394 lines
17 KiB
C
394 lines
17 KiB
C
#include "math.h"
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#include "ruby.h"
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#include "igraph.h"
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//#define DEBUG
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//Classes
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extern VALUE cIGraph;
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extern VALUE cIGraphError;
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extern VALUE cIGraphMatrix;
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extern igraph_attribute_table_t cIGraph_attribute_table;
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//Error and warning handling functions
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void cIGraph_error_handler(const char *reason, const char *file,
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int line, int igraph_errno);
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void cIGraph_warning_handler(const char *reason, const char *file,
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int line, int igraph_errno);
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//IGraph specific utility functions
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igraph_integer_t cIGraph_get_vertex_id(VALUE graph, VALUE v);
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VALUE cIGraph_get_vertex_object(VALUE graph, igraph_integer_t n);
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int cIGraph_vertex_arr_to_id_vec(VALUE graph, VALUE va, igraph_vector_t *nv);
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VALUE cIGraph_include(VALUE self, VALUE v);
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//IGraph allocation, destruction and intialization
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void Init_igraph(void);
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void cIGraph_free(void *p);
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void cIGraph_mark(void *p);
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VALUE cIGraph_alloc(VALUE klass);
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VALUE cIGraph_initialize(int argc, VALUE *argv, VALUE self);
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VALUE cIGraph_init_copy(VALUE copy, VALUE orig);
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//Graph generators
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VALUE cIGraph_adjacency(VALUE self, VALUE matrix, VALUE mode);
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VALUE cIGraph_star (VALUE self, VALUE n, VALUE mode, VALUE center);
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VALUE cIGraph_lattice (VALUE self, VALUE dim, VALUE directed, VALUE mutual, VALUE circular);
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VALUE cIGraph_ring(VALUE self, VALUE n, VALUE directed, VALUE mutual, VALUE circular);
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VALUE cIGraph_tree(VALUE self, VALUE n, VALUE children, VALUE type);
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VALUE cIGraph_full(VALUE self, VALUE n, VALUE directed, VALUE loops);
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VALUE cIGraph_atlas(VALUE self, VALUE n);
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VALUE cIGraph_extended_chordal_ring(VALUE self, VALUE n, VALUE matrix);
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VALUE cIGraph_connect_neighborhood(VALUE self, VALUE order, VALUE mode);
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//Random graph generators
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VALUE cIGraph_grg_game (VALUE self, VALUE nodes,
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VALUE radius, VALUE torus);
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VALUE cIGraph_barabasi_game(VALUE self, VALUE nodes,
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VALUE m, VALUE outpref, VALUE directed);
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VALUE cIGraph_nonlinear_barabasi_game(VALUE self, VALUE nodes, VALUE power,
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VALUE m, VALUE outpref, VALUE zeroappeal, VALUE directed);
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VALUE cIGraph_erdos_renyi_game (VALUE self, VALUE type, VALUE nodes, VALUE mp, VALUE directed, VALUE loops);
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VALUE cIGraph_watts_strogatz_game(VALUE self, VALUE dim, VALUE size, VALUE nei, VALUE p);
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VALUE cIGraph_degree_sequence_game(VALUE self, VALUE out_deg, VALUE in_deg);
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VALUE cIGraph_growing_random_game(VALUE self, VALUE n, VALUE m, VALUE directed, VALUE citation);
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VALUE cIGraph_callaway_traits_game(VALUE self, VALUE nodes, VALUE types, VALUE e_per_step, VALUE type_dist, VALUE pref_matrix, VALUE directed);
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VALUE cIGraph_establishment_game(VALUE self, VALUE nodes, VALUE types, VALUE k, VALUE type_dist, VALUE pref_matrix, VALUE directed);
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VALUE cIGraph_preference_game(VALUE self, VALUE nodes, VALUE types, VALUE type_dist, VALUE pref_matrix, VALUE directed, VALUE loops);
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VALUE cIGraph_asymmetric_preference_game(VALUE self, VALUE nodes, VALUE types, VALUE type_dist_matrix, VALUE pref_matrix, VALUE loops);
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VALUE cIGraph_recent_degree_game(VALUE self, VALUE n, VALUE power, VALUE window, VALUE m, VALUE outpref, VALUE zero_appeal, VALUE directed);
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VALUE cIGraph_barabasi_aging_game(VALUE self, VALUE nodes, VALUE m, VALUE outpref, VALUE pa_exp, VALUE aging_exp, VALUE aging_bin, VALUE zero_deg_appeal, VALUE zero_age_appeal, VALUE deg_coef, VALUE age_coef, VALUE directed);
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VALUE cIGraph_recent_degree_aging_game(VALUE self, VALUE nodes, VALUE m, VALUE outpref, VALUE pa_exp, VALUE aging_exp, VALUE aging_bin, VALUE time_window, VALUE zero_appeal, VALUE directed);
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VALUE cIGraph_cited_type_game(VALUE self, VALUE nodes, VALUE types, VALUE pref, VALUE e_per_s, VALUE directed);
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VALUE cIGraph_citing_cited_type_game(VALUE self, VALUE nodes, VALUE types, VALUE pref, VALUE e_per_s, VALUE directed);
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VALUE cIGraph_rewire_edges(VALUE self, VALUE prop);
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VALUE cIGraph_rewire(VALUE self, VALUE n, VALUE mode);
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//Attribute accessors
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int replace_i(VALUE key, VALUE val, VALUE hash);
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VALUE cIGraph_get_edge_attr(VALUE self, VALUE from, VALUE to);
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VALUE cIGraph_set_edge_attr(VALUE self, VALUE from, VALUE to, VALUE attr);
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VALUE cIGraph_graph_attributes(VALUE self);
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igraph_i_attribute_record_t cIGraph_create_record(VALUE v);
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//Iterators
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VALUE cIGraph_each_vertex (VALUE self);
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VALUE cIGraph_each_edge (VALUE self, VALUE order);
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VALUE cIGraph_each_edge_eid(VALUE self, VALUE order);
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//Selectors
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VALUE cIGraph_all_v (VALUE self);
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VALUE cIGraph_adj_v (VALUE self, VALUE v, VALUE mode);
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VALUE cIGraph_nonadj_v(VALUE self, VALUE v, VALUE mode);
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VALUE cIGraph_all_e (VALUE self, VALUE mode);
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VALUE cIGraph_adj_e (VALUE self, VALUE v, VALUE mode);
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//Basic query operations
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VALUE cIGraph_vcount (VALUE self);
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VALUE cIGraph_ecount (VALUE self);
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VALUE cIGraph_edge (VALUE self, VALUE eid);
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VALUE cIGraph_get_eid (VALUE self, VALUE from, VALUE to, VALUE directed);
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VALUE cIGraph_neighbors (VALUE self, VALUE v, VALUE mode);
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VALUE cIGraph_adjacent (VALUE self, VALUE v, VALUE mode);
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VALUE cIGraph_is_directed(VALUE self);
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VALUE cIGraph_degree (VALUE self, VALUE v, VALUE mode, VALUE loops);
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//Adding and eleting vertices and edges
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VALUE cIGraph_add_edges (int argc, VALUE *argv, VALUE self);
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VALUE cIGraph_add_edge (int argc, VALUE *argv, VALUE self);
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VALUE cIGraph_add_vertices (VALUE self, VALUE vs);
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VALUE cIGraph_delete_edge (VALUE self, VALUE from, VALUE to);
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VALUE cIGraph_delete_edges (VALUE self, VALUE edges);
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VALUE cIGraph_delete_vertices(VALUE self, VALUE vs);
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VALUE cIGraph_delete_vertex (VALUE self, VALUE v);
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VALUE cIGraph_add_vertex (VALUE self, VALUE v);
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//Basic properties
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VALUE cIGraph_are_connected(VALUE self, VALUE from, VALUE to);
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//Shortest Path Related Functions
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VALUE cIGraph_shortest_paths (VALUE self, VALUE from, VALUE mode);
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VALUE cIGraph_get_shortest_paths (VALUE self, VALUE from, VALUE to, VALUE mode);
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VALUE cIGraph_get_all_shortest_paths(VALUE self, VALUE from, VALUE to, VALUE mode);
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VALUE cIGraph_average_path_length (VALUE self, VALUE directed, VALUE unconn);
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VALUE cIGraph_diameter (VALUE self, VALUE directed, VALUE unconn);
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VALUE cIGraph_girth (VALUE self);
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VALUE cIGraph_dijkstra_shortest_paths(VALUE self, VALUE from, VALUE weights, VALUE mode);
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int igraph_dijkstra_shortest_paths(const igraph_t *graph,
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igraph_matrix_t *res,
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const igraph_vs_t from,
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const igraph_vector_t *wghts,
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igraph_neimode_t mode);
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//Vertex neighbourhood functions
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VALUE cIGraph_neighborhood_size (VALUE self, VALUE from, VALUE order, VALUE mode);
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VALUE cIGraph_neighborhood (VALUE self, VALUE from, VALUE order, VALUE mode);
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VALUE cIGraph_neighborhood_graphs(VALUE self, VALUE from, VALUE order, VALUE mode);
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//Component functions
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VALUE cIGraph_subcomponent(VALUE self, VALUE v, VALUE mode);
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VALUE cIGraph_subgraph (VALUE self, VALUE vs);
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VALUE cIGraph_clusters (VALUE self, VALUE mode);
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VALUE cIGraph_decompose (int argc, VALUE *argv, VALUE self);
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//Centrality measures
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VALUE cIGraph_closeness (VALUE self, VALUE vs, VALUE mode);
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VALUE cIGraph_betweenness (VALUE self, VALUE vs, VALUE directed);
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VALUE cIGraph_edge_betweenness(VALUE self, VALUE directed);
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VALUE cIGraph_pagerank (VALUE self, VALUE vs, VALUE directed, VALUE niter, VALUE eps, VALUE damping);
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VALUE cIGraph_constraint (int argc, VALUE *argv, VALUE self);
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VALUE cIGraph_maxdegree (VALUE self, VALUE vs, VALUE mode, VALUE loops);
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//Spanning trees
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VALUE cIGraph_minimum_spanning_tree_prim (VALUE self, VALUE weights);
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VALUE cIGraph_minimum_spanning_tree_unweighted(VALUE self);
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//Transitivity
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VALUE cIGraph_transitivity (VALUE self);
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VALUE cIGraph_transitivity_local (VALUE self, VALUE vs);
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VALUE cIGraph_transitivity_avglocal(VALUE self);
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//Directedness conversion
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VALUE cIGraph_to_directed (VALUE self, VALUE mode);
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VALUE cIGraph_to_undirected(VALUE self, VALUE mode);
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//Spectral properties
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VALUE cIGraph_laplacian(VALUE self, VALUE mode);
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//K-Cores
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VALUE cIGraph_coreness(VALUE self, VALUE mode);
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//Topological sorting
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VALUE cIGraph_topological_sorting(VALUE self, VALUE mode);
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//Other operations
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VALUE cIGraph_density (VALUE self, VALUE loops);
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VALUE cIGraph_simplify (VALUE self, VALUE mult, VALUE loops);
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VALUE cIGraph_reciprocity (VALUE self, VALUE loops);
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VALUE cIGraph_bibcoupling (VALUE self, VALUE vs);
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VALUE cIGraph_cocitation (VALUE self, VALUE vs);
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VALUE cIGraph_get_adjacency(VALUE self, VALUE mode);
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//Cliques
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VALUE cIGraph_cliques(VALUE self, VALUE min, VALUE max);
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VALUE cIGraph_largest_cliques(VALUE self);
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VALUE cIGraph_maximal_cliques(VALUE self);
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VALUE cIGraph_clique_number(VALUE self);
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//Independent vertex sets
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VALUE cIGraph_independent_vertex_sets(VALUE self, VALUE min, VALUE max);
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VALUE cIGraph_largest_independent_vertex_sets(VALUE self);
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VALUE cIGraph_maximal_independent_vertex_sets(VALUE self);
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VALUE cIGraph_independence_number(VALUE self);
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//Graph isomorphism
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VALUE cIGraph_isomorphic (VALUE self, VALUE g);
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VALUE cIGraph_isomorphic_vf2 (VALUE self, VALUE g);
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VALUE cIGraph_isoclass (VALUE self);
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VALUE cIGraph_isoclass_subgraph(VALUE self, VALUE vs);
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VALUE cIGraph_isoclass_create (VALUE self, VALUE vn, VALUE iso, VALUE dir);
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//Motifs
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VALUE cIGraph_motifs_randesu (VALUE self, VALUE size, VALUE cuts);
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VALUE cIGraph_motifs_randesu_no (VALUE self, VALUE size, VALUE cuts);
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VALUE cIGraph_motifs_randesu_estimate(VALUE self, VALUE size, VALUE cuts,
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VALUE samplen, VALUE samplev);
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//File handling
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VALUE cIGraph_read_graph_edgelist (VALUE self, VALUE file, VALUE mode);
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VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file);
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VALUE cIGraph_read_graph_ncol (VALUE self, VALUE file, VALUE predefnames, VALUE names, VALUE weights, VALUE directed);
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VALUE cIGraph_write_graph_ncol (VALUE self, VALUE file, VALUE names, VALUE weights);
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VALUE cIGraph_read_graph_lgl (VALUE self, VALUE file, VALUE names, VALUE weights);
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VALUE cIGraph_write_graph_lgl (VALUE self, VALUE file, VALUE names, VALUE weights, VALUE isolates);
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VALUE cIGraph_read_graph_dimacs (VALUE self, VALUE file, VALUE directed);
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VALUE cIGraph_write_graph_dimacs (VALUE self, VALUE file, VALUE source, VALUE target, VALUE capacity);
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VALUE cIGraph_read_graph_graphdb (VALUE self, VALUE file, VALUE directed);
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VALUE cIGraph_read_graph_graphml (VALUE self, VALUE file, VALUE index);
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VALUE cIGraph_write_graph_graphml (VALUE self, VALUE file);
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VALUE cIGraph_read_graph_gml (VALUE self, VALUE file);
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VALUE cIGraph_write_graph_gml (VALUE self, VALUE file);
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VALUE cIGraph_read_graph_pajek (VALUE self, VALUE file);
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VALUE cIGraph_write_graph_pajek (VALUE self, VALUE file);
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//Layouts
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VALUE cIGraph_layout_random (VALUE self);
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VALUE cIGraph_layout_circle (VALUE self);
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VALUE cIGraph_layout_fruchterman_reingold(VALUE self,
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VALUE niter,
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VALUE maxdelta,
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VALUE area,
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VALUE coolexp,
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VALUE repulserad,
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VALUE use_seed);
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VALUE cIGraph_layout_kamada_kawai (VALUE self,
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VALUE niter,
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VALUE sigma,
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VALUE initemp,
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VALUE coolexp,
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VALUE kkconst);
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VALUE cIGraph_layout_reingold_tilford (VALUE self,
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VALUE root);
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VALUE cIGraph_layout_reingold_tilford_circular(VALUE self,
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VALUE root);
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VALUE cIGraph_layout_grid_fruchterman_reingold(VALUE self,
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VALUE niter,
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VALUE maxdelta,
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VALUE area,
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VALUE coolexp,
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VALUE repulserad,
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VALUE cellsize,
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VALUE use_seed);
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VALUE cIGraph_layout_lgl(VALUE self,
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VALUE maxit,
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VALUE maxdelta,
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VALUE area,
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VALUE coolexp,
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VALUE repulserad,
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VALUE cellsize,
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VALUE proot);
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VALUE cIGraph_layout_random_3d(VALUE self);
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VALUE cIGraph_layout_sphere (VALUE self);
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VALUE cIGraph_layout_fruchterman_reingold_3d(VALUE self,
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VALUE niter,
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VALUE maxdelta,
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VALUE volume,
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VALUE coolexp,
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VALUE repulserad,
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VALUE use_seed);
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VALUE cIGraph_layout_kamada_kawai_3d (VALUE self,
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VALUE niter,
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VALUE sigma,
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VALUE initemp,
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VALUE coolexp,
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VALUE kkconst);
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VALUE cIGraph_layout_merge_dla(VALUE self, VALUE graphs, VALUE layouts);
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//Min cuts
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VALUE cIGraph_maxflow_value (VALUE self, VALUE source, VALUE target, VALUE capacity);
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VALUE cIGraph_st_mincut_value(VALUE self, VALUE source, VALUE target, VALUE capacity);
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VALUE cIGraph_mincut_value (VALUE self, VALUE capacity);
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VALUE cIGraph_mincut (VALUE self, VALUE capacity);
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//Connectivity
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VALUE cIGraph_st_edge_connectivity (VALUE self, VALUE source, VALUE target);
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VALUE cIGraph_edge_connectivity (VALUE self);
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VALUE cIGraph_st_vertex_connectivity(VALUE self, VALUE source, VALUE target, VALUE neighbours);
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VALUE cIGraph_vertex_connectivity (VALUE self);
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VALUE cIGraph_edge_disjoint_paths (VALUE self, VALUE source, VALUE target);
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VALUE cIGraph_vertex_disjoint_paths (VALUE self, VALUE source, VALUE target);
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VALUE cIGraph_adhesion(VALUE self);
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VALUE cIGraph_cohesion(VALUE self);
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//Community
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VALUE cIGraph_modularity (VALUE self, VALUE groups);
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VALUE cIGraph_community_to_membership (VALUE self, VALUE merge,
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VALUE steps);
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VALUE cIGraph_community_spinglass (VALUE self, VALUE weights,
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VALUE spins,
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VALUE parupdate,
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VALUE starttemp,
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VALUE stoptemp,
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VALUE coolfact,
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VALUE update_rule,
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VALUE gamma);
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VALUE cIGraph_community_spinglass_single (VALUE self, VALUE weights,
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VALUE vertex,
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VALUE spins,
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VALUE update_rule,
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VALUE gamma);
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VALUE cIGraph_community_leading_eigenvector (VALUE self, VALUE steps);
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VALUE cIGraph_community_leading_eigenvector_naive(VALUE self, VALUE steps);
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VALUE cIGraph_community_leading_eigenvector_step (VALUE self,
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VALUE membership,
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VALUE steps);
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//Attributes
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int cIGraph_attribute_init(igraph_t *graph,
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igraph_vector_ptr_t *attr);
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void cIGraph_attribute_destroy(igraph_t *graph);
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int cIGraph_attribute_copy(igraph_t *to,
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const igraph_t *from);
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int cIGraph_attribute_add_vertices(igraph_t *graph,
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long int nv,
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igraph_vector_ptr_t *attr);
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void cIGraph_attribute_delete_edges(igraph_t *graph,
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const igraph_vector_t *idx);
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void cIGraph_attribute_delete_vertices(igraph_t *graph,
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const igraph_vector_t *eidx,
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const igraph_vector_t *vidx);
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int cIGraph_attribute_add_edges(igraph_t *graph,
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const igraph_vector_t *edges,
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igraph_vector_ptr_t *attr);
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void cIGraph_attribute_delete_edges(igraph_t *graph,
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const igraph_vector_t *idx);
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int cIGraph_attribute_permute_edges(igraph_t *graph,
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const igraph_vector_t *idx);
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int cIGraph_attribute_get_info(const igraph_t *graph,
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igraph_strvector_t *gnames,
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igraph_vector_t *gtypes,
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igraph_strvector_t *vnames,
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igraph_vector_t *vtypes,
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igraph_strvector_t *enames,
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igraph_vector_t *etypes);
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igraph_bool_t cIGraph_attribute_has_attr(const igraph_t *graph,
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igraph_attribute_elemtype_t type,
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const char* name);
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int cIGraph_attribute_get_type(const igraph_t *graph,
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igraph_attribute_type_t *type,
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igraph_attribute_elemtype_t elemtype,
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const char *name);
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int cIGraph_get_numeric_graph_attr(const igraph_t *graph,
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const char *name,
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igraph_vector_t *value);
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int cIGraph_get_string_graph_attr(const igraph_t *graph,
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const char *name,
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igraph_strvector_t *value);
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int cIGraph_get_numeric_vertex_attr(const igraph_t *graph,
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const char *name,
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igraph_vs_t vs,
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igraph_vector_t *value);
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int cIGraph_get_string_vertex_attr(const igraph_t *graph,
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const char *name,
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igraph_vs_t vs,
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igraph_strvector_t *value);
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int cIGraph_get_numeric_edge_attr(const igraph_t *graph,
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const char *name,
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igraph_es_t es,
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igraph_vector_t *value);
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int cIGraph_get_string_edge_attr(const igraph_t *graph,
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const char *name,
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igraph_es_t es,
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igraph_strvector_t *value);
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//Matrix functions
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void cIGraph_matrix_free(void *p);
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VALUE cIGraph_matrix_alloc(VALUE klass);
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VALUE cIGraph_matrix_init_copy(VALUE copy, VALUE orig);
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VALUE cIGraph_matrix_initialize(int argc, VALUE *argv, VALUE self);
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void Init_igraphmatrix();
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VALUE cIGraph_matrix_each(VALUE self);
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VALUE cIGraph_matrix_get (VALUE self, VALUE i, VALUE j);
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VALUE cIGraph_matrix_set (VALUE self, VALUE i, VALUE j, VALUE x);
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VALUE cIGraph_matrix_size(VALUE self);
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VALUE cIGraph_matrix_nrow(VALUE self);
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VALUE cIGraph_matrix_ncol(VALUE self);
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VALUE cIGraph_matrix_max (VALUE self);
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VALUE cIGraph_matrix_multiply(VALUE self, VALUE x);
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VALUE cIGraph_matrix_toa(VALUE self);
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//Not implemented yet
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//VALUE cIGraph_add_rows(VALUE self, VALUE n);
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//VALUE cIGraph_add_cols(VALUE self, VALUE n);
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//VALUE cIGraph_matrix_resize(VALUE self, VALUE nrow, VALUE ncol);
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