int main() {
igraph_t g;
igraph_vector_ptr_t result;
igraph_es_t es;
igraph_integer_t omega;
long int i, j, n;
const int params[] = {4, -1, 2, 2, 0, 0, -1, -1};
igraph_set_warning_handler(warning_handler_ignore);
igraph_vector_ptr_init(&result, 0);
igraph_full(&g, 6, 0, 0);
igraph_es_pairs_small(&es, 0, 0, 1, 0, 2, 3, 5, -1);
igraph_delete_edges(&g, es);
igraph_es_destroy(&es);
for (j=0; j<sizeof(params)/(2*sizeof(params[0])); j++) {
if (params[2*j+1] != 0) {
igraph_cliques(&g, &result, params[2*j], params[2*j+1]);
} else {
igraph_largest_cliques(&g, &result);
}
n = igraph_vector_ptr_size(&result);
printf("%ld cliques found\n", (long)n);
canonicalize_list(&result);
for (i=0; i<n; i++) {
igraph_vector_t* v = (igraph_vector_t*) igraph_vector_ptr_e(&result,i);
print_vector(v);
igraph_vector_destroy(v);
free(v);
}
}
igraph_clique_number(&g, &omega);
printf("omega=%ld\n", (long)omega);
test_callback(&g);
igraph_destroy(&g);
igraph_tree(&g, 5, 2, IGRAPH_TREE_OUT);
igraph_cliques(&g, &result, 5, 5);
if (igraph_vector_ptr_size(&result) != 0) return 1;
igraph_destroy(&g);
igraph_vector_ptr_destroy(&result);
return 0;
}
int main() {
igraph_t g;
igraph_vector_t v, res, reset, weights;
igraph_arpack_options_t arpack_options;
igraph_real_t value;
int ret;
igraph_pagerank_power_options_t power_options;
/* Test graphs taken from http://www.iprcom.com/papers/pagerank/ */
igraph_vector_init(&v, 10);
VECTOR(v)[0]=0; VECTOR(v)[1]=1;
VECTOR(v)[2]=1; VECTOR(v)[3]=2;
VECTOR(v)[4]=2; VECTOR(v)[5]=0;
VECTOR(v)[6]=3; VECTOR(v)[7]=2;
VECTOR(v)[8]=0; VECTOR(v)[9]=2;
igraph_create(&g, &v, 0, 1);
igraph_vector_init(&res, 0);
oldwarn=igraph_set_warning_handler(warning_handler_stdout);
igraph_pagerank_old(&g, &res, igraph_vss_all(), 1, 1000, 0.001, 0.85, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&res);
igraph_vector_destroy(&v);
igraph_destroy(&g);
igraph_vector_init(&v, 28);
VECTOR(v)[ 0]=0; VECTOR(v)[ 1]=1;
VECTOR(v)[ 2]=0; VECTOR(v)[ 3]=2;
VECTOR(v)[ 4]=0; VECTOR(v)[ 5]=3;
VECTOR(v)[ 6]=1; VECTOR(v)[ 7]=0;
VECTOR(v)[ 8]=2; VECTOR(v)[ 9]=0;
VECTOR(v)[10]=3; VECTOR(v)[11]=0;
VECTOR(v)[12]=3; VECTOR(v)[13]=4;
VECTOR(v)[14]=3; VECTOR(v)[15]=5;
VECTOR(v)[16]=3; VECTOR(v)[17]=6;
VECTOR(v)[18]=3; VECTOR(v)[19]=7;
VECTOR(v)[20]=4; VECTOR(v)[21]=0;
VECTOR(v)[22]=5; VECTOR(v)[23]=0;
VECTOR(v)[24]=6; VECTOR(v)[25]=0;
VECTOR(v)[26]=7; VECTOR(v)[27]=0;
igraph_create(&g, &v, 0, 1);
igraph_vector_init(&res, 0);
igraph_pagerank_old(&g, &res, igraph_vss_all(), 1, 10000, 0.0001, 0.85, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&res);
igraph_vector_destroy(&v);
igraph_destroy(&g);
igraph_set_warning_handler(oldwarn);
/* New PageRank */
igraph_star(&g, 11, IGRAPH_STAR_UNDIRECTED, 0);
igraph_vector_init(&res, 0);
igraph_arpack_options_init(&arpack_options);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
/* Check twice more for consistency */
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, 0, 0);
print_vector(&res, stdout);
/* Check personalized PageRank */
igraph_personalized_pagerank_vs(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.5,
igraph_vss_1(1), 0, &arpack_options);
print_vector(&res, stdout);
igraph_personalized_pagerank_vs(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.5,
igraph_vss_1(1), 0, 0);
print_vector(&res, stdout);
/* Errors */
power_options.niter = -1; power_options.eps=0.0001;
igraph_set_error_handler(igraph_error_handler_ignore);
igraph_set_warning_handler(igraph_warning_handler_ignore);
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 0.85,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 1;
}
power_options.niter=10000; power_options.eps=-1;
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 0.85,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 2;
}
power_options.niter=10000; power_options.eps=0.0001;
ret=igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_POWER, &res,
/*value=*/ 0, igraph_vss_all(), 1, 1.2,
/*weights=*/ 0, &power_options);
if (ret != IGRAPH_EINVAL) {
return 3;
}
igraph_vector_init(&reset, 2);
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 0, 0.85, &reset, 0,
&arpack_options);
if (ret != IGRAPH_EINVAL) {
return 4;
}
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 0, 0.85, &reset, 0, 0);
if (ret != IGRAPH_EINVAL) {
return 4;
}
igraph_vector_resize(&reset, 10);
igraph_vector_fill(&reset, 0);
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK,
&res, 0, igraph_vss_all(), 0, 0.85,
&reset, 0, &arpack_options);
if (ret != IGRAPH_EINVAL) {
return 5;
}
ret=igraph_personalized_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK,
&res, 0, igraph_vss_all(), 0, 0.85,
&reset, 0, 0);
if (ret != IGRAPH_EINVAL) {
return 5;
}
igraph_vector_destroy(&reset);
igraph_destroy(&g);
igraph_set_error_handler(igraph_error_handler_abort);
/* Special cases: check for empty graph */
igraph_empty(&g, 10, 0);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, &value,
igraph_vss_all(), 1, 0.85, 0, &arpack_options);
if (value != 1.0) {
return 6;
}
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, &value,
igraph_vss_all(), 1, 0.85, 0, 0);
if (value != 1.0) {
return 6;
}
print_vector(&res, stdout);
igraph_destroy(&g);
/* Special cases: check for full graph, zero weights */
igraph_full(&g, 10, 0, 0);
igraph_vector_init(&v, 45);
igraph_vector_fill(&v, 0);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, &value,
igraph_vss_all(), 1, 0.85, &v, &arpack_options);
if (value != 1.0) {
return 7;
}
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, &value,
igraph_vss_all(), 1, 0.85, &v, 0);
if (value != 1.0) {
return 7;
}
igraph_vector_destroy(&v);
print_vector(&res, stdout);
igraph_destroy(&g);
/* Another test case for PageRank (bug #792352) */
igraph_small(&g, 9, 1, 0, 5, 1, 5, 2, 0, 3, 1, 5, 4, 5, 7, 6, 0, 8, 0, 8, 1, -1);
igraph_vector_init(&weights, 9);
VECTOR(weights)[0] = 4; VECTOR(weights)[1] = 5; VECTOR(weights)[2] = 5;
VECTOR(weights)[3] = 4; VECTOR(weights)[4] = 4; VECTOR(weights)[5] = 4;
VECTOR(weights)[6] = 3; VECTOR(weights)[7] = 4; VECTOR(weights)[8] = 4;
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_ARPACK, &res, 0,
igraph_vss_all(), 1, 0.85, &weights, &arpack_options);
print_vector(&res, stdout);
igraph_pagerank(&g, IGRAPH_PAGERANK_ALGO_PRPACK, &res, 0,
igraph_vss_all(), 1, 0.85, &weights, 0);
print_vector(&res, stdout);
igraph_vector_destroy(&weights);
igraph_destroy(&g);
igraph_vector_destroy(&res);
return 0;
}
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 */
}
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;
}
