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= 0.1 2007-06-29
* First version

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History.txt
License.txt
Manifest.txt
README.txt
ext/cIGraph.c
ext/cIGraph.h
ext/cIGraph_add_delete.c
ext/cIGraph_basic_properties.c
ext/cIGraph_basic_query.c
ext/cIGraph_error_handlers.c
ext/cIGraph_shortest_paths.c
ext/cIGraph_utility.c
test/tc_add_delete.rb
test/tc_basic_properties.rb
test/tc_basic_query.rb
test/tc_create.rb
test/tc_error_handling.rb
test/tc_shortest_paths.rb
test/test_all.rb

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== Introduction
IGraph
IGraph
IGraph
== Installation
A working igraph library installation is required.
An IGraph gem is available as well as a package using setup.rb. In each case the installation requires the location of your igraph library to compile the extension. If you download the setup.rb package use these incantations:
ruby setup.rb config -- --with-igraph-dir=$R_HOME
ruby setup.rb setup
ruby setup.rb install
Using gems it is almost the same:
gem install igraph -- --with-igraph-dir=$R_HOME
== Documentation
Here is a very quick and simple example:
require 'igraph'
graph = IGraph.new([],true)
== License
Copyright (C) 2006 Alex Gutteridge
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

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require 'hoe'
$LOAD_PATH.unshift("./lib")
$LOAD_PATH.unshift("./ext")
hoe = Hoe.new("igraph",'0.1') do |p|
p.author = "Alex Gutteridge"
p.email = "alexg@kuicr.kyoto-u.ac.jp"
p.url = "http://web.kuicr.kyoto-u.ac.jp/~alexg/igraph/"
p.description = p.paragraphs_of("README.txt",1..3)[0]
p.summary = p.paragraphs_of("README.txt",1)[0]
p.changes = p.paragraphs_of("History.txt",0..1).join("\n\n")
p.clean_globs = ["ext/*.o","ext/*.so","ext/Makefile","ext/mkmf.log","**/*~","email.txt","manual.{aux,log,out,toc,pdf}"]
p.rdoc_pattern = /(^ext\/.*\.c$|^README|^History|^License)/
p.spec_extras = {
:extensions => ['ext/extconf.rb'],
:require_paths => ['test'],
:has_rdoc => true,
:extra_rdoc_files => ["README.txt","History.txt","License.txt"],
:rdoc_options => ["--exclude", "test/*", "--main", "README.txt", "--inline-source"]
}
task :setup_rb_package => [:clean, :package, :build_manual] do
package_dir = "#{p.name}-#{p.version}"
cp("setup.rb","pkg/#{package_dir}")
cp("manual.pdf","pkg/#{package_dir}")
Dir.chdir("pkg")
system("tar -czf #{p.name}-#{p.version}.tgz #{package_dir}")
Dir.chdir("..")
end
end
hoe.spec.dependencies.delete_if{|dep| dep.name == "hoe"}
desc "Uses extconf.rb and make to build the extension"
task :build_extension => ['ext/igraph.so']
SRC = FileList['ext/*.c'] + FileList['ext/*.h']
file 'ext/igraph.so' => SRC do
Dir.chdir('ext')
system("ruby extconf.rb --with-igraph-dir=$IGRAPH_HOME")
system("make")
Dir.chdir('..')
end
task :test => [:build_extension]
desc "Build PDF manual"
task :build_manual => ["manual.pdf"]
file "manual.pdf" => ["manual.tex"] do
out = 'Rerun'
while out.match(/Rerun/)
out = `pdflatex manual.tex`
end
end
task :build_manual_clean => [:build_manual] do
system("rm manual.{aux,log,out,toc}")
end

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
void cIGraph_free(void *p){
igraph_destroy(p);
}
VALUE cIGraph_alloc(VALUE klass){
igraph_t *graph = malloc(sizeof(igraph_t));
VALUE obj;
igraph_empty(graph, 0, 1);
obj = Data_Wrap_Struct(klass, 0, cIGraph_free, graph);
return obj;
}
/* call-seq:
* IGraph.new(edges,directed) -> graph
*
* Creates a new IGraph graph with the edges specified in the edge 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.
* The boolean value directed specifies whether a directed or undirected
* graph is created.
*/
VALUE cIGraph_initialize(VALUE self, VALUE edges, VALUE directed){
igraph_t *graph;
igraph_vector_t edge_v;
VALUE vertex;
VALUE object_h;
VALUE id_h;
int vertex_n = 0;
int current_vertex_id;
igraph_set_error_handler(cIGraph_error_handler);
igraph_set_warning_handler(cIGraph_warning_handler);
//New hash for mapping vertex objects to floats used by iGraph
object_h = rb_iv_set(self,"@object_ids",rb_hash_new());
id_h = rb_iv_set(self,"@id_objects",rb_hash_new());
//Initialize edge vector
igraph_vector_init_int(&edge_v,0);
Data_Get_Struct(self, igraph_t, graph);
if(!directed)
igraph_to_undirected(graph,IGRAPH_TO_UNDIRECTED_COLLAPSE);
//Loop through objects in edge Array
vertex = rb_ary_shift(edges);
while(vertex != Qnil){
if(rb_funcall(object_h,rb_intern("has_key?"),1,vertex)){
//If @vertices includes this vertex then look up the vertex number
current_vertex_id = NUM2INT(rb_hash_aref(object_h,vertex));
} else {
//otherwise add a new entry to Hash
rb_hash_aset(object_h,vertex,INT2NUM(vertex_n));
rb_hash_aset(id_h, INT2NUM(vertex_n),vertex);
current_vertex_id = vertex_n;
vertex_n++;
}
igraph_vector_push_back(&edge_v,current_vertex_id);
vertex = rb_ary_shift(edges);
}
if(igraph_vector_size(&edge_v) > 0){
igraph_add_vertices(graph,vertex_n,0);
igraph_add_edges(graph,&edge_v,0);
}
igraph_vector_destroy(&edge_v);
return self;
}
/* Interface to the iGraph[http://cneurocvs.rmki.kfki.hu/igraph/] library
* for graph computation
*/
void Init_igraph(){
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, 2);
rb_define_method(cIGraph, "include?", cIGraph_include, 1);
rb_define_method(cIGraph, "vcount", cIGraph_vcount, 0);
rb_define_method(cIGraph, "ecount", cIGraph_ecount, 0);
rb_define_method(cIGraph, "edge", cIGraph_edge, 1);
rb_define_method(cIGraph, "get_eid", cIGraph_get_eid, 2);
rb_define_method(cIGraph, "neighbors", cIGraph_neighbors,2);
rb_define_method(cIGraph, "neighbours", cIGraph_neighbors,2);
rb_define_method(cIGraph, "adjacent", cIGraph_adjacent,2);
rb_define_const(cIGraph, "IGRAPH_OUT", INT2NUM(1));
rb_define_const(cIGraph, "IGRAPH_IN", INT2NUM(2));
rb_define_const(cIGraph, "IGRAPH_ALL", INT2NUM(3));
rb_define_const(cIGraph, "IGRAPH_TOTAL", INT2NUM(4));
rb_define_method(cIGraph, "is_directed", cIGraph_is_directed,0);
rb_define_method(cIGraph, "is_directed?", cIGraph_is_directed,0);
rb_define_method(cIGraph, "degree", cIGraph_degree,3);
rb_define_method(cIGraph, "add_edges", cIGraph_add_edges,1);
rb_define_method(cIGraph, "add_vertices", cIGraph_add_vertices,1);
rb_define_method(cIGraph, "are_connected", cIGraph_are_connected,2);
rb_define_method(cIGraph, "are_connected?", cIGraph_are_connected,2);
rb_define_method(cIGraph, "shortest_paths", cIGraph_shortest_paths,2);
rb_define_method(cIGraph, "get_shortest_paths", cIGraph_get_shortest_paths,3);
}

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//Classes
VALUE cIGraph;
VALUE cIGraphError;
//Error and warning handling functions
void cIGraph_error_handler(const char *reason, const char *file,
int line, int igraph_errno);
void cIGraph_warning_handler(const char *reason, const char *file,
int line, int igraph_errno);
//IGraph specific utility functions
igraph_integer_t cIGraph_get_vertex_id(VALUE graph, VALUE v);
VALUE cIGraph_get_vertex_object(VALUE graph, igraph_integer_t n);
int cIGraph_vertex_arr_to_id_vec(VALUE graph, VALUE va, igraph_vector_t *nv);
VALUE cIGraph_include(VALUE self, VALUE v);
//IGraph allocation, destruction and intialization
void Init_igraph(void);
void cIGraph_free(void *p);
VALUE cIGraph_alloc(VALUE klass);
VALUE cIGraph_initialize(VALUE self, VALUE edges, VALUE directed);
//Basic query operations
VALUE cIGraph_vcount (VALUE self);
VALUE cIGraph_ecount (VALUE self);
VALUE cIGraph_edge (VALUE self, VALUE eid);
VALUE cIGraph_get_eid (VALUE self, VALUE from, VALUE to, VALUE directed);
VALUE cIGraph_neighbors (VALUE self, VALUE v, VALUE mode);
VALUE cIGraph_adjacent (VALUE self, VALUE v, VALUE mode);
VALUE cIGraph_is_directed(VALUE self);
VALUE cIGraph_degree (VALUE self, VALUE v, VALUE mode, VALUE loops);
//Adding and eleting vertices and edges
VALUE cIGraph_add_edges (VALUE self, VALUE edges);
VALUE cIGraph_add_vertices (VALUE self, VALUE vs);
VALUE cIGraph_delete_edges (VALUE self, VALUE edges);
VALUE cIGraph_delete_vertices(VALUE self, VALUE vs);
//Basic properties
VALUE cIGraph_are_connected(VALUE self, VALUE from, VALUE to);
//Shortest Path Related Functions
VALUE cIGraph_shortest_paths (VALUE self, VALUE from, VALUE mode);
VALUE cIGraph_get_shortest_paths(VALUE self, VALUE from, VALUE to, VALUE mode);

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
VALUE cIGraph_add_edges(VALUE self, VALUE edges){
igraph_t *graph;
igraph_vector_t edge_v;
VALUE vertex;
VALUE object_h;
int vid;
int code = 0;
//Initialize edge vector
igraph_vector_init_int(&edge_v,0);
object_h = rb_iv_get(self,"@object_ids");
Data_Get_Struct(self, igraph_t, graph);
//Loop through objects in edge Array
vertex = rb_ary_shift(edges);
while(vertex != Qnil){
if(rb_funcall(object_h,rb_intern("has_key?"),1,vertex)){
//If @vertices includes this vertex then look up the vertex number
vid = NUM2INT(rb_hash_aref(object_h,vertex));
} else {
rb_raise(cIGraphError, "Unknown vertex in edge array. Use add_vertices first");
}
igraph_vector_push_back(&edge_v,vid);
vertex = rb_ary_shift(edges);
}
if(igraph_vector_size(&edge_v) > 0){
code = igraph_add_edges(graph,&edge_v,0);
}
igraph_vector_destroy(&edge_v);
return INT2NUM(code);
}
VALUE cIGraph_add_vertices(VALUE self, VALUE vs){
igraph_t *graph;
VALUE vertex;
VALUE object_h;
VALUE id_h;
int vertex_n;
int code = 0;
int length;
object_h = rb_iv_get(self,"@object_ids");
id_h = rb_iv_get(self,"@id_objects");
length = NUM2INT(rb_funcall(vs, rb_intern("length"),0));
vertex_n = NUM2INT(rb_funcall(object_h,rb_intern("length"),0));
Data_Get_Struct(self, igraph_t, graph);
//Loop through objects in vertex array
vertex = rb_ary_shift(vs);
while(vertex != Qnil){
if(rb_funcall(object_h,rb_intern("has_key?"),1,vertex)){
//If @vertices includes this vertex then raise an error
rb_raise(cIGraphError, "Vertex already added to graph");
} else {
//otherwise add a new entry to Hash
rb_hash_aset(object_h,vertex,INT2NUM(vertex_n));
rb_hash_aset(id_h, INT2NUM(vertex_n),vertex);
vertex_n++;
}
vertex = rb_ary_shift(vs);
}
code = igraph_add_vertices(graph,length,0);
return INT2NUM(code);
}

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
VALUE cIGraph_are_connected(VALUE self, VALUE from, VALUE to){
igraph_t *graph;
igraph_integer_t from_i;
igraph_integer_t to_i;
igraph_bool_t res;
Data_Get_Struct(self, igraph_t, graph);
from_i = cIGraph_get_vertex_id(self,from);
to_i = cIGraph_get_vertex_id(self,to);
igraph_are_connected(graph,from_i,to_i,&res);
return res ? Qtrue : Qfalse;
}

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
VALUE cIGraph_vcount(VALUE self){
igraph_t *graph;
Data_Get_Struct(self, igraph_t, graph);
return INT2NUM(igraph_vcount(graph));
}
VALUE cIGraph_ecount(VALUE self){
igraph_t *graph;
Data_Get_Struct(self, igraph_t, graph);
return INT2NUM(igraph_ecount(graph));
}
VALUE cIGraph_edge(VALUE self, VALUE eid){
igraph_t *graph;
igraph_integer_t from = 0;
igraph_integer_t to = 0;
VALUE from_r;
VALUE to_r;
Data_Get_Struct(self, igraph_t, graph);
igraph_edge(graph,NUM2INT(eid),&from,&to);
from_r = cIGraph_get_vertex_object(self,from);
to_r = cIGraph_get_vertex_object(self,to);
return rb_ary_new3(2, from_r, to_r);
}
VALUE cIGraph_get_eid(VALUE self, VALUE from, VALUE to, VALUE directed){
igraph_t *graph;
igraph_integer_t eid = 0;
int from_i;
int to_i;
igraph_bool_t directed_b = 0;
Data_Get_Struct(self, igraph_t, graph);
from_i = cIGraph_get_vertex_id(self,from);
to_i = cIGraph_get_vertex_id(self,to);
if(directed)
directed_b = 1;
igraph_get_eid(graph,&eid,from_i,to_i,directed_b);
return INT2NUM(eid);
}
VALUE cIGraph_neighbors(VALUE self, VALUE v, VALUE mode){
igraph_t *graph;
igraph_integer_t pnode;
igraph_neimode_t pmode = NUM2INT(mode);
igraph_vector_t neis;
int i;
VALUE neighbors = rb_ary_new();
igraph_vector_init_int(&neis,0);
Data_Get_Struct(self, igraph_t, graph);
pnode = cIGraph_get_vertex_id(self,v);
igraph_neighbors(graph,&neis,pnode,pmode);
for(i=0;i<igraph_vector_size(&neis);i++){
rb_ary_push(neighbors,cIGraph_get_vertex_object(self,VECTOR(neis)[i]));
}
igraph_vector_destroy(&neis);
return neighbors;
}
VALUE cIGraph_adjacent(VALUE self, VALUE v, VALUE mode){
igraph_t *graph;
igraph_integer_t pnode;
igraph_neimode_t pmode = NUM2INT(mode);
igraph_vector_t eids;
int i;
VALUE eids_r = rb_ary_new();
igraph_vector_init_int(&eids,0);
Data_Get_Struct(self, igraph_t, graph);
pnode = cIGraph_get_vertex_id(self,v);
igraph_adjacent(graph,&eids,pnode,pmode);
for(i=0;i<igraph_vector_size(&eids);i++){
rb_ary_push(eids_r,INT2NUM(VECTOR(eids)[i]));
}
igraph_vector_destroy(&eids);
return eids_r;
}
VALUE cIGraph_is_directed(VALUE self){
igraph_t *graph;
Data_Get_Struct(self, igraph_t, graph);
return igraph_is_directed(graph) ? Qtrue : Qfalse;
}
VALUE cIGraph_degree(VALUE self, VALUE v, VALUE mode, VALUE loops){
igraph_t *graph;
igraph_vs_t vids;
igraph_vector_t vidv;
igraph_neimode_t pmode = NUM2INT(mode);
igraph_bool_t loop_mode = loops ? 1 : 0;
igraph_vector_t res;
int i;
VALUE degree_r = rb_ary_new();
//vector to hold the results of the degree calculations
igraph_vector_init_int(&res,0);
Data_Get_Struct(self, igraph_t, graph);
//Convert an array of vertices to a vector of vertex ids
cIGraph_vertex_arr_to_id_vec(self,v,&vidv);
//create vertex selector from the vecotr of ids
igraph_vs_vector(&vids,&vidv);
igraph_degree(graph,&res,vids,pmode,loop_mode);
for(i=0;i<igraph_vector_size(&res);i++){
rb_ary_push(degree_r,INT2NUM(VECTOR(res)[i]));
}
igraph_vector_destroy(&vidv);
igraph_vector_destroy(&res);
igraph_vs_destroy(&vids);
return degree_r;
}

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
void cIGraph_error_handler(const char *reason, const char *file,
int line, int igraph_errno) {
rb_raise(cIGraphError, reason);
}
void cIGraph_warning_handler(const char *reason, const char *file,
int line, int igraph_errno) {
rb_warning(reason);
}

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
VALUE cIGraph_shortest_paths(VALUE self, VALUE from, VALUE mode){
igraph_t *graph;
igraph_vs_t vids;
igraph_vector_t vidv;
igraph_neimode_t pmode = NUM2INT(mode);
igraph_matrix_t res;
int i;
int j;
VALUE row;
VALUE matrix = rb_ary_new();
int n_row;
int n_col;
Data_Get_Struct(self, igraph_t, graph);
n_row = NUM2INT(rb_funcall(from,rb_intern("length"),0));
n_col = igraph_vcount(graph);
//matrix to hold the results of the calculations
igraph_matrix_init(&res,n_row,n_col);
//Convert an array of vertices to a vector of vertex ids
cIGraph_vertex_arr_to_id_vec(self,from,&vidv);
//create vertex selector from the vecotr of ids
igraph_vs_vector(&vids,&vidv);
igraph_shortest_paths(graph,&res,vids,pmode);
for(i=0; i<igraph_matrix_nrow(&res); i++){
row = rb_ary_new();
rb_ary_push(matrix,row);
for(j=0; j<igraph_matrix_ncol(&res); j++){
rb_ary_push(row,INT2NUM(MATRIX(res,i,j)));
}
}
igraph_vector_destroy(&vidv);
igraph_matrix_destroy(&res);
igraph_vs_destroy(&vids);
return matrix;
}
VALUE cIGraph_get_shortest_paths(VALUE self, VALUE from, VALUE to, VALUE mode){
igraph_t *graph;
igraph_integer_t from_vid;
igraph_vs_t to_vids;
igraph_vector_t to_vidv;
igraph_neimode_t pmode = NUM2INT(mode);
igraph_vector_ptr_t res;
igraph_vector_t *path_v;
int i;
int j;
VALUE path;
VALUE matrix = rb_ary_new();
int n_paths;
Data_Get_Struct(self, igraph_t, graph);
n_paths = NUM2INT(rb_funcall(to,rb_intern("length"),0));
//vector to hold the results of the calculations
igraph_vector_ptr_init(&res,0);
for(i=0;i<n_paths;i++){
path_v = malloc(sizeof(igraph_vector_t));
igraph_vector_init(path_v,0);
igraph_vector_ptr_push_back(&res,path_v);
}
//Convert an array of vertices to a vector of vertex ids
cIGraph_vertex_arr_to_id_vec(self,to,&to_vidv);
//create vertex selector from the vecotr of ids
igraph_vs_vector(&to_vids,&to_vidv);
//The id of the vertex from where we are counting
from_vid = cIGraph_get_vertex_id(self, from);
igraph_get_shortest_paths(graph,&res,from_vid,to_vids,pmode);
for(i=0; i<n_paths; i++){
path = rb_ary_new();
rb_ary_push(matrix,path);
for(j=0; j<igraph_vector_size(VECTOR(res)[i]); j++){
path_v = VECTOR(res)[i];
rb_ary_push(path,cIGraph_get_vertex_object(self,VECTOR(*path_v)[j]));
}
}
for(i=0;i<n_paths;i++){
igraph_vector_destroy(VECTOR(res)[i]);
}
igraph_vector_destroy(&to_vidv);
igraph_vector_ptr_destroy(&res);
igraph_vs_destroy(&to_vids);
return matrix;
}

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#include "igraph.h"
#include "ruby.h"
#include "cIGraph.h"
igraph_integer_t cIGraph_get_vertex_id(VALUE graph, VALUE v){
VALUE vertex_h;
vertex_h = rb_iv_get(graph,"@object_ids");
if(rb_funcall(vertex_h,rb_intern("has_key?"),1,v))
return NUM2INT(rb_hash_aref(vertex_h,v));
return -1;
}
VALUE cIGraph_get_vertex_object(VALUE graph, igraph_integer_t n){
VALUE vertex_h;
vertex_h = rb_iv_get(graph,"@id_objects");
if(rb_funcall(vertex_h,rb_intern("has_key?"),1,INT2NUM(n)))
return rb_hash_aref(vertex_h,INT2NUM(n));
return Qnil;
}
int cIGraph_vertex_arr_to_id_vec(VALUE graph, VALUE va, igraph_vector_t *nv){
VALUE vertex;
//Initialize edge vector
igraph_vector_init_int(nv,0);
vertex = rb_ary_shift(va);
while(vertex != Qnil){
igraph_vector_push_back(nv,cIGraph_get_vertex_id(graph, vertex));
vertex = rb_ary_shift(va);
}
return 0;
}
VALUE cIGraph_include(VALUE self, VALUE v){
VALUE vertex_h = rb_iv_get(self,"@object_ids");
return rb_funcall(vertex_h,rb_intern("has_key?"),1,v);
}

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require 'mkmf'
dir_config('igraph')
unless have_library("igraph")
$stderr.puts "\nERROR: Cannot find the iGraph library, aborting."
exit 1
end
unless have_header("igraph.h")
$stderr.puts "\nERROR: Cannot find the iGraph header, aborting."
exit 1
end
create_makefile("igraph")

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require 'igraph'
require 'kgml'
require 'benchmark'
xmlfiles = Dir.glob(ARGV[0])
pathway =
DirectedBipartiteMetabolicPathway.new(File.open(xmlfiles.shift).read)
pathway = xmlfiles.inject(pathway){|p,file|
p + DirectedBipartiteMetabolicPathway.new(File.open(file).read)
}
igraph = IGraph.new([],0,true);
pathway.reactions.each do |reaction|
reaction_name = reaction.name.gsub(/rn:/,'')
unless igraph.include?(reaction_name)
igraph.add_vertices([reaction_name])
end
reaction.substrates.each do |s_name|
s_name.gsub!(/cpd:/,'')
unless igraph.include?(s_name)
igraph.add_vertices([s_name])
end
igraph.add_edges([s_name,reaction_name])
if reaction.type == 'reversible'
igraph.add_edges([reaction_name,s_name])
end
end
reaction.products.each do |p_name|
p_name.gsub!(/cpd:/,'')
unless igraph.include?(p_name)
igraph.add_vertices([p_name])
end
igraph.add_edges([reaction_name,p_name])
if reaction.type == 'reversible'
igraph.add_edges([p_name,reaction_name])
end
end
end
include Benchmark
graph = pathway.graph
bm(6) do |x|
x.report("igraph"){
100.times{
igraph.get_shortest_paths("R02740",["C00074"])
}
}
x.report("hashgraph"){
100.times{
h = {}
graph.dijkstra_shortest_paths({
:root => "R02740",
:target => "C00074",
:predecessor => h
})
graph.route("C00074",h)
}
}
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_add_edges
graph = IGraph.new(['A','B','C','D'],true)
graph.add_edges(['A','C'])
assert_equal [2], graph.degree(['A'],IGraph::IGRAPH_ALL,true)
end
def test_add_vertices
graph = IGraph.new(['A','B','C','D'],true)
assert_equal 4, graph.vcount
graph.add_vertices(['E','F','G','H'])
assert_equal 8, graph.vcount
assert_equal [0], graph.degree(['E'],IGraph::IGRAPH_ALL,true)
end
def test_add_to_empty_graph
graph = IGraph.new([],true)
assert_equal 0, graph.vcount
graph.add_vertices(['A','B'])
assert_equal 2, graph.vcount
graph.add_edges(['A','B'])
assert_equal 1, graph.ecount
end
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_are_connected
graph = IGraph.new(['A','B','C','D'],true)
assert graph.are_connected('A','B')
assert !(graph.are_connected('A','C'))
end
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_graph_size
assert_equal 4, IGraph.new([1,2,3,4],true).vcount
assert_equal 2, IGraph.new([1,2,3,4],true).ecount
end
def test_eid_get_edge
assert_nothing_raised do
IGraph.new(['A','B','C','D'],true).get_eid('A','B')
end
graph = IGraph.new(['A','B','C','D'],true)
eid1 = graph.get_eid('A','B')
eid2 = graph.get_eid('C','D')
assert_equal ['A','B'], graph.edge(eid1)
assert_equal ['C','D'], graph.edge(eid2);
assert_not_equal eid1,eid2
end
def test_neighbours
assert_nothing_raised do
IGraph.new(['A','B','C','D'],true).neighbors('A',IGraph::IGRAPH_ALL)
end
graph = IGraph.new(['A','B','C','D'],true)
assert_equal ['B'], graph.neighbors('A',IGraph::IGRAPH_ALL)
assert_equal ['D'], graph.neighbors('C',IGraph::IGRAPH_ALL)
end
def test_adjacent
assert_nothing_raised do
IGraph.new(['A','B','C','D'],true).adjacent('A',IGraph::IGRAPH_ALL)
end
graph = IGraph.new(['A','B','C','D'],true)
eid1 = graph.get_eid('A','B')
eid2 = graph.adjacent('A',IGraph::IGRAPH_ALL)[0]
assert_equal eid1, eid2
end
def test_directed
assert IGraph.new(['A','B','C','D'],true).is_directed?
assert !(IGraph.new(['A','B','C','D'],false).is_directed?)
end
def test_degree
graph = IGraph.new(['A','B','C','D'],true)
assert_equal [1], graph.degree(['A'], IGraph::IGRAPH_ALL,true)
assert_equal [1,1],graph.degree(['A','B'],IGraph::IGRAPH_ALL,true)
end
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_graph
assert_nothing_raised{IGraph.new([],true)}
assert_nothing_raised{IGraph.new(['A','B','C','D'],true)}
end
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_edge_fail
assert_raise IGraphError do
IGraph.new([1,2,3],true)
end
end
end

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require 'test/unit'
require 'igraph'
class TestGraph < Test::Unit::TestCase
def test_shortest_paths
graph = IGraph.new(['A','B','C','D'],true)
m = graph.shortest_paths(['A'],IGraph::IGRAPH_ALL)
assert_equal 1, m[0][1]
assert_equal 0, m[0][0]
assert_equal graph.vcount, m[0].size
assert_equal graph.vcount, m[0][2]
end
def test_get_shortest_paths
graph = IGraph.new(['A','B','C','D'],true)
m = graph.get_shortest_paths('A',['B','C'],IGraph::IGRAPH_ALL)
assert_equal ['A','B'], m[0]
assert_equal [], m[1]
end
end

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#Tests all test cases for rsruby
require 'test/unit'
require 'tc_create'
require 'tc_add_delete'
require 'tc_basic_query'
require 'tc_basic_properties'
require 'tc_error_handling'
require 'tc_shortest_paths'