Bio::Ontology
Relationship
Summary
Relationship - a relationship for an ontology
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$rel = Bio::Ontology::Relationship->new( -identifier => "16847",
-parent_term => $parent,
-child_term => $child,
-relationship_type => $type );
Description
This is a basic implementation of Bio::Ontology::RelationshipI.
Methods
Methods description
Title : new
Usage : $rel = Bio::Ontology::Relationship->new( -identifier => "16847",
-parent_term => $parent,
-child_term => $child,
-relationship_type => $type );
Function: Creates a new Bio::Ontology::Relationship.
Returns : A new Bio::Ontology::Relationship object.
Args : -identifier => the identifier of this relationship [scalar]
-parent_term => the parent term [Bio::Ontology::TermI]
-child_term => the child term [Bio::Ontology::TermI]
-relationship_type => the relationship type [Bio::Ontology::TermI] |
Title : init()
Usage : $rel->init();
Function: Initializes this Relationship to all undef.
Returns :
Args : |
Title : identifier
Usage : $rel->identifier( "100050" );
or
print $rel->identifier();
Function: Set/get for the identifier of this Relationship.
Returns : The identifier [scalar].
Args : The identifier [scalar] (optional). |
Title : parent_term
Usage : $rel->parent_term( $parent );
or
$parent = $rel->parent_term();
Function: Set/get for the parent term of this Relationship.
Returns : The parent term [Bio::Ontology::TermI].
Args : The parent term [Bio::Ontology::TermI] (optional). |
Title : child_term
Usage : $rel->child_term( $child );
or
$child = $rel->child_term();
Function: Set/get for the child term of this Relationship.
Returns : The child term [Bio::Ontology::TermI].
Args : The child term [Bio::Ontology::TermI] (optional). |
Title : relationship_type
Usage : $rel->relationship_type( $type );
or
$type = $rel->relationship_type();
Function: Set/get for the relationship type of this relationship.
Returns : The relationship type [Bio::Ontology::TermI].
Args : The relationship type [Bio::Ontology::TermI] (optional). |
Title : to_string()
Usage : print $rel->to_string();
Function: to_string method for Relationship.
Returns : A string representation of this Relationship.
Args : |
Methods code
sub new
{
my( $class, @args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $identifier,
$parent_term,
$child_term,
$relationship_type )
= $self->_rearrange( [ qw( IDENTIFIER
PARENT_TERM
CHILD_TERM
RELATIONSHIP_TYPE ) ], @args );
$self->init();
$identifier && $self->identifier( $identifier );
$parent_term && $self->parent_term( $parent_term );
$child_term && $self->child_term( $child_term );
$relationship_type && $self->relationship_type( $relationship_type );
return $self;
}
} | sub init
{ my( $self ) = @_;
$self->{ "_identifier" } = undef;
$self->{ "_parent_term" } = undef;
$self->{ "_child_term" } = undef;
$self->{ "_relationship_type" } = undef;
}
} | sub identifier
{ my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{ "_identifier" } = $value;
}
return $self->{ "_identifier" };
}
} | sub parent_term
{ my ( $self, $term ) = @_;
if ( defined $term ) {
$self->_check_class( $term, "Bio::Ontology::TermI" );
$self->{ "_parent_term" } = $term;
}
return $self->{ "_parent_term" };
}
} | sub child_term
{ my ( $self, $term ) = @_;
if ( defined $term ) {
$self->_check_class( $term, "Bio::Ontology::TermI" );
$self->{ "_child_term" } = $term;
}
return $self->{ "_child_term" };} | sub relationship_type
{ my ( $self, $term ) = @_;
if ( defined $term ) {
$self->_check_class( $term, "Bio::Ontology::TermI" );
$self->{ "_relationship_type" } = $term;
}
return $self->{ "_relationship_type" };} | sub to_string
{ my( $self ) = @_;
local $^W = 0;
my $s = "";
$s .= "-- Identifier:\n";
$s .= $self->identifier()."\n";
$s .= "-- Parent Term Identifier:\n";
$s .= $self->parent_term()->identifier()."\n";
$s .= "-- Child Term Identifier:\n";
$s .= $self->child_term()->identifier()."\n";
$s .= "-- Relationship Type Identifier:\n";
$s .= $self->relationship_type()->identifier();
return $s;
}
} | 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" );
}
}
} | General documentation
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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _