&g2);
/* ****************************************************** */
igraph_destroy(&g);
return 0;
}
int main() {
igraph_t g;
igraph_matrix_t mat;
int m[4][4] = { { 0, 1, 2, 0 }, { 2, 0, 0, 1 }, { 0, 0, 1, 0 }, { 0, 1, 0, 0 } };
long int i, j;
igraph_matrix_init(&mat, 4, 4);
for (i=0; i<4; i++) for (j=0; j<4; j++) MATRIX(mat, i, j) = m[i][j];
igraph_i_set_attribute_table(&igraph_cattribute_table);
/* [ 0 1 2 0 ]
[ 2 0 0 1 ]
[ 0 0 1 0 ]
[ 0 1 0 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_DIRECTED, 0);
print(&g);
igraph_destroy(&g);
/* [ 0 1 2 0 ]
[ - 0 0 1 ]
[ - - 1 0 ]
[ - - - 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_UPPER, 0);
print(&g);
igraph_destroy(&g);
/* [ 0 - - - ]
[ 2 0 - - ]
[ 0 0 1 - ]
[ 0 1 0 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_LOWER, 0);
print(&g);
igraph_destroy(&g);
/* [ 0 1 0 0 ]
[ 1 0 0 1 ]
[ 0 0 1 0 ]
[ 0 1 0 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_MIN, 0);
print(&g);
igraph_destroy(&g);
/* [ 0 2 2 0 ]
[ 2 0 0 1 ]
[ 2 0 1 0 ]
[ 0 1 0 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_MAX, 0);
print(&g);
igraph_destroy(&g);
/* [ 0 3 2 0 ]
[ 3 0 0 2 ]
[ 2 0 1 0 ]
[ 0 2 0 0 ] */
igraph_weighted_adjacency(&g, &mat, IGRAPH_ADJ_PLUS, 0);
print(&g);
igraph_destroy(&g);
igraph_matrix_destroy(&mat);
if (IGRAPH_FINALLY_STACK_SIZE() != 0) return 1;
return 0;
}
int main() {
igraph_t g, g2;
igraph_vector_t weight;
igraph_attribute_combination_t comb;
igraph_i_set_attribute_table(&igraph_cattribute_table);
igraph_small(&g, 4, IGRAPH_DIRECTED,
0, 1, 0, 1, 0, 1,
1, 2, 2, 3,
-1);
igraph_vector_init_seq(&weight, 1, igraph_ecount(&g));
SETEANV(&g, "weight", &weight);
igraph_vector_destroy(&weight);
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_SUM,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_PROD,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_MIN,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_MAX,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_FIRST,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_LAST,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_MEAN,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"weight", IGRAPH_ATTRIBUTE_COMBINE_FUNCTION, mf,
"", IGRAPH_ATTRIBUTE_COMBINE_IGNORE,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
/* ****************************************************** */
igraph_copy(&g2, &g);
igraph_attribute_combination(&comb,
"", IGRAPH_ATTRIBUTE_COMBINE_MEAN,
IGRAPH_NO_MORE_ATTRIBUTES);
igraph_simplify(&g2, /*multiple=*/ 1, /*loops=*/ 1, &comb);
igraph_attribute_combination_destroy(&comb);
igraph_write_graph_graphml(&g2, stdout);
igraph_destroy(&g2);
/* ****************************************************** */
igraph_destroy(&g);
return 0;
}
int main(int argc,char** argv)
{
int c;
int option_index = 0;
int status = 0;
// parse options
while(1)
{
c = getopt_long(argc, argv, short_opts,long_options, &option_index);
if(c == -1)
break;
switch(c)
{
case 0:
break;
case 'r':
rngfname = optarg;
break;
case 'o':
outfname = optarg;
break;
case 'i':
infname = optarg;
break;
case 'n':
name = optarg;
break;
case 'h':
ask_help = 1;
break;
case 'V':
ask_version =1;
break;
case 'f':
logfname = optarg;
break;
case 'l':
logval = optarg;
break;
default:
fprintf(stderr,"ggen bug: someone forgot how to write a switch\n");
exit(EXIT_FAILURE);
case '?':
fprintf(stderr,"ggen bug: getopt failed miserably\n");
exit(EXIT_FAILURE);
}
}
// forget the parsed part of argv
argc -= optind;
argv = &(argv[optind]);
if(ask_full_help)
{
print_full_help();
exit(EXIT_SUCCESS);
}
if(ask_version)
{
print_version();
exit(EXIT_SUCCESS);
}
if(argc == 0)
{
print_help(general_help);
exit(EXIT_FAILURE);
}
// initialize logging
if(logfname != NULL)
{
logfile = fopen(logfname,"w");
if(!logfile)
{
fprintf(stderr,"failed to open file %s for logging, using stderr instead\n",logfname);
logfile = stderr;
logfname = NULL;
}
}
else
logfile = stderr;
status = log_init(logfile,"ggen");
if(status)
{
fprintf(stderr,"error during log initialization\n");
exit(EXIT_FAILURE);
}
// now set level according to options
unsigned long l;
if(logval != NULL)
{
status = s2ul(logval,&l);
if(status)
{
warning("Cannot convert log level option to int\n");
l = LOG_NORMAL;
}
else if(l < LOG_QUIET || l > LOG_DEBUG)
{
warning("Incorrect log level value, must be between %d and %d\n",LOG_QUIET,LOG_DEBUG);
l = LOG_NORMAL;
}
}
else
l = LOG_NORMAL;
log_filter_above((enum log_level)l);
normal("Logging facility initialized\n");
// initialize igraph attributes for all commands
igraph_i_set_attribute_table(&igraph_cattribute_table);
// find the command to launch
info("Searching for command %s\n",argv[0]);
for(int i = 0; i < ARRAY_SIZE(cmd_table); i++)
{
struct first_lvl_cmd *c = cmd_table+i;
if(!strcmp(c->name,argv[0]))
{
argc--;
argv++;
status = handle_first_lvl(argc,argv,c);
goto end;
}
}
status = EXIT_FAILURE;
error("Command not found\n");
end:
// close logging
normal("Closing log\n");
if(logfname)
{
fclose(logfile);
}
return status;
}
int main() {
igraph_t g, g2;
FILE *ifile;
igraph_vector_t gtypes, vtypes, etypes;
igraph_strvector_t gnames, vnames, enames;
long int i;
igraph_vector_t y;
igraph_strvector_t id;
char str[20];
/* turn on attribute handling */
igraph_i_set_attribute_table(&igraph_cattribute_table);
ifile=fopen("LINKS.NET", "r");
if (ifile==0) {
return 10;
}
igraph_read_graph_pajek(&g, ifile);
fclose(ifile);
igraph_vector_init(>ypes, 0);
igraph_vector_init(&vtypes, 0);
igraph_vector_init(&etypes, 0);
igraph_strvector_init(&gnames, 0);
igraph_strvector_init(&vnames, 0);
igraph_strvector_init(&enames, 0);
igraph_cattribute_list(&g, &gnames, >ypes, &vnames, &vtypes,
&enames, &etypes);
/* List attribute names and types */
printf("Graph attributes: ");
for (i=0; i<igraph_strvector_size(&gnames); i++) {
printf("%s (%i) ", STR(gnames, i), (int)VECTOR(gtypes)[i]);
}
printf("\n");
printf("Vertex attributes: ");
for (i=0; i<igraph_strvector_size(&vnames); i++) {
printf("%s (%i) ", STR(vnames, i), (int)VECTOR(vtypes)[i]);
}
printf("\n");
printf("Edge attributes: ");
for (i=0; i<igraph_strvector_size(&enames); i++) {
printf("%s (%i) ", STR(enames, i), (int)VECTOR(etypes)[i]);
}
printf("\n");
print_attributes(&g);
/* Copying a graph */
igraph_copy(&g2, &g);
print_attributes(&g2);
igraph_destroy(&g2);
/* Adding vertices */
igraph_add_vertices(&g, 3, 0);
print_attributes(&g);
/* Adding edges */
igraph_add_edge(&g, 1, 1);
igraph_add_edge(&g, 2, 5);
igraph_add_edge(&g, 3, 6);
print_attributes(&g);
/* Deleting vertices */
igraph_delete_vertices(&g, igraph_vss_1(1));
igraph_delete_vertices(&g, igraph_vss_1(4));
print_attributes(&g);
/* Deleting edges */
igraph_delete_edges(&g, igraph_ess_1(igraph_ecount(&g)-1));
igraph_delete_edges(&g, igraph_ess_1(0));
print_attributes(&g);
/* Set graph attributes */
SETGAN(&g, "id", 10);
if (GAN(&g, "id") != 10) {
return 11;
}
SETGAS(&g, "name", "toy");
if (strcmp(GAS(&g, "name"), "toy")) {
return 12;
}
/* Delete graph attributes */
DELGA(&g, "id");
DELGA(&g, "name");
igraph_cattribute_list(&g, &gnames, 0,0,0,0,0);
if (igraph_strvector_size(&gnames) != 0) {
return 14;
}
/* Delete vertex attributes */
DELVA(&g, "x");
DELVA(&g, "shape");
DELVA(&g, "xfact");
DELVA(&g, "yfact");
igraph_cattribute_list(&g, 0,0, &vnames, 0,0,0);
if (igraph_strvector_size(&vnames) != 2) {
return 15;
}
/* Delete edge attributes */
igraph_cattribute_list(&g, 0,0,0,0,&enames,0);
i=igraph_strvector_size(&enames);
DELEA(&g, "hook1");
DELEA(&g, "hook2");
DELEA(&g, "label");
igraph_cattribute_list(&g, 0,0,0,0,&enames,0);
if (igraph_strvector_size(&enames) != i-3) {
return 16;
}
/* Set vertex attributes */
SETVAN(&g, "y", 0, -1);
SETVAN(&g, "y", 1, 2.1);
if (VAN(&g, "y", 0) != -1 ||
VAN(&g, "y", 1) != 2.1) {
return 17;
}
SETVAS(&g, "id", 0, "foo");
SETVAS(&g, "id", 1, "bar");
if (strcmp(VAS(&g, "id", 0), "foo") ||
strcmp(VAS(&g, "id", 1), "bar")) {
return 18;
}
/* Set edge attributes */
SETEAN(&g, "weight", 2, 100.0);
SETEAN(&g, "weight", 0, -100.1);
if (EAN(&g, "weight", 2) != 100.0 ||
EAN(&g, "weight", 0) != -100.1) {
return 19;
}
SETEAS(&g, "color", 2, "RED");
SETEAS(&g, "color", 0, "Blue");
if (strcmp(EAS(&g, "color", 2), "RED") ||
strcmp(EAS(&g, "color", 0), "Blue")) {
return 20;
}
/* Set vector attributes as vector */
igraph_vector_init(&y, igraph_vcount(&g));
igraph_vector_fill(&y, 1.23);
SETVANV(&g, "y", &y);
igraph_vector_destroy(&y);
for (i=0; i<igraph_vcount(&g); i++) {
if (VAN(&g, "y", i) != 1.23) {
return 21;
}
}
igraph_vector_init_seq(&y, 0, igraph_vcount(&g)-1);
SETVANV(&g, "foobar", &y);
igraph_vector_destroy(&y);
for (i=0; i<igraph_vcount(&g); i++) {
if (VAN(&g, "foobar", i) != i) {
return 22;
}
}
igraph_strvector_init(&id, igraph_vcount(&g));
for (i=0; i<igraph_vcount(&g); i++) {
snprintf(str, sizeof(str)-1, "%li", i);
igraph_strvector_set(&id, i, str);
}
SETVASV(&g, "foo", &id);
igraph_strvector_destroy(&id);
for (i=0; i<igraph_vcount(&g); i++) {
printf("%s ", VAS(&g, "foo", i));
}
printf("\n");
igraph_strvector_init(&id, igraph_vcount(&g));
for (i=0; i<igraph_vcount(&g); i++) {
snprintf(str, sizeof(str)-1, "%li", i);
igraph_strvector_set(&id, i, str);
}
SETVASV(&g, "id", &id);
igraph_strvector_destroy(&id);
for (i=0; i<igraph_vcount(&g); i++) {
printf("%s ", VAS(&g, "id", i));
}
printf("\n");
/* Set edge attributes as vector */
igraph_vector_init(&y, igraph_ecount(&g));
igraph_vector_fill(&y, 12.3);
SETEANV(&g, "weight", &y);
igraph_vector_destroy(&y);
for (i=0; i<igraph_ecount(&g); i++) {
if (EAN(&g, "weight", i) != 12.3) {
return 23;
}
}
igraph_vector_init_seq(&y, 0, igraph_ecount(&g)-1);
SETEANV(&g, "foobar", &y);
igraph_vector_destroy(&y);
for (i=0; i<igraph_ecount(&g); i++) {
if (VAN(&g, "foobar", i) != i) {
return 24;
}
}
igraph_strvector_init(&id, igraph_ecount(&g));
for (i=0; i<igraph_ecount(&g); i++) {
snprintf(str, sizeof(str)-1, "%li", i);
igraph_strvector_set(&id, i, str);
}
SETEASV(&g, "foo", &id);
igraph_strvector_destroy(&id);
for (i=0; i<igraph_ecount(&g); i++) {
printf("%s ", EAS(&g, "foo", i));
}
printf("\n");
igraph_strvector_init(&id, igraph_ecount(&g));
for (i=0; i<igraph_ecount(&g); i++) {
snprintf(str, sizeof(str)-1, "%li", i);
igraph_strvector_set(&id, i, str);
}
SETEASV(&g, "color", &id);
igraph_strvector_destroy(&id);
for (i=0; i<igraph_ecount(&g); i++) {
printf("%s ", EAS(&g, "color", i));
}
printf("\n");
/* Delete all remaining attributes */
DELALL(&g);
igraph_cattribute_list(&g, &gnames, >ypes, &vnames, &vtypes, &enames, &etypes);
if (igraph_strvector_size(&gnames) != 0 ||
igraph_strvector_size(&vnames) != 0 ||
igraph_strvector_size(&enames) != 0) {
return 25;
}
/* Destroy */
igraph_vector_destroy(>ypes);
igraph_vector_destroy(&vtypes);
igraph_vector_destroy(&etypes);
igraph_strvector_destroy(&gnames);
igraph_strvector_destroy(&vnames);
igraph_strvector_destroy(&enames);
igraph_destroy(&g);
return 0;
}
//-------------------------------------------------------------------------------------------------
int main(int argc, char **argv) {
igraph_set_error_handler(igraph_error_handler_printignore);
igraph_i_set_attribute_table(&igraph_cattribute_table);
drawingcontrol=1;
runningcontrol=0;
cleared=1;
graphisloaded=0;
newgraph=1;
usesteady=0;
ispii=0;
haveout=0;
isrelaxed=0;
havecstop=0;
isdissipating=0;
//RANDOM NUMBER GENERATOR INITIALISE
init_genrand(0); //srand(3);
//preloaded graph:
{
latticedim=2;
latticeside=5;
istoro=1;
islattice=1;
isclustered=0;
israndomER1=0;
generatelattice(2,5,1,0,0,0,0);
//inizializations
igraph_matrix_init(&state, 0, 0);
igraph_matrix_init(&density, 0, 0);
igraph_matrix_init(&densityold,0,0);
igraph_matrix_init(&statenew, 0, 0);
igraph_matrix_init(&flux, 0, 0);
igraph_matrix_init(&loss, 0, 0);
beginner=(nodesnumber/2);
InitialStateTAS(beginner,0,totrun);
igraph_vector_init(&gain,nodesnumber);
graphisloaded=1;
newgraph=1;
haveloadedstate=0;
drnodes=1;
drlinks=1;
drfluxes=0;
}
havepath=0;
sprintf(path,"No path");
logDebug("\n DEFAULT ADJ MATRIX:\n");
print_matrix_ur(&admatrix,stdout);
printf("\n");
printf("\n");
rewrite=1;
CreateMyWindow();
//Fl::add_timeout(1.0,mainidle_cb);
Fl::add_idle(mainidle_cb, 0);
Fl::run();
histdist.Clear();
igraph_destroy(&graph);
igraph_destroy(&sgraph);
igraph_matrix_destroy(&admatrix);
igraph_matrix_destroy(&layout);
igraph_matrix_destroy(&density);
igraph_matrix_destroy(&densityold);
igraph_matrix_destroy(&state);
igraph_matrix_destroy(&loadedstate);
igraph_matrix_destroy(&statenew);
igraph_matrix_destroy(&flux);
igraph_vector_destroy(&gain);
igraph_matrix_destroy(&loss);
igraph_vector_destroy(&statstate);
igraph_matrix_destroy(&estates);
closeout();
return 0;
}
int main(int argc, char **argv) {
igraph_t g;
igraph_error_handler_t* oldhandler;
igraph_warning_handler_t* oldwarnhandler;
int result;
FILE *ifile, *ofile;
igraph_i_set_attribute_table(&igraph_cattribute_table);
/* GraphML */
ifile=fopen("test.gxl", "r");
if (ifile==0) {
return 10;
}
oldhandler=igraph_set_error_handler(igraph_error_handler_ignore);
oldwarnhandler=igraph_set_warning_handler(custom_warning_handler);
if ((result=igraph_read_graph_graphml(&g, ifile, 0))) {
/* maybe it is simply disabled at compile-time */
if (result == IGRAPH_UNIMPLEMENTED) return 77;
return 1;
}
igraph_set_error_handler(oldhandler);
fclose(ifile);
/* Write it back */
ofile=fopen("test2.gxl", "w");
/* If we can't create the test file, just skip the test */
if (ofile) {
if ((result=igraph_write_graph_graphml(&g, ofile, /*prefixattr=*/ 1))) {
return 1;
}
fclose(ofile);
unlink("test2.gxl");
}
dump_graph("The directed graph:\n", &g);
igraph_destroy(&g);
/* The same with undirected graph */
ifile=fopen("test.gxl", "r");
if ((result=igraph_read_graph_graphml(&g, ifile, 0))) {
return 1;
}
fclose(ifile);
dump_graph("The undirected graph:\n", &g);
igraph_destroy(&g);
/* Test a GraphML file with default attributes */
ifile=fopen("graphml-default-attrs.xml", "r");
if ((result=igraph_read_graph_graphml(&g, ifile, 0))) {
return 1;
}
fclose(ifile);
dump_graph("The directed graph:\n", &g);
dump_vertex_attribute_bool("type", &g);
dump_vertex_attribute_string("gender", &g);
dump_vertex_attribute_numeric("age", &g);
dump_vertex_attribute_bool("retired", &g);
igraph_destroy(&g);
/* Test a GraphML file with namespaces */
ifile=fopen("graphml-namespace.xml", "r");
if ((result=igraph_read_graph_graphml(&g, ifile, 0))) {
return 1;
}
fclose(ifile);
dump_graph("The undirected graph:\n", &g);
igraph_destroy(&g);
/* Restore the old warning handler */
igraph_set_warning_handler(oldwarnhandler);
/* There were sometimes problems with this file */
/* Only if called from R though, and only on random occasions, once in every
ten reads. Do testing here doesn't make much sense, but if we have the file
then let's do it anyway. */
ifile=fopen("graphml-hsa05010.xml", "r");
igraph_read_graph_graphml(&g, ifile, 0);
fclose(ifile);
igraph_destroy(&g);
return 0;
}
