Fixed GC problem.

git-svn-id: http://igraph.rubyforge.org/svn/trunk@26 71f48855-0bbf-4aa5-930d-4df415e86613

ext/cIGraph.c

@@ -10,6 +10,11 @@ void cIGraph_free(void *p){
   igraph_destroy(p);
 }
 
+void cIGraph_mark(void *p){
+  rb_gc_mark(((VALUE*)((igraph_t*)p)->attr)[0]);
+  rb_gc_mark(((VALUE*)((igraph_t*)p)->attr)[1]);
+}
+
 VALUE cIGraph_alloc(VALUE klass){
 
   igraph_t *graph = malloc(sizeof(igraph_t));
@@ -17,7 +22,7 @@ VALUE cIGraph_alloc(VALUE klass){
 
   igraph_empty(graph, 0, 1);
 
-  obj = Data_Wrap_Struct(klass, 0, cIGraph_free, graph);
+  obj = Data_Wrap_Struct(klass, cIGraph_mark, cIGraph_free, graph);
 
   return obj;
   
@@ -228,4 +233,29 @@ void Init_igraph(){
   rb_define_singleton_method(cIGraph, "read_graph_edgelist", cIGraph_read_graph_edgelist, 2); /* in cIGraph_file.c */
   rb_define_method(cIGraph, "write_graph_edgelist", cIGraph_write_graph_edgelist, 1);         /* in cIGraph_file.c */
 
+  rb_define_method(cIGraph, "layout_random", cIGraph_layout_random, 0);
+  rb_define_method(cIGraph, "layout_circle", cIGraph_layout_circle, 0);
+  rb_define_method(cIGraph, "layout_fruchterman_reingold", cIGraph_layout_fruchterman_reingold, 6);
+
+  //Matrix class
+  cIGraphMatrix = rb_define_class("IGraphMatrix", rb_cObject);
+
+  rb_define_alloc_func(cIGraphMatrix, cIGraph_matrix_alloc);
+  rb_define_method(cIGraphMatrix, "initialize",      cIGraph_matrix_initialize, -1);
+  rb_define_method(cIGraphMatrix, "initialize_copy", cIGraph_matrix_init_copy,   1);
+  //rb_define_singleton_method(cIGraphMatrix, "[]",    cIGraph_matrix_initialize, -1);
+  rb_include_module(cIGraphMatrix, rb_mEnumerable);
+  rb_define_method (cIGraphMatrix, "each", cIGraph_matrix_each,0);
+ 
+  rb_define_method(cIGraphMatrix, "[]",   cIGraph_matrix_get,  2);
+  rb_define_method(cIGraphMatrix, "[]=",  cIGraph_matrix_set,  3);
+  rb_define_method(cIGraphMatrix, "size", cIGraph_matrix_size, 0);
+  rb_define_method(cIGraphMatrix, "nrow", cIGraph_matrix_nrow, 0);
+  rb_define_method(cIGraphMatrix, "ncol", cIGraph_matrix_ncol, 0);
+  rb_define_method(cIGraphMatrix, "max",  cIGraph_matrix_max,  0);
+
+  rb_define_method(cIGraphMatrix, "*", cIGraph_matrix_multiply, 1);
+
+  rb_define_method(cIGraphMatrix, "to_a", cIGraph_matrix_toa, 0);
+
 }

ext/cIGraph.h

@@ -1,6 +1,7 @@
 //Classes
 extern VALUE cIGraph;
 extern VALUE cIGraphError;
+extern VALUE cIGraphMatrix;
 extern igraph_attribute_table_t cIGraph_attribute_table;
 
 //Error and warning handling functions
@@ -18,6 +19,7 @@ VALUE cIGraph_include(VALUE self, VALUE v);
 //IGraph allocation, destruction and intialization
 void Init_igraph(void);
 void cIGraph_free(void *p);
+void cIGraph_mark(void *p);
 VALUE cIGraph_alloc(VALUE klass);
 VALUE cIGraph_initialize(int argc, VALUE *argv, VALUE self);
 VALUE cIGraph_init_copy(VALUE copy, VALUE orig);
@@ -82,6 +84,18 @@ VALUE cIGraph_topological_sorting(VALUE self, VALUE mode);
 VALUE cIGraph_read_graph_edgelist (VALUE self, VALUE file, VALUE mode);
 VALUE cIGraph_write_graph_edgelist(VALUE self, VALUE file);
 
+
+//Layouts
+VALUE cIGraph_layout_random(VALUE self);
+VALUE cIGraph_layout_circle(VALUE self);
+VALUE cIGraph_layout_fruchterman_reingold(VALUE self,
+					  VALUE niter,
+					  VALUE maxdelta,
+					  VALUE area,
+					  VALUE coolexp,
+					  VALUE repulserad,
+					  VALUE use_seed);
+
 //Attributes
 int cIGraph_attribute_init(igraph_t *graph, 
 			   igraph_vector_ptr_t *attr);
@@ -139,3 +153,29 @@ int cIGraph_get_string_edge_attr(const igraph_t *graph,
 				 const char *name,
 				 igraph_es_t es,
 				 igraph_strvector_t *value);
+
+
+//Matrix functions
+void cIGraph_matrix_free(void *p);
+VALUE cIGraph_matrix_alloc(VALUE klass);
+VALUE cIGraph_matrix_init_copy(VALUE copy, VALUE orig);
+VALUE cIGraph_matrix_initialize(int argc, VALUE *argv, VALUE self);
+void Init_igraphmatrix();
+
+VALUE cIGraph_matrix_each(VALUE self);
+
+VALUE cIGraph_matrix_get (VALUE self, VALUE i, VALUE j);
+VALUE cIGraph_matrix_set (VALUE self, VALUE i, VALUE j, VALUE x);
+VALUE cIGraph_matrix_size(VALUE self);
+VALUE cIGraph_matrix_nrow(VALUE self);
+VALUE cIGraph_matrix_ncol(VALUE self);
+VALUE cIGraph_matrix_max (VALUE self);
+
+VALUE cIGraph_matrix_multiply(VALUE self, VALUE x);
+
+VALUE cIGraph_matrix_toa(VALUE self);
+
+//Not implemented yet
+//VALUE cIGraph_add_rows(VALUE self, VALUE n);
+//VALUE cIGraph_add_cols(VALUE self, VALUE n);
+//VALUE cIGraph_matrix_resize(VALUE self, VALUE nrow, VALUE ncol);

ext/cIGraph_attribute_handler.c

@@ -68,7 +68,8 @@ int cIGraph_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr) {
 
   VALUE* attrs;
 
-  attrs = (VALUE*)calloc(2, sizeof(VALUE));
+  //attrs = (VALUE*)calloc(2, sizeof(VALUE));
+  attrs = ALLOC_N(VALUE, 2);
 
   if(!attrs)
     IGRAPH_ERROR("Error allocating Arrays\n", IGRAPH_ENOMEM);
@@ -76,7 +77,7 @@ int cIGraph_attribute_init(igraph_t *graph, igraph_vector_ptr_t *attr) {
   //[0] is vertex array, [1] is edge array
   attrs[0] = rb_ary_new();
   attrs[1] = rb_ary_new();
-
+ 
   graph->attr = attrs;
 
   return IGRAPH_SUCCESS;
@@ -91,10 +92,12 @@ void cIGraph_attribute_destroy(igraph_t *graph) {
 /* Copying */
 int cIGraph_attribute_copy(igraph_t *to, const igraph_t *from) {
 
+  VALUE* attrs;
   VALUE vertex_array = ((VALUE*)from->attr)[0];
   VALUE edge_array   = ((VALUE*)from->attr)[1];
 
-  VALUE* attrs = (VALUE*)calloc(2, sizeof(VALUE));
+  //VALUE* attrs = (VALUE*)calloc(2, sizeof(VALUE));
+  attrs = ALLOC_N(VALUE, 2);
 
   attrs[0] = rb_ary_dup(vertex_array);
   attrs[1] = rb_ary_dup(edge_array);
@@ -182,7 +185,19 @@ void cIGraph_attribute_delete_edges(igraph_t *graph, const igraph_vector_t *idx)
 
 /* Permuting edges */
 int cIGraph_attribute_permute_edges(igraph_t *graph,
-						  const igraph_vector_t *idx) {   return 0;
+				    const igraph_vector_t *idx) {
+
+  int i;
+  VALUE edge_array = ((VALUE*)graph->attr)[1];
+  VALUE n_e_ary = rb_ary_new();
+
+  for(i=0;i<igraph_vector_size(idx);i++){
+    rb_ary_push(n_e_ary,rb_ary_entry(edge_array,VECTOR(*idx)[i]));
+  }
+
+  ((VALUE*)graph->attr)[1] = n_e_ary;
+  
+  return 0;
 }
 
 /* Getting attribute names and types */