Summary

Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for
Bio::Ontology::SimpleGOEngine

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  use Bio::Ontology::SimpleGOEngine::GraphAdaptor;

  my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;

Description

This is a think adaptor to simplify use of the old and new versions of
the standard CPAN Graph module (old is versions 0.2x; new is 0.5x and
beyond) within Bio::Ontology::SimpleGOEngine.
This module implements only those Graph methods used by
SimpleGOEngine. It is far from a complete compatibility layer! It
also implements workarounds for cerain performance problems in the
current versions of Graph v0.5x.
This class provides a 'new' method that determines which version of
Graph is available. The object returned by 'new' is blessed into this
class if the new version of Graph is available, else into the subclass

  Bio::Ontology::SimpleGOEngine::GraphAdaptor02

This class provides implementations for the required graph methods
using the new version of Graph. In most cases, these are simple
pass-throughs. Methods that differ in v0.2x are implemented in the
subclass.
The methods implemented here or in the subclasses are listed below.
In all cases, we implemented the Graph v0.5x interface. Consult the
Graph v0.5x man page for details.

  add_vertex
  has_vertex
  add_edge
  has_edge
  vertices
  edges
  edges_at
  predecessors
  successors
  set_vertex_attribute
  get_vertex_attribute
  set_edge_attribute
  get_edge_attribute
  source_vertices
  sink_vertices

Methods

Methods description

 Title   : new
 Usage   : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new()
 Function: Creates a new graph
 Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or 
           Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object, 
           depending on which Graph version is available
 Args    : none

 Title   : _graph
 Usage   : $self->_graph();
 Function: Internal method to access 'real' graph
 Returns : Graph::Directed object 
 Args    : none

 Title   : _vertex_attributes
 Usage   : $self->vertex_attributes();
 Function: Internal method to access HASH used to store vertex attributes
 Returns : Graph::Directed object 
 Args    : none

 Title   : _edge_attributes
 Usage   : $self->edge_attributes();
 Function: Internal method to access HASH used to store edge attributes
 Returns : Graph::Directed object 
 Args    : none

 Title   : _vertex2attributes
 Usage   : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
           $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
 Function: Internal method to access attributes for a specific vertex
 Returns : HASH
 Args    : none

 Title   : _edge2attributes
 Usage   : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE};
           $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value;
 Function: Internal method to access HASH used to store edge attributes
 Returns : HASH
 Args    : none

Methods code

sub new {

  my( $class ) = @_;
  $class = ref $class || $class;

  my $self=
    ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ?
      bless ( {}, $class ) :
	bless ( {}, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor02' );
  $self->{_graph}=new Graph::Directed;
  $self->{_vertex_attributes}={};
  $self->{_edge_attributes}={};
  return $self;

}

sub add_vertex {

  my $self=shift;
  $self->_graph->add_vertex(@_);

}

sub has_vertex {

  my $self=shift;
  $self->_graph->has_vertex(@_);

}

sub add_edge {

  my $self=shift;
  $self->_graph->add_edge(@_);

}

sub has_edge {

  my $self=shift;
  $self->_graph->has_edge(@_);

}

sub vertices {

  my $self=shift;
  $self->_graph->vertices(@_);

}

sub edges {

  my $self=shift;
  $self->_graph->edges(@_);

}

sub edges_at {

  my $self=shift;
  $self->_graph->edges_at(@_);

}

sub predecessors {

  my $self=shift;
  $self->_graph->predecessors(@_);

}

sub successors {

  my $self=shift;
  $self->_graph->successors(@_);

}

sub source_vertices {

  my $self=shift;
  $self->_graph->source_vertices();

}

sub sink_vertices {

  my $self=shift;
  $self->_graph->sink_vertices();

}

sub set_vertex_attribute {

  my($self,$v,$attribute,$value)=@_;
  $self->_vertex2attributes($v)->{$attribute}=$value;

}

sub get_vertex_attribute {

  my($self,$v,$attribute)=@_;
  $self->_vertex2attributes($v)->{$attribute};

}

sub set_edge_attribute {

  my($self,$u,$v,$attribute,$value)=@_;
  $self->_edge2attributes($u,$v)->{$attribute}=$value;

}

sub get_edge_attribute {

  my($self,$u,$v,$attribute)=@_;
  $self->_edge2attributes($u,$v)->{$attribute};

}

sub _graph {

$_[0]->{_graph};

}

sub _vertex_attributes {

$_[0]->{_vertex_attributes};

}

sub _edge_attributes {

$_[0]->{_edge_attributes};

}

sub _vertex2attributes {

  my($self,$vertex)=@_;
  $self->_vertex_attributes->{$vertex} or $self->_vertex_attributes->{$vertex}={};

}

sub _edge2attributes {

  my($self,$u,$v)=@_;
  $self->_edge_attributes->{$u,$v} or $self->_edge_attributes->{$u,$v}={};

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Nat Goodman
Email: natg at shore.net
Address:

  Institute for Systems Biology
  1441 N 34th St
  Seattle, WA 98103-8904

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _