#include "igraph.h" #include "ruby.h" #include "cIGraph.h" //Classes VALUE cIGraph; VALUE cIGraphError; void cIGraph_free(void *p){ igraph_destroy(p); free(p); } void cIGraph_mark(void *p){ rb_gc_mark(((VALUE*)((igraph_t*)p)->attr)[0]); rb_gc_mark(((VALUE*)((igraph_t*)p)->attr)[1]); rb_gc_mark(((VALUE*)((igraph_t*)p)->attr)[2]); } VALUE cIGraph_alloc(VALUE klass){ igraph_t *graph = malloc(sizeof(igraph_t)); VALUE obj; igraph_empty(graph, 0, 1); obj = Data_Wrap_Struct(klass, cIGraph_mark, cIGraph_free, graph); return obj; } /* Document-method: initialize_copy * * Internal method for copying IGraph objects. */ VALUE cIGraph_init_copy(VALUE copy, VALUE orig){ igraph_t *orig_graph; igraph_t *copy_graph; if (copy == orig) return copy; if(TYPE(orig) != T_DATA || RDATA(orig)->dfree != (RUBY_DATA_FUNC)cIGraph_free){ rb_raise(rb_eTypeError, "Wrong argument type."); } Data_Get_Struct(copy, igraph_t, copy_graph); Data_Get_Struct(orig, igraph_t, orig_graph); IGRAPH_CHECK(igraph_copy(copy_graph,orig_graph)); return copy; } /* call-seq: * IGraph.new(edges,directed) -> IGraph * * Creates a new IGraph graph with the edges specified in the edges Array. * The first two elements define the first edge (the order is from,to for * directed graphs). The next two define the second edge and so on. The * Array should contain an even number of elements. Graph elements can be * any ruby object. * * The boolean value directed specifies whether a directed or undirected * graph is created. * * Example: * * IGraph.new([1,2,3,4],true) * * Creates a graph with four vertices. Vertex 1 is connected to vertex 2. * Vertex 3 is connected to vertex 4. */ VALUE cIGraph_initialize(int argc, VALUE *argv, VALUE self){ igraph_t *graph; igraph_vector_t edge_v; VALUE vertex; VALUE directed; VALUE edges; VALUE attrs; VALUE v_ary; int vertex_n = 0; int current_vertex_id; int i; igraph_vector_ptr_t vertex_attr; igraph_vector_ptr_t edge_attr; igraph_i_attribute_record_t v_attr_rec; v_attr_rec.name = "__RUBY__"; v_attr_rec.type = IGRAPH_ATTRIBUTE_PY_OBJECT; v_attr_rec.value = (void*)rb_ary_new(); igraph_i_attribute_record_t e_attr_rec; e_attr_rec.name = "__RUBY__"; e_attr_rec.type = IGRAPH_ATTRIBUTE_PY_OBJECT; e_attr_rec.value = (void*)rb_ary_new(); rb_scan_args(argc,argv,"12", &edges, &directed, &attrs); //Initialize edge vector IGRAPH_FINALLY(igraph_vector_destroy,&edge_v); IGRAPH_FINALLY(igraph_vector_ptr_destroy,&vertex_attr); IGRAPH_FINALLY(igraph_vector_ptr_destroy,&edge_attr); IGRAPH_CHECK(igraph_vector_init_int(&edge_v,0)); IGRAPH_CHECK(igraph_vector_ptr_init(&vertex_attr,0)); IGRAPH_CHECK(igraph_vector_ptr_init(&edge_attr,0)); Data_Get_Struct(self, igraph_t, graph); v_ary = rb_ary_new(); if(!directed) IGRAPH_CHECK(igraph_to_undirected(graph,IGRAPH_TO_UNDIRECTED_COLLAPSE)); //Loop through objects in edge Array for (i=0; i 0){ IGRAPH_CHECK(igraph_add_vertices(graph,vertex_n,&vertex_attr)); IGRAPH_CHECK(igraph_add_edges(graph,&edge_v,&edge_attr)); } igraph_vector_destroy(&edge_v); igraph_vector_ptr_destroy(&vertex_attr); igraph_vector_ptr_destroy(&edge_attr); IGRAPH_FINALLY_CLEAN(3); return self; } VALUE cIGraph_unavailable_method(int argc, VALUE *argv, VALUE self){ rb_raise(rb_eNoMethodError,"Method not available on OSX"); } /* Interface to the iGraph[http://cneurocvs.rmki.kfki.hu/igraph/] library * for graph and network computation. * * Basic graph operations are defined on the IGraph class itself, but many * other operations are defined in Modules included into IGraph: * * - Deterministic graph generation: IGraph::Generate * - Random graph generation: IGraph::GenerateRandom * - Graph randomisation: IGraph::Randomise * - Shortest paths: IGraph::ShortestPaths * - Vertex neighborhoods: IGraph::Neighborhood * - Graph components: IGraph::Components * - Closeness centrality calculations: IGraph::Closeness * - Spanning tree: IGraph::Spanning * - Transitivity calculations: IGraph::Transitivity * - Spectral properties: IGraph::Spectral * - Coreness: IGraph::KCores * - Other operations: IGraph::OtherOperations * - Clique calculations: IGraph::Cliques * - Independent vertex sets: IGraph::IndependentVertexSets * - Graph isomorphism: IGraph::Isomorphism * - Motifs: IGraph::Motifs * - Sorting: IGraph::Sorting * - File read/write: IGraph::FileRead, IGraph::FileWrite * - Graph layout algorithms: IGraph::Layout * - Minimum cuts: IGraph::MinimumCuts * - Connectivity: IGraph::Connectivity * - Community: IGraph::Community * * Some methods return (or require as a paramter) an IGraphMatrix object. This * class wraps the igraph C matrix type. */ 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 */ }