Bio::Ontology
GOterm
Summary
GOterm - representation of GO terms
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$term = Bio::Ontology::GOterm->new
( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
$term->add_definition_references( @refs );
$term->add_secondary_GO_ids( @ids );
$term->add_aliases( @aliases );
foreach my $dr ( $term->each_definition_reference() ) {
print $dr, "\n";
}
# etc.
Description
This is "dumb" class for GO terms (it provides no functionality related to graphs).
Implements Bio::Ontology::TermI.
Methods
Methods description
Title : new
Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::GOterm.
Returns : A new Bio::Ontology::GOterm object.
Args : -go_id => the goid of this GO term [GO:nnnnnnn]
or [nnnnnnn] (nnnnnnn is a zero-padded
integer of seven digits)
-name => the name of this GO term [scalar]
-definition => the definition of this GO term [scalar]
-category => a relationship between this Term and another Term [TermI or scalar]
-version => version information [scalar]
-is_obsolete => the obsoleteness of this GO term [0 or 1]
-comment => a comment [scalar] |
Title : init()
Usage : $term->init();
Function: Initializes this GOterm to all "" and empty lists.
Returns :
Args : |
Title : GO_id
Usage : $term->GO_id( "GO:0003947" );
or
print $term->GO_id();
Function: Set/get for the goid of this GO term.
This is essentially an alias to identifier(), with added
format checking.
Returns : The goid [GO:nnnnnnn].
Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
zero-padded integer of seven digits) (optional). |
Title : each_dblink()
Usage : @ds = $term->each_dblink();
Function: Returns a list of each dblinks of this GO term.
Returns : A list of dblinks [array of [scalars]].
Args : |
Title : add_dblinks
Usage : $term->add_dblinks( @dbls );
or
$term->add_dblinks( $dbl );
Function: Pushes one or more dblinks
into the list of dblinks.
Returns :
Args : One dblink [scalar] or a list of
dblinks [array of [scalars]]. |
Title : remove_dblinks()
Usage : $term->remove_dblinks();
Function: Deletes (and returns) the definition references of this GO term.
Returns : A list of definition references [array of [scalars]].
Args : |
Title : each_secondary_GO_id()
Usage : @ids = $term->each_secondary_GO_id();
Function: Returns a list of secondary goids of this Term.
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args : |
Title : add_secondary_GO_ids
Usage : $term->add_secondary_GO_ids( @ids );
or
$term->add_secondary_GO_ids( $id );
Function: Pushes one or more secondary goids into
the list of secondary goids.
Returns :
Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits). |
Title : remove_secondary_GO_ids()
Usage : $term->remove_secondary_GO_ids();
Function: Deletes (and returns) the secondary goids of this Term.
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args : |
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for GO terms.
Returns : A string representation of this GOterm.
Args : |
Methods code
sub new
{
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $GO_id )
= $self->_rearrange( [ qw( GO_ID ) ], @args );
$GO_id && $self->GO_id( $GO_id );
return $self;
}
} | sub init
{
my $self = shift;
$self->SUPER::init(@_);
$self->GO_id( GOID_DEFAULT );
$self->remove_dblinks();
$self->remove_secondary_GO_ids();
$self->remove_synonyms();
}
} | sub GO_id
{ my $self = shift;
my $value;
if ( @_ ) {
$value = $self->_check_go_id( shift );
unshift(@_, $value);
}
return $self->identifier( @_ );
}
} | sub each_dblink
{ my ( $self ) = @_;
if ( $self->{ "_dblinks" } ) {
return @{ $self->{ "_dblinks" } };
}
else {
return my @a = ();
}
}
} | sub add_dblinks
{ my ( $self, @values ) = @_;
return unless( @values );
push( @{ $self->{ "_dblinks" } }, @values );
}
} | sub remove_dblinks
{ my ( $self ) = @_;
my @a = $self->each_dblink();
$self->{ "_dblinks" } = [];
return @a;
}
} | sub each_secondary_GO_id
{ my ( $self ) = @_;
if ( $self->{ "_secondary_GO_ids" } ) {
return @{ $self->{ "_secondary_GO_ids" } };
}
else {
return my @a = ();
}
}
} | sub add_secondary_GO_ids
{ my ( $self, @values ) = @_;
return unless( @values );
foreach my $value ( @values ) {
$value = $self->_check_go_id( $value );
}
push( @{ $self->{ "_secondary_GO_ids" } }, @values );
}
} | sub remove_secondary_GO_ids
{ my ( $self ) = @_;
my @a = $self->each_secondary_GO_id();
$self->{ "_secondary_GO_ids" } = [];
return @a;
}
} | sub to_string
{ my( $self ) = @_;
my $s = "";
$s .= "-- GO id:\n";
$s .= $self->GO_id()."\n";
$s .= "-- Name:\n";
$s .= ($self->name() || '') ."\n";
$s .= "-- Definition:\n";
$s .= ($self->definition() || '') ."\n";
$s .= "-- Category:\n";
if ( defined( $self->category() ) ) {
$s .= $self->category()->name()."\n";
}
else {
$s .= "\n";
}
$s .= "-- Version:\n";
$s .= ($self->version() || '') ."\n";
$s .= "-- Is obsolete:\n";
$s .= $self->is_obsolete()."\n";
$s .= "-- Comment:\n";
$s .= ($self->comment() || '') ."\n";
$s .= "-- Definition references:\n";
$s .= $self->_array_to_string( $self->each_dblink() )."\n";
$s .= "-- Secondary GO ids:\n";
$s .= $self->_array_to_string( $self->each_secondary_GO_id() )."\n";
$s .= "-- Aliases:\n";
$s .= $self->_array_to_string( $self->each_synonym() );
return $s;
}
} | sub _check_go_id
{ my ( $self, $value ) = @_;
unless ( $value =~ /^(GO:)?\d{7}$/ || $value eq GOID_DEFAULT ) {
$self->throw( "Found [" . $value
. "] where [GO:nnnnnnn] or [nnnnnnn] expected" );
}
unless ( $value =~ /^GO:/ ) {
$value = "GO:".$value;
}
return $value;
}
} | | _array_to_string | description | prev | next | Top |
sub _array_to_string
{ my( $self, @value ) = @_;
my $s = "";
for ( my $i = 0; $i < scalar( @value ); ++$i ) {
if ( ! ref( $value[ $i ] ) ) {
$s .= "#" . $i . "\n-- " . $value[ $i ] . "\n";
}
}
return $s;
}
} | General documentation
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The rest of the documentation details each of the object
methods.