Bio::Ontology SimpleOntologyEngine
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Summary
Bio::Ontology::SimpleOntologyEngine - Implementation of OntologyEngineI interface
Package variables
No package variables defined.
Included modules
Bio::Ontology::RelationshipFactory
Carp
Data::Dumper
Inherit
Bio::Ontology::OntologyEngineI Bio::Root::Root
Synopsis
  my $soe = Bio::Ontology::SimpleOntologyEngine->new;
Description
This is a "simple" implementation of Bio::Ontology::OntologyEngineI.
Methods
newDescriptionCode
_instantiated_terms_storeDescriptionCode
mark_instantiatedDescriptionCode
mark_uninstantiatedDescriptionCode
_term_storeDescriptionCode
add_termDescriptionCode
get_term_by_identifierDescriptionCode
_get_number_relsDescriptionCode
_get_number_termsDescriptionCode
_relationship_storeDescriptionCode
_inverted_relationship_storeDescriptionCode
_relationship_type_storeDescriptionCode
_add_relationship_simpleDescriptionCode
add_relationshipDescriptionCode
get_relationshipsDescriptionCode
get_all_relationshipsDescriptionCode
get_predicate_termsDescriptionCode
_is_rel_typeDescriptionCode
_typed_traversalDescriptionCode
get_child_termsDescriptionCode
get_descendant_termsDescriptionCode
get_parent_termsDescriptionCode
get_ancestor_termsDescriptionCode
get_leaf_termsDescriptionCode
get_root_termsDescriptionCode
_filter_repeatedDescriptionCode
get_all_termsDescriptionCode
find_termsDescriptionCode
relationship_factoryDescriptionCode
term_factoryDescriptionCode
_filter_unmarkedDescriptionCode
remove_term_by_idDescriptionCode
to_stringDescriptionCode
_unique_termidDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : $soe = Bio::Ontology::SimpleOntologyEngine->new;
Function: Initializes the ontology engine.
Example : $soe = Bio::Ontology::SimpleOntologyEngine->new;
Returns : Object of class SimpleOntologyEngine.
Args :
_instantiated_terms_storecodeprevnextTop
 Title   : _instantiated_terms_store
Usage : $obj->_instantiated_terms_store($newval)
Function:
Example :
Returns : hash
Args : empty hash
mark_instantiatedcodeprevnextTop
 Title   : mark_instantiated
Usage : $self->mark_instantiated(TermI terms): TermI
Function: Marks TermI objects as fully instantiated,
allowing for proper counting of the number of terms in the term store.
The TermI objects has to be already stored in the term store in order
to be marked.
Example : $self->mark_instantiated($term);
Returns : its argument or throws an exception if a term is not
in the term store.
Args : array of objects of class TermI.
mark_uninstantiatedcodeprevnextTop
 Title   : mark_uninstantiated
Usage : $self->mark_uninstantiated(TermI terms): TermI
Function: Marks TermI objects as not fully instantiated,
Example : $self->mark_uninstantiated($term);
Returns : its argument or throws an exception if a term is not
in the term store(if the term is not marked it does nothing).
Args : array of objects of class TermI.
_term_storecodeprevnextTop
 Title   : term_store
Usage : $obj->_term_store($newval)
Function:
Example :
Returns : reference to an array of Bio::Ontology::TermI objects
Args : reference to an array of Bio::Ontology::TermI objects
add_termcodeprevnextTop
 Title   : add_term
Usage : add_term(TermI term): TermI
Function: Adds TermI object to the ontology engine term store.
Marks the term fully instantiated by default.
Example : $soe->add_term($term)
Returns : its argument.
Args : object of class TermI.
get_term_by_identifiercodeprevnextTop
 Title   : get_term_by_identifier
Usage : get_term_by_identifier(String id): TermI
Function: Retrieves terms from the term store by their identifier
field, or an empty list if not there.
Example : $term = $soe->get_term_by_identifier("IPR000001");
Returns : An array of zero or more Bio::Ontology::TermI objects.
Args : An array of identifier strings
_get_number_relscodeprevnextTop
 Title   : get_number_rels
Usage :
Function:
Example :
Returns :
Args :
_get_number_termscodeprevnextTop
 Title   : _get_number_terms
Usage :
Function:
Example :
Returns :
Args :
_relationship_storecodeprevnextTop
 Title   : _storerelationship_store
Usage : $obj->relationship_store($newval)
Function:
Example :
Returns : reference to an array of Bio::Ontology::TermI objects
Args : reference to an array of Bio::Ontology::TermI objects
_inverted_relationship_storecodeprevnextTop
 Title   : _inverted_relationship_store
Usage :
Function:
Example :
Returns : reference to an array of Bio::Ontology::TermI objects
Args : reference to an array of Bio::Ontology::TermI objects
_relationship_type_storecodeprevnextTop
 Title   : _relationship_type_store
Usage : $obj->_relationship_type_store($newval)
Function:
Example :
Returns : reference to an array of Bio::Ontology::RelationshipType objects
Args : reference to an array of Bio::Ontology::RelationshipType objects
_add_relationship_simplecodeprevnextTop
 Title   : _add_relationship_simple
Usage :
Function:
Example :
Returns :
Args :
add_relationshipcodeprevnextTop
 Title   : add_relationship
Usage : add_relationship(RelationshipI relationship): RelationshipI
Function: Adds a relationship object to the ontology engine.
Example :
Returns : Its argument.
Args : A RelationshipI object.
get_relationshipscodeprevnextTop
 Title   : get_relationships
Usage : get_relationships(): RelationshipI
Function: Retrieves all relationship objects.
Example :
Returns : Array of RelationshipI objects
Args :
get_all_relationshipscodeprevnextTop
 Title   : get_all_relationships
Usage : get_all_relationships(): RelationshipI
Function: Retrieves all relationship objects.
Example :
Returns : Array of RelationshipI objects
Args :
get_predicate_termscodeprevnextTop
 Title   : get_predicate_terms
Usage : get_predicate_terms(): TermI
Function: Retrives all relationship types stored in the engine
Example :
Returns : reference to an array of Bio::Ontology::RelationshipType objects
Args :
_is_rel_typecodeprevnextTop
 Title   : _is_rel_type
Usage :
Function:
Example :
Returns :
Args :
_typed_traversalcodeprevnextTop
 Title   : _typed_traversal
Usage :
Function:
Example :
Returns :
Args :
get_child_termscodeprevnextTop
 Title   : get_child_terms
Usage : get_child_terms(TermI term, TermI predicate_terms): TermI
get_child_terms(TermI term, RelationshipType predicate_terms): TermI
Function: Retrieves all child terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_child_terms is a special
case of get_descendant_terms, limiting the search to the
direct descendants.
Example :
Returns : Array of TermI objects.
Args : First argument is the term of interest, second is the list of
relationship type terms.
get_descendant_termscodeprevnextTop
 Title   : get_descendant_terms
Usage : get_descendant_terms(TermI term, TermI rel_types): TermI
get_child_terms(TermI term, RelationshipType predicate_terms): TermI
Function: Retrieves all descendant terms of a given term, that
satisfy a relationship among those that are specified in
the second argument or undef otherwise. Uses
_typed_traversal to find all descendants.
Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.
get_parent_termscodeprevnextTop
 Title   : get_parent_terms
Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI
get_child_terms(TermI term, RelationshipType predicate_terms): TermI
Function: Retrieves all parent terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_parent_terms is a special
case of get_ancestor_terms, limiting the search to the
direct ancestors.
Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.
get_ancestor_termscodeprevnextTop
 Title   : get_ancestor_terms
Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI
get_child_terms(TermI term, RelationshipType predicate_terms): TermI
Function: Retrieves all ancestor terms of a given term, that satisfy
a relationship among those that are specified in the second
argument or undef otherwise. Uses _typed_traversal to find
all ancestors.
Example : Returns : Array of TermI objects. Args : First argument is the term of interest, second is the list of relationship type terms.
get_leaf_termscodeprevnextTop
 Title   : get_leaf_terms
Usage : get_leaf_terms(): TermI
Function: Retrieves all leaf terms from the ontology. Leaf term is a term w/o descendants.
Example : @leaf_terms = $obj->get_leaf_terms()
Returns : Array of TermI objects.
Args :
get_root_termscodeprevnextTop
 Title   : get_root_terms
Usage : get_root_terms(): TermI
Function: Retrieves all root terms from the ontology. Root term is a term w/o descendants.
Example : @root_terms = $obj->get_root_terms()
Returns : Array of TermI objects.
Args :
_filter_repeatedcodeprevnextTop
 Title   : _filter_repeated
Usage : @lst = $self->_filter_repeated(@old_lst);
Function: Removes repeated terms
Example :
Returns : List of unique TermI objects
Args : List of TermI objects
get_all_termscodeprevnextTop
 Title   : get_all_terms
Usage : get_all_terms(): TermI
Function: Retrieves all terms currently stored in the ontology.
Example : @all_terms = $obj->get_all_terms()
Returns : Array of TermI objects.
Args :
find_termscodeprevnextTop
 Title   : find_terms
Usage : ($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
relationship_factorycodeprevnextTop
 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
term_factorycodeprevnextTop
 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
_filter_unmarkedcodeprevnextTop
 Title   : _filter_unmarked
Usage : _filter_unmarked(TermI terms): TermI
Function: Removes the uninstantiated terms from the list of terms
Example :
Returns : array of fully instantiated TermI objects
Args : array of TermI objects
remove_term_by_idcodeprevnextTop
 Title   : remove_term_by_id
Usage : remove_term_by_id(String id): TermI
Function: Removes TermI object from the ontology engine using the
string id as an identifier. Current implementation does not
enforce consistency of the relationships using that term.
Example : $term = $soe->remove_term_by_id($id);
Returns : Object of class TermI or undef if not found.
Args : The string identifier of a term.
to_stringcodeprevnextTop
 Title   : to_string
Usage : print $sv->to_string();
Function: Currently returns formatted string containing the number of
terms and number of relationships from the ontology engine.
Example : print $sv->to_string();
Returns :
Args :
_unique_termidcodeprevnextTop
 Title   : _unique_termid
Usage :
Function: Returns a string that can be used as ID using fail-over
approaches.
If the identifier attribute is not set, it uses the combination of name and ontology name, provided both are set. If they are not, it returns the name alone. Note that this is a private method. Call from inheriting classes but not from outside. Example : Returns : a string Args : a Bio::Ontology::TermI compliant object
Methods code
newdescriptionprevnextTop
sub new {
    my ( $class, @args ) = @_;
    my $self = $class->SUPER::new(@args);

    #   my %param = @args;
$self->_term_store( {} ); $self->_relationship_store( {} ); $self->_inverted_relationship_store( {} ); $self->_relationship_type_store( {} ); $self->_instantiated_terms_store( {} ); # set defaults for the factories
$self->relationship_factory( Bio::Ontology::RelationshipFactory->new( -type => "Bio::Ontology::Relationship" ) ); return $self;
}
_instantiated_terms_storedescriptionprevnextTop
sub _instantiated_terms_store {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        $self->{'_instantiated_terms_store'} = $value;
    }
    return $self->{'_instantiated_terms_store'};
}
mark_instantiateddescriptionprevnextTop
sub mark_instantiated {
    my ( $self, @terms ) = @_;

    foreach my $term (@terms) {
        $self->throw( "term " . $term->identifier . " not in the term store\n" )
            if !defined $self->_term_store->{ $term->identifier };
        $self->_instantiated_terms_store->{ $term->identifier } = 1;
    }

    return @terms;
}
mark_uninstantiateddescriptionprevnextTop
sub mark_uninstantiated {
    my ( $self, @terms ) = @_;

    foreach my $term (@terms) {
        $self->throw( "term " . $term->identifier . " not in the term store\n" )
            if !defined $self->_term_store->{ $term->identifier };
        delete $self->_instantiated_terms_store->{ $term->identifier }
            if defined $self->_instantiated_terms_store->{ $term->identifier };
    }

    return @terms;
}
_term_storedescriptionprevnextTop
sub _term_store {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        if ( defined $self->{'_term_store'} ) {
            $self->throw("_term_store already defined\n");
        } else {
            $self->{'_term_store'} = $value;
        }
    }

    return $self->{'_term_store'};
}
add_termdescriptionprevnextTop
sub add_term {
    my ( $self, $term ) = @_;
    my $term_store = $self->_term_store;

    if ( defined $term_store->{ $term->identifier } && $self->_instantiated_terms_store->{ $term->identifier }) {
        $self->throw( "term " . $term->identifier . " already defined\n" );
    } else {
        $term_store->{ $term->identifier } = $term;
        $self->_instantiated_terms_store->{ $term->identifier } = 1;
    }

    return $term;
}
get_term_by_identifierdescriptionprevnextTop
sub get_term_by_identifier {
    my ( $self, @ids ) = @_;
    my @ans = ();

    foreach my $id (@ids) {
        my $term = $self->_term_store->{$id};
        push @ans, $term if defined $term;
    }

    return @ans;
}
_get_number_relsdescriptionprevnextTop
sub _get_number_rels {
    my ($self) = @_;
    my $num_rels = 0;

    foreach my $entry ( $self->_relationship_store ) {
        $num_rels += scalar keys %$entry;
    }
    return $num_rels;
}
_get_number_termsdescriptionprevnextTop
sub _get_number_terms {
    my ($self) = @_;

    return scalar $self->_filter_unmarked( values %{ $self->_term_store } );
}
_relationship_storedescriptionprevnextTop
sub _relationship_store {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        if ( defined $self->{'_relationship_store'} ) {
            $self->throw("_relationship_store already defined\n");
        } else {
            $self->{'_relationship_store'} = $value;
        }
    }

    return $self->{'_relationship_store'};
}
_inverted_relationship_storedescriptionprevnextTop
sub _inverted_relationship_store {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        if ( defined $self->{'_inverted_relationship_store'} ) {
            $self->throw("_inverted_relationship_store already defined\n");
        } else {
            $self->{'_inverted_relationship_store'} = $value;
        }
    }

    return $self->{'_inverted_relationship_store'};
}
_relationship_type_storedescriptionprevnextTop
sub _relationship_type_store {
    my ( $self, $value ) = @_;

    if ( defined $value ) {
        if ( defined $self->{'_relationship_type_store'} ) {
            $self->throw("_relationship_type_store already defined\n");
        } else {
            $self->{'_relationship_type_store'} = $value;
        }
    }

    return $self->{'_relationship_type_store'};
}
_add_relationship_simpledescriptionprevnextTop
sub _add_relationship_simple {
    my ( $self, $store, $rel, $inverted ) = @_;

    my $subject = $rel->subject_term
        or $self->throw('cannot add relationship, relationship has no subject_term');
    my $object  = $rel->object_term
        or $self->throw('cannot add relationship, relationship has no object_term');

    my ( $parent_id, $child_id ) = ( $object->identifier, $subject->identifier );
    ( $parent_id, $child_id ) = ( $child_id, $parent_id ) if $inverted;

    if (     defined $store->{$parent_id}
         &&  defined $store->{$parent_id}->{$child_id}
         && $store->{$parent_id}->{$child_id}->name ne $rel->predicate_term->name
     ) {
        $self->throw( "relationship "
                . $rel->predicate_term->name
                . " between "
                . $parent_id . " and "
                . $child_id
                . " already defined as "
                . $store->{$parent_id}->{$child_id}->name
                . "\n" );
    }

    # all is well if we get here
$store->{$parent_id}->{$child_id} = $rel->predicate_term;
}
add_relationshipdescriptionprevnextTop
sub add_relationship {
    my ( $self, $rel ) = @_;

    $self->_add_relationship_simple( $self->_relationship_store,          $rel, 0 );
    $self->_add_relationship_simple( $self->_inverted_relationship_store, $rel, 1 );
    $self->_relationship_type_store->{ $self->_unique_termid( $rel->predicate_term ) } =
        $rel->predicate_term;

    return $rel;
}
get_relationshipsdescriptionprevnextTop
sub get_relationships {
    my $self = shift;
    my $term = shift;
    my @rels;
    my $store   = $self->_relationship_store;
    my $relfact = $self->relationship_factory();

    my @parent_ids = $term
        ?

        # if a term is supplied then only get the term's parents
( map { $_->identifier(); } $self->get_parent_terms($term) ) : # otherwise use all parent ids
( keys %{$store} ); # add the term as a parent too if one is supplied
push( @parent_ids, $term->identifier ) if $term; foreach my $parent_id (@parent_ids) { my $parent_entry = $store->{$parent_id}; # if a term is supplied, add a relationship for the parent to the term
# except if the parent is the term itself (we added that one before)
if ( $term && ( $parent_id ne $term->identifier() ) ) { my @parent_terms = $self->get_term_by_identifier($parent_id); foreach my $parent_term (@parent_terms) { push( @rels, $relfact->create_object( -object_term => $parent_term, -subject_term => $term, -predicate_term => $parent_entry->{ $term->identifier }, -ontology => $term->ontology() ) ); } } else { # otherwise, i.e., no term supplied, or the parent equals the
# supplied term
my @parent_terms = $term ? ($term) : $self->get_term_by_identifier($parent_id); foreach my $child_id ( keys %$parent_entry ) { my $rel_info = $parent_entry->{$child_id}; my ($subj_term) = $self->get_term_by_identifier($child_id); foreach my $parent_term (@parent_terms) { push( @rels, $relfact->create_object( -object_term => $parent_term, -subject_term => $subj_term, -predicate_term => $rel_info, -ontology => $parent_term->ontology ) ); } } } } return @rels;
}
get_all_relationshipsdescriptionprevnextTop
sub get_all_relationships {
    return shift->get_relationships();
}
get_predicate_termsdescriptionprevnextTop
sub get_predicate_terms {
    my ($self) = @_;

    return values %{ $self->_relationship_type_store };
}
_is_rel_typedescriptionprevnextTop
sub _is_rel_type {
    my ( $self, $term, @rel_types ) = @_;

    foreach my $rel_type (@rel_types) {
        if ( $rel_type->identifier || $term->identifier ) {
            return 1 if $rel_type->identifier eq $term->identifier;
        } else {
            return 1 if $rel_type->name eq $term->name;
        }
    }

    return 0;
}
_typed_traversaldescriptionprevnextTop
sub _typed_traversal {
    my ( $self, $rel_store, $level, $term_id, @rel_types ) = @_;
    return if !defined( $rel_store->{$term_id} );
    my %parent_entry = %{ $rel_store->{$term_id} };
    my @children     = keys %parent_entry;

    my @ans;

    if ( @rel_types > 0 ) {
        @ans = ();

        foreach my $child_id (@children) {
            push @ans, $child_id
                if $self->_is_rel_type( $rel_store->{$term_id}->{$child_id}, @rel_types );
        }
    } else {
        @ans = @children;
    }
    if ( $level < 1 ) {
        my @ans1 = ();

        foreach my $child_id (@ans) {
            push @ans1, $self->_typed_traversal( $rel_store, $level - 1, $child_id, @rel_types )
                if defined $rel_store->{$child_id};
        }
        push @ans, @ans1;
    }

    return @ans;
}
get_child_termsdescriptionprevnextTop
sub get_child_terms {
    my ( $self, $term, @relationship_types ) = @_;

    $self->throw("must provide TermI compliant object")
        unless defined($term) && $term->isa("Bio::Ontology::TermI");

    return $self->_filter_unmarked(
        $self->get_term_by_identifier(
            $self->_typed_traversal(
                $self->_relationship_store, 1, $term->identifier, @relationship_types
            )
        )
    );
}
get_descendant_termsdescriptionprevnextTop
sub get_descendant_terms {
    my ( $self, $term, @relationship_types ) = @_;

    $self->throw("must provide TermI compliant object")
        unless defined($term) && $term->isa("Bio::Ontology::TermI");

    return $self->_filter_unmarked(
        $self->_filter_repeated(
            $self->get_term_by_identifier(
                $self->_typed_traversal(
                    $self->_relationship_store, 0, $term->identifier, @relationship_types
                )
            )
        )
    );
}
get_parent_termsdescriptionprevnextTop
sub get_parent_terms {
    my ( $self, $term, @relationship_types ) = @_;
    $self->throw("term must be a valid object, not undef") unless defined $term;

    return $self->_filter_unmarked(
        $self->get_term_by_identifier(
            $self->_typed_traversal(
                $self->_inverted_relationship_store,
                1, $term->identifier, @relationship_types
            )
        )
    );
}
get_ancestor_termsdescriptionprevnextTop
sub get_ancestor_terms {
    my ( $self, $term, @relationship_types ) = @_;
    $self->throw("term must be a valid object, not undef") unless defined $term;

    return $self->_filter_unmarked(
        $self->_filter_repeated(
            $self->get_term_by_identifier(
                $self->_typed_traversal(
                    $self->_inverted_relationship_store, 0,
                    $term->identifier,                   @relationship_types
                )
            )
        )
    );
}
get_leaf_termsdescriptionprevnextTop
sub get_leaf_terms {
    my ($self) = @_;
    my @leaf_terms;

    foreach my $term ( values %{ $self->_term_store } ) {
        push @leaf_terms, $term
            if !defined $self->_relationship_store->{ $term->identifier }
                && defined $self->_instantiated_terms_store->{ $term->identifier };
    }

    return @leaf_terms;
}
get_root_termsdescriptionprevnextTop
sub get_root_terms {
    my ($self) = @_;
    my @root_terms;

    foreach my $term ( values %{ $self->_term_store } ) {
        push @root_terms, $term
            if !defined $self->_inverted_relationship_store->{ $term->identifier }
                && defined $self->_instantiated_terms_store->{ $term->identifier };
    }

    return @root_terms;
}
_filter_repeateddescriptionprevnextTop
sub _filter_repeated {
    my ( $self, @args ) = @_;
    my %h;

    foreach my $element (@args) {
        $h{ $element->identifier } = $element if !defined $h{ $element->identifier };
    }

    return values %h;
}
get_all_termsdescriptionprevnextTop
sub get_all_terms {
    my ($self) = @_;

    return $self->_filter_unmarked( values %{ $self->_term_store } );
}
find_termsdescriptionprevnextTop
sub find_terms {
    my ( $self, @args ) = @_;
    my @terms;

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

    if ( defined($id) ) {
        @terms = $self->get_term_by_identifier($id);
    } else {
        @terms = $self->get_all_terms();
    }
    if ( defined($name) ) {
        @terms = grep { $_->name() eq $name; } @terms;
    }
    return @terms;
}
relationship_factorydescriptionprevnextTop
sub relationship_factory {
    my $self = shift;

    return $self->{'relationship_factory'} = shift if @_;
    return $self->{'relationship_factory'};
}
term_factorydescriptionprevnextTop
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'};
}
_filter_unmarkeddescriptionprevnextTop
sub _filter_unmarked {
    my ( $self, @terms ) = @_;
    my @filtered_terms = ();

    if ( scalar(@terms) >= 1 ) {
        foreach my $term (@terms) {
            push @filtered_terms, $term
                if defined $self->_instantiated_terms_store->{ $term->identifier };
        }
    }

    return @filtered_terms;
}
remove_term_by_iddescriptionprevnextTop
sub remove_term_by_id {
    my ( $self, $id ) = @_;

    if ( $self->get_term_by_identifier($id) ) {
        my $term = $self->{_term_store}->{$id};
        delete $self->{_term_store}->{$id};
        return $term;
    } else {
        $self->warn("Term with id '$id' is not in the term store");
        return;
    }
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($self) = @_;
    my $s = "";

    $s .= "-- # Terms:\n";
    $s .= scalar( $self->get_all_terms ) . "\n";
    $s .= "-- # Relationships:\n";
    $s .= $self->_get_number_rels . "\n";

    return $s;
}
_unique_termiddescriptionprevnextTop
sub _unique_termid {
    my $self = shift;
    my $term = shift;

    return $term->identifier() if $term->identifier();
    my $id = $term->ontology->name() if $term->ontology();
    if ($id) {
        $id .= '|';
    } else {
        $id = '';
    }
    $id .= $term->name();
}

#################################################################
# aliases
#################################################################
*get_relationship_types =\& get_predicate_terms; 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Peter DimitrovTop
Email dimitrov@gnf.org
CONTRIBUTORSTop
Hilmar Lapp, hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _