libbio-perl-perl 1.6.923-1 / usr / share / perl5 / Bio / Ontology / OBOEngine.pm

#
# BioPerl module for Bio::Ontology::OBOEngine
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Ontology::OBOEngine - An Ontology Engine for OBO style flat file
format from the Gene Ontology Consortium

=head1 SYNOPSIS

  use Bio::Ontology::OBOEngine;

  my $parser = Bio::Ontology::OBOEngine->new
        ( -file => "gene_ontology.obo" );

  my $engine = $parser->parse();

=head1 DESCRIPTION

Needs Graph.pm from CPAN.

This module replaces SimpleGOEngine.pm, which is deprecated.

=head1 FEEDBACK

=head2 Mailing Lists

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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<bioperl-l@bioperl.org>

rather than to the module maintainer directly. Many experienced and 
reponsive experts will be able look at the problem and quickly 
address it. Please include a thorough description of the problem 
with code and data examples if at all possible.

=head2 Reporting Bugs

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:

  https://redmine.open-bio.org/projects/bioperl/

=head1 AUTHOR

Sohel Merchant

Email: s-merchant@northwestern.edu

Address:

  Northwestern University
  Center for Genetic Medicine (CGM), dictyBase
  Suite 1206,
  676 St. Clair st
  Chicago IL 60611

=head2 CONTRIBUTOR

 Hilmar Lapp, hlapp at gmx.net
 Chris Mungall,   cjm at fruitfly.org

=head1 APPENDIX

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

=cut

package Bio::Ontology::OBOEngine;

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

use strict;
use Bio::Ontology::RelationshipType;
use Bio::Ontology::RelationshipFactory;
use Data::Dumper;

use constant TRUE       => 1;
use constant FALSE      => 0;
use constant IS_A       => "IS_A";
use constant PART_OF    => "PART_OF";
use constant RELATED_TO => "RELATED_TO";
use constant TERM       => "TERM";
use constant TYPE       => "TYPE";
use constant ONTOLOGY   => "ONTOLOGY";
use constant REGULATES   => "REGULATES";
use constant POSITIVELY_REGULATES   => "POSITIVELY_REGULATES";
use constant NEGATIVELY_REGULATES   => "NEGATIVELY_REGULATES";


use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI);



=head2 new

 Title   : new
 Usage   : $engine = Bio::Ontology::OBOEngine->new()
 Function: Creates a new OBOEngine
 Returns : A new OBOEngine object
 Args    :

=cut

sub new {
    my( $class, @args ) = @_;

    my $self = $class->SUPER::new( @args );

    $self->init();

    return $self;
} # new



=head2 init

 Title   : init()
 Usage   : $engine->init();
 Function: Initializes this Engine.
 Returns :
 Args    :

=cut

sub init {
    my ( $self ) = @_;

    $self->{ "_is_a_relationship" }       = Bio::Ontology::RelationshipType->get_instance( IS_A );
    $self->{ "_part_of_relationship" }    = Bio::Ontology::RelationshipType->get_instance( PART_OF );
    $self->{ "_related_to_relationship" } = Bio::Ontology::RelationshipType->get_instance( RELATED_TO );

    $self->{'_regulates_relationship'} = Bio::Ontology::RelationshipType->get_instance(REGULATES);
    $self->{'_positively_regulate'} = Bio::Ontology::RelationshipType->get_instance(POSITIVELY_REGULATES);
    $self->{'_negatively_regulate'} = Bio::Ontology::RelationshipType->get_instance(NEGATIVELY_REGULATES);
    

    $self->graph( Bio::Ontology::SimpleGOEngine::GraphAdaptor->new() );        # NG 05-02-16

    # set defaults for the factories
    $self->relationship_factory(Bio::Ontology::RelationshipFactory->new(
                                     -type => "Bio::Ontology::Relationship"));

} # init



=head2 is_a_relationship

 Title   : is_a_relationship()
 Usage   : $IS_A = $engine->is_a_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "is-a"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "IS_A"
 Args    :

=cut

sub is_a_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_is_a_relationship" };
} # is_a_relationship



=head2 part_of_relationship

 Title   : part_of_relationship()
 Usage   : $PART_OF = $engine->part_of_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "part-of"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "PART_OF"
 Args    :

=cut

sub part_of_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_part_of_relationship" };
} # part_of_relationship


=head2 related_to_relationship

 Title   : related_to_relationship()
 Usage   : $RELATED_TO = $engine->related_to_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "related-to"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "RELATED_TO"
 Args    :

=cut

sub related_to_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_related_to_relationship" };
} # related_to_relationship

=head2 regulates_relationship

 Title   : regulates_relationship()
 Usage   : $REGULATES = $engine->regulates_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "regulates"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "REGULATES"
 Args    :

=cut

sub regulates_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_regulates_relationship" };
} # is_a_relationship

=head2 positively_regulates_relationship

 Title   : positively_regulates_relationship()
 Usage   : $REGULATES = $engine->positively_regulates_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "positively_regulates"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
 Args    :

=cut

sub positively_regulates_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_positively_regulate" };
} 

=head2 negatively_regulates_relationship

 Title   : negatively_regulates_relationship()
 Usage   : $REGULATES = $engine->negatively_regulates_relationship();
 Function: Returns a Bio::Ontology::RelationshipType object for "negatively_regulates"
           relationships
 Returns : Bio::Ontology::RelationshipType set to "POSITIVELY_REGULATES"
 Args    :

=cut

sub negatively_regulates_relationship {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->throw( "Attempted to change immutable field" );
    }

    return $self->{ "_negatively_regulate" };
} 


=head2 add_term

 Title   : add_term
 Usage   : $engine->add_term( $term_obj );
 Function: Adds a Bio::Ontology::TermI to this engine
 Returns : true if the term was added and false otherwise (e.g., if the
           term already existed in the ontology engine)
 Args    : Bio::Ontology::TermI

=cut

sub add_term {
    my ( $self, $term ) = @_;

    return FALSE if $self->has_term( $term );

    my $goid = $self->_get_id($term);

    $self->graph()->add_vertex( $goid );
    $self->graph()->set_vertex_attribute( $goid, TERM, $term );        # NG 05-02-16
    return TRUE;

} # add_term



=head2 has_term

 Title   : has_term
 Usage   : $engine->has_term( $term );
 Function: Checks whether this engine contains a particular term
 Returns : true or false
 Args    : Bio::Ontology::TermI
           or
           Term identifier (e.g. "GO:0012345")

=cut

sub has_term {
    my ( $self, $term ) = @_;
    $term = $self->_get_id( $term );
    if ( $self->graph()->has_vertex( $term ) ) {
        return TRUE;
    }
    else {
        return FALSE;
    }

} # has_term


=head2 add_relationship_type

 Title   : add_relationship_type
 Usage   : $engine->add_relationship_type( $type_name, $ont );
 Function: Adds a new relationship type to the engine.  Use
           get_relationship_type($type_name) to retrieve.
 Returns : true if successfully added, false otherwise
 Args    : relationship type name to add (scalar)
           ontology to which to assign the relationship type

=cut

sub add_relationship_type{
   my ($self,@args) = @_;

   if(scalar(@_) == 3){
         my $type_name = $args[0];
         my $ont = $args[1];
         $self->{ "_extra_relationship_types" }{$type_name} = Bio::Ontology::RelationshipType->get_instance($type_name,$ont);
#warn Dumper($self->{"_extra_relationship_types"}{$type_name});
         return 1;
   }
   return 0;
}


=head2 get_relationship_type

 Title   : get_relationship_type
 Usage   : $engine->get_relationship_type( $type_name );
 Function: Gets a Bio::Ontology::RelationshipI object corresponding
           to $type_name
 Returns : a Bio::Ontology::RelationshipI object
 Args    :

=cut

sub get_relationship_type{
   my ($self,$type_name) = @_;
   return $self->{ "_extra_relationship_types" }{$type_name};
}

=head2 add_relationship

 Title   : add_relationship
 Usage   : $engine->add_relationship( $relationship );
           $engine->add_relatioship( $subject_term, $predicate_term,
                                     $object_term, $ontology );
           $engine->add_relatioship( $subject_id, $predicate_id,
                                     $object_id, $ontology);
 Function: Adds a relationship to this engine
 Returns : true if successfully added, false otherwise
 Args    : The relationship in one of three ways:

             a) subject (or child) term id, Bio::Ontology::TermI
                (rel.type), object (or parent) term id, ontology

           or

             b) subject Bio::Ontology::TermI, predicate
                Bio::Ontology::TermI (rel.type), object
                Bio::Ontology::TermI, ontology

           or

             c) Bio::Ontology::RelationshipI-compliant object

=cut

# term objs or term ids
sub add_relationship {
    my ( $self, $child, $type, $parent, $ont ) = @_;

    if ( scalar( @_ ) == 2 ) {
        $self->_check_class( $child, "Bio::Ontology::RelationshipI" );
        $type   = $child->predicate_term();
        $parent = $child->object_term();
        $ont    = $child->ontology();
        $child  = $child->subject_term();
    }


    $self->_check_class( $type, "Bio::Ontology::TermI" );

    my $parentid = $self->_get_id( $parent );
    my $childid = $self->_get_id( $child );

    my $g = $self->graph();

    $self->add_term($child) unless $g->has_vertex( $childid );
    $self->add_term($parent) unless $g->has_vertex( $parentid );

    # This prevents multi graphs.
    if ( $g->has_edge( $parentid, $childid ) ) {
        return FALSE;
    }

    $g->add_edge( $parentid, $childid );
    $g->set_edge_attribute( $parentid, $childid, TYPE, $type );           # NG 05-02-16
    $g->set_edge_attribute( $parentid, $childid, ONTOLOGY, $ont ); # NG 05-02-16

    return TRUE;

} # add_relationship




=head2 get_relationships


 Title   : get_relationships
 Usage   : $engine->get_relationships( $term );
 Function: Returns all relationships of a term, or all relationships in
           the graph if no term is specified.
 Returns : Relationship
 Args    : term id
           or
           Bio::Ontology::TermI

=cut

sub get_relationships {
    my ( $self, $term ) = @_;

    my $g = $self->graph();

    # obtain the ID if term provided
    my $termid;
    if($term) {
        $termid = $self->_get_id( $term );
        # check for presence in the graph
        if ( ! $g->has_vertex( $termid ) ) {
            $self->throw( "no term with identifier \"$termid\" in ontology" );
        }
    }

    # now build the relationships
    my $relfact = $self->relationship_factory();
    # we'll build the relationships from edges
    my @rels = ();
    my @edges = $termid ? $g->edges_at( $termid ) : $g->edges(); # NG 05-02-13
    while(@edges) {
      my ( $startid, $endid ) = @{ shift @edges }; # NG 05-02-16
      my $rel = $relfact->create_object
        (-subject_term   => $self->get_terms($endid),
         -object_term    => $self->get_terms($startid),
         -predicate_term => $g->get_edge_attribute($startid, $endid, TYPE),
         -ontology       => $g->get_edge_attribute($startid, $endid, ONTOLOGY));
      push( @rels, $rel );

    }

    return @rels;

} # get_relationships

=head2 get_all_relationships


 Title   : get_all_relationships
 Usage   : @rels = $engine->get_all_relationships();
 Function: Returns all relationships in the graph.
 Returns : Relationship
 Args    :

=cut

sub get_all_relationships {
    return shift->get_relationships(@_);
} # get_all_relationships



=head2 get_predicate_terms

 Title   : get_predicate_terms
 Usage   : $engine->get_predicate_terms();
 Function: Returns the types of relationships this engine contains
 Returns : Bio::Ontology::RelationshipType
 Args    :

=cut

sub get_predicate_terms {
    my ( $self ) = @_;

    my @a = (
            $self->is_a_relationship(),
            $self->part_of_relationship(),
            $self->related_to_relationship(),
            $self->regulates_relationship(),
            $self->positively_regulates_relationship(),
            $self->negatively_regulates_relationship(),
           );

    foreach my $termname (keys %{$self->{ "_extra_relationship_types" }}){
      push @a, $self->{ "_extra_relationship_types" }{ $termname };
    }

    return @a;
} # get_predicate_terms




=head2 get_child_terms

 Title   : get_child_terms
 Usage   : $engine->get_child_terms( $term_obj, @rel_types );
           $engine->get_child_terms( $term_id, @rel_types );
 Function: Returns the children of this term
 Returns : Bio::Ontology::TermI
 Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
           or
           term id, Bio::Ontology::RelationshipType

           if NO Bio::Ontology::RelationshipType is indicated: children
           of ALL types are returned

=cut

sub get_child_terms {
    my ( $self, $term, @types ) = @_;

    return $self->_get_child_parent_terms_helper( $term, TRUE, @types );

} # get_child_terms


=head2 get_descendant_terms

 Title   : get_descendant_terms
 Usage   : $engine->get_descendant_terms( $term_obj, @rel_types );
           $engine->get_descendant_terms( $term_id, @rel_types );
 Function: Returns the descendants of this term
 Returns : Bio::Ontology::TermI
 Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
           or
           term id, Bio::Ontology::RelationshipType

           if NO Bio::Ontology::RelationshipType is indicated:
           descendants of ALL types are returned

=cut

sub get_descendant_terms {
    my ( $self, $term, @types ) = @_;

    my %ids = ();
    my @ids = ();

    $term = $self->_get_id( $term );

    if ( ! $self->graph()->has_vertex( $term ) ) {
        $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
    }

    $self->_get_descendant_terms_helper( $term, \%ids, \@types );

    while( ( my $id ) = each ( %ids ) ) {
        push( @ids, $id );
    }

    return $self->get_terms( @ids );

} # get_descendant_terms


=head2 get_parent_terms

 Title   : get_parent_terms
 Usage   : $engine->get_parent_terms( $term_obj, @rel_types );
           $engine->get_parent_terms( $term_id, @rel_types );
 Function: Returns the parents of this term
 Returns : Bio::Ontology::TermI
 Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
           or
           term id, Bio::Ontology::RelationshipType

           if NO Bio::Ontology::RelationshipType is indicated:
           parents of ALL types are returned

=cut

sub get_parent_terms {
    my ( $self, $term, @types ) = @_;

    return $self->_get_child_parent_terms_helper( $term, FALSE, @types );

} # get_parent_terms



=head2 get_ancestor_terms

 Title   : get_ancestor_terms
 Usage   : $engine->get_ancestor_terms( $term_obj, @rel_types );
           $engine->get_ancestor_terms( $term_id, @rel_types );
 Function: Returns the ancestors of this term
 Returns : Bio::Ontology::TermI
 Args    : Bio::Ontology::TermI, Bio::Ontology::RelationshipType
           or
           term id, Bio::Ontology::RelationshipType

           if NO Bio::Ontology::RelationshipType is indicated:
           ancestors of ALL types are returned

=cut

sub get_ancestor_terms {
    my ( $self, $term, @types ) = @_;

    my %ids = ();
    my @ids = ();

    $term = $self->_get_id( $term );

    if ( ! $self->graph()->has_vertex( $term ) ) {
        $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
    }

    $self->_get_ancestor_terms_helper( $term, \%ids, \@types );

    while( ( my $id ) = each ( %ids ) ) {
        push( @ids, $id );
    }

    return $self->get_terms( @ids );

} # get_ancestor_terms





=head2 get_leaf_terms

 Title   : get_leaf_terms
 Usage   : $engine->get_leaf_terms();
 Function: Returns the leaf terms
 Returns : Bio::Ontology::TermI
 Args    :

=cut

sub get_leaf_terms {
    my ( $self ) = @_;

    my @a = $self->graph()->sink_vertices();

    return $self->get_terms( @a );

}



=head2 get_root_terms()

 Title   : get_root_terms
 Usage   : $engine->get_root_terms();
 Function: Returns the root terms
 Returns : Bio::Ontology::TermI
 Args    :

=cut

sub get_root_terms {
    my ( $self ) = @_;


    my @a = $self->graph()->source_vertices();

    return $self->get_terms( @a );

}


=head2 get_terms

 Title   : get_terms
 Usage   : @terms = $engine->get_terms( "GO:1234567", "GO:2234567" );
 Function: Returns term objects with given identifiers
 Returns : Bio::Ontology::TermI, or the term corresponding to the
           first identifier if called in scalar context
 Args    : term ids

=cut

sub get_terms {
    my ( $self, @ids ) = @_;

    my @terms = ();

    foreach my $id ( @ids ) {
        if ( $self->graph()->has_vertex( $id ) ) {
          push( @terms, $self->graph()->get_vertex_attribute( $id, TERM ) ); # NG 05-02-16
        }
    }

    return wantarray ? @terms : shift(@terms);

} # get_terms


=head2 get_all_terms

 Title   : get_all_terms
 Usage   : $engine->get_all_terms();
 Function: Returns all terms in this engine
 Returns : Bio::Ontology::TermI
 Args    :

=cut

sub get_all_terms {
    my ( $self ) = @_;

    return( $self->get_terms( $self->graph()->vertices() ) );

} # get_all_terms


=head2 find_terms

 Title   : find_terms
 Usage   : ($term) = $oe->find_terms(-identifier => "SO:0000263");
 Function: Find term instances matching queries for their attributes.

           This implementation can efficiently resolve queries by
           identifier.

 Example :
 Returns : an array of zero or more Bio::Ontology::TermI objects
 Args    : Named parameters. The following parameters should be recognized
           by any implementations:

              -identifier    query by the given identifier
              -name          query by the given name

=cut

sub find_terms{
    my ($self,@args) = @_;
    my @terms;

    my ($id,$name) = $self->_rearrange([qw(IDENTIFIER NAME)],@args);

    if(defined($id)) {
        @terms = $self->get_terms($id);
    } else {
        @terms = $self->get_all_terms();
    }
    if(defined($name)) {
        @terms = grep { $_->name() eq $name; } @terms;
    }
    return @terms;
}


=head2 find_identically_named_terms

 Title   : find_identically_named_terms
 Usage   : ($term) = $oe->find_identically_named_terms($term0);
 Function: Find term instances where names match the query term
           name exactly
 Example :
 Returns : an array of zero or more Bio::Ontology::TermI objects
 Args    : a Bio::Ontology::TermI object

=cut

sub find_identically_named_terms{
    my ($self,$qterm) = @_;
    $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
        unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");

    my %matching_terms;

    foreach my $term ($self->get_all_terms) {
        $matching_terms{$term->identifier} = $term and next
            if $term->name eq $qterm->name;
    }
    return values %matching_terms;
}


=head2 find_identical_terms

 Title   : find_identical_terms
 Usage   : ($term) = $oe->find_identical_terms($term0);
 Function: Find term instances where name or synonym
           matches the query exactly
 Example :
 Returns : an array of zero or more Bio::Ontology::TermI objects
 Args    : a Bio::Ontology::TermI object

=cut

sub find_identical_terms{
    my ($self,$qterm) = @_;
    $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
        unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");

    my %matching_terms;

    foreach my $qstring ($qterm->name, $qterm->each_synonym) {
        foreach my $term ($self->get_all_terms) {
            foreach my $string ( $term->name, $term->each_synonym() ) {
                $matching_terms{$term->identifier} = $term and next
                    if $string eq $qstring;
            }
        }
    }
    return values %matching_terms;
}

=head2 find_similar_terms

 Title   : find_similar_terms
 Usage   : ($term) = $oe->find_similar_terms($term0);
 Function: Find term instances where name or synonym, or part of one,
           matches the query.
 Example :
 Returns : an array of zero or more Bio::Ontology::TermI objects
 Args    : a Bio::Ontology::TermI object

=cut

sub find_similar_terms{
    my ($self,$qterm) = @_;
    $self->throw("Argument doesn't implement Bio::Ontology::TermI. " . "Bummer." )
        unless defined $qterm and $qterm->isa("Bio::Ontology::TermI");

    my %matching_terms;

    foreach my $qstring ($qterm->name, $qterm->each_synonym) {
        foreach my $term ($self->get_all_terms) {

            foreach my $string ( $term->name, $term->each_synonym() ) {
                $matching_terms{$term->identifier} = $term and next
                    if $string =~ /\Q$qstring\E/ or $qstring =~ /\Q$string\E/;
            }
        }
    }
    return values %matching_terms;
}


=head2 relationship_factory

 Title   : relationship_factory
 Usage   : $fact = $obj->relationship_factory()
 Function: Get/set the object factory to be used when relationship
           objects are created by the implementation on-the-fly.

 Example :
 Returns : value of relationship_factory (a Bio::Factory::ObjectFactoryI
           compliant object)
 Args    : on set, a Bio::Factory::ObjectFactoryI compliant object

=cut

sub relationship_factory{
    my $self = shift;

    return $self->{'relationship_factory'} = shift if @_;
    return $self->{'relationship_factory'};
}

=head2 term_factory

 Title   : term_factory
 Usage   : $fact = $obj->term_factory()
 Function: Get/set the object factory to be used when term objects are
           created by the implementation on-the-fly.

           Note that this ontology engine implementation does not
           create term objects on the fly, and therefore setting this
           attribute is meaningless.

 Example :
 Returns : value of term_factory (a Bio::Factory::ObjectFactoryI
           compliant object)
 Args    : on set, a Bio::Factory::ObjectFactoryI compliant object

=cut

sub term_factory{
    my $self = shift;

    if(@_) {
        $self->warn("setting term factory, but ".ref($self).
                    " does not create terms on-the-fly");
        return $self->{'term_factory'} = shift;
    }
    return $self->{'term_factory'};
}

=head2 graph

 Title   : graph()
 Usage   : $engine->graph();
 Function: Returns the Graph this engine is based on
 Returns : Graph
 Args    :

=cut

sub graph {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->_check_class( $value, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor' ); # NG 05-02-16
        $self->{ "_graph" } = $value;
    }

    return $self->{ "_graph" };
} # graph


# Internal methods
# ----------------
# Checks the correct format of a GOBO-formatted id
# Gets the id out of a term or id string
sub _get_id {
    my ( $self, $term ) = @_;
    my $id = $term;

    if ( ref($term) ) {

        # use TermI standard API
        $self->throw(
            "Object doesn't implement Bio::Ontology::TermI. " . "Bummer." )
          unless $term->isa("Bio::Ontology::TermI");
        $id = $term->identifier();

        # if there is no ID, we need to fake one from ontology name and name
        # in order to achieve uniqueness
        if ( !$id ) {
            $id = $term->ontology->name() if $term->ontology();
            $id = $id ? $id . '|' : '';
            $id .= $term->name();
        }
    }

    return $id

#        if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
      if $term->isa("Bio::Ontology::OBOterm") || ( $id =~ /^\w+:\w+$/ );

    # prefix with something if only numbers
    #     if($id =~ /^\d+$/) {
    #         $self->warn(ref($self).": identifier [$id] is only numbers - ".
    #                     "prefixing with 'GO:'");
    #         return "GO:" . $id;
    #     }
    # we shouldn't have gotten here if it's at least a remotely decent ID
    $self->throw( ref($self) . ": non-standard identifier '$id'\n" )
      unless $id =~ /\|/;
    return $id;
}    # _get_id

# Helper for getting children and parent terms
sub _get_child_parent_terms_helper {
    my ( $self, $term, $do_get_child_terms, @types ) = @_;

    foreach my $type ( @types ) {
        $self->_check_class( $type, "Bio::Ontology::TermI" );
    }

    my @relative_terms = ();

    $term = $self->_get_id( $term );
    if ( ! $self->graph()->has_vertex( $term ) ) {
        $self->throw( "Ontology does not contain a term with an identifier of \"$term\"" );
    }

    my @all_relative_terms = ();
    if ( $do_get_child_terms ) {
        @all_relative_terms = $self->graph()->successors( $term );
    }
    else {
        @all_relative_terms = $self->graph()->predecessors( $term );
    }

    foreach my $relative ( @all_relative_terms ) {
        if ( scalar( @types ) > 0 ) {
            foreach my $type ( @types ) {
                my $relative_type;
                if ( $do_get_child_terms ) {
                  $relative_type = $self->graph()->get_edge_attribute ($term, $relative, TYPE );  # NG 05-02-16
                }
                else {
                  $relative_type = $self->graph()->get_edge_attribute ($relative, $term, TYPE ); # NG 05-02-16
                }
                if ( $relative_type->equals( $type ) ) {
                    push( @relative_terms, $relative );
                }
            }
        }
        else {
            push( @relative_terms, $relative );
        }
    }

    return $self->get_terms( @relative_terms );

} # get_child_terms


# Recursive helper
sub _get_descendant_terms_helper {
    my ( $self, $term, $ids_ref, $types_ref ) = @_;

    my @child_terms = $self->get_child_terms( $term, @$types_ref );

    if ( scalar( @child_terms ) < 1 ) {
        return;
    }

    foreach my $child_term ( @child_terms ) {
        my $child_term_id = $self->_get_id($child_term->identifier());
        $ids_ref->{ $child_term_id } = 0;
        $self->_get_descendant_terms_helper( $child_term_id, $ids_ref, $types_ref );
    }

} # _get_descendant_terms_helper


# Recursive helper
sub _get_ancestor_terms_helper {
    my ( $self, $term, $ids_ref, $types_ref ) = @_;

    my @parent_terms = $self->get_parent_terms( $term, @$types_ref );

    if ( scalar( @parent_terms ) < 1 ) {
        return;
    }

    foreach my $parent_term ( @parent_terms ) {
        my $parent_term_id = $self->_get_id($parent_term->identifier());
        $ids_ref->{ $parent_term_id } = 0;
        $self->_get_ancestor_terms_helper( $parent_term_id, $ids_ref, $types_ref );
    }

} # get_ancestor_terms_helper

sub _check_class {
    my ( $self, $value, $expected_class ) = @_;

    if ( ! defined( $value ) ) {
        $self->throw( "Found [undef] where [$expected_class] expected" );
    }
    elsif ( ! ref( $value ) ) {
        $self->throw( "Found [scalar] where [$expected_class] expected" );
    }
    elsif ( ! $value->isa( $expected_class ) ) {
        $self->throw( "Found [" . ref( $value ) . "] where [$expected_class] expected" );
    }

} # _check_class

#################################################################
# aliases
#################################################################

*get_relationship_types = \&get_predicate_terms;




1;