Bio::Ontology GOterm
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Summary
Bio::Ontology::GOterm - representation of GO terms
Package variables
No package variables defined.
Inherit
Bio::Ontology::Term
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
newDescriptionCode
initDescriptionCode
GO_idDescriptionCode
get_secondary_GO_idsDescriptionCode
add_secondary_GO_idDescriptionCode
remove_secondary_GO_idsDescriptionCode
to_stringDescriptionCode
_check_go_id
No description
Code
_array_to_string
No description
Code
Methods description
newcode    nextTop
 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]
-ontology => the ontology for this term (a
Bio::Ontology::OntologyI compliant object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this GO term [0 or 1]
-comment => a comment [scalar]
initcodeprevnextTop
 Title   : init()
Usage : $term->init();
Function: Initializes this GOterm to all "" and empty lists.
Returns :
Args :
GO_idcodeprevnextTop
 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).
get_secondary_GO_idscodeprevnextTop
 Title   : get_secondary_GO_ids
Usage : @ids = $term->get_secondary_GO_ids();
Function: Returns a list of secondary goids of this Term.
This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args :
add_secondary_GO_idcodeprevnextTop
 Title   : add_secondary_GO_id
Usage : $term->add_secondary_GO_id( @ids );
or
$term->add_secondary_GO_id( $id );
Function: Pushes one or more secondary goids into
the list of secondary goids.
This is aliased to remove_secondary_ids(). 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).
remove_secondary_GO_idscodeprevnextTop
 Title   : remove_secondary_GO_ids()
Usage : $term->remove_secondary_GO_ids();
Function: Deletes (and returns) the secondary goids of this Term.
This is aliased to remove_secondary_ids(). Returns : A list of secondary goids [array of [GO:nnnnnnn]] (nnnnnnn is a zero-padded integer of seven digits). Args :
to_stringcodeprevnextTop
 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
newdescriptionprevnextTop
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;
    
} # new
}
initdescriptionprevnextTop
sub init {
    my $self = shift;

    # first call the inherited version to properly chain up the hierarchy
$self->SUPER::init(@_); # then only initialize what we implement ourselves here
#$self->GO_id( GOID_DEFAULT );
} # init
}
GO_iddescriptionprevnextTop
sub GO_id {
    my $self = shift;
    my $value;

    if ( @_ ) {
        $value = $self->_check_go_id( shift );
	unshift(@_, $value);
    }

    return $self->identifier( @_ );

} # GO_id
}
get_secondary_GO_idsdescriptionprevnextTop
sub get_secondary_GO_ids {
    return shift->get_secondary_ids(@_);
} # get_secondary_GO_ids
}
add_secondary_GO_iddescriptionprevnextTop
sub add_secondary_GO_id {
    return shift->add_secondary_id(@_);
} # add_secondary_GO_id
}
remove_secondary_GO_idsdescriptionprevnextTop
sub remove_secondary_GO_ids {
    return shift->remove_secondary_ids(@_);
} # remove_secondary_GO_ids
}
to_stringdescriptionprevnextTop
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->ontology() ) ) {
        $s .= $self->ontology()->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->get_dbxrefs() )."\n";
    $s .= "-- Secondary GO ids:\n";
    $s .= $self->_array_to_string( $self->get_secondary_GO_ids() )."\n";
    $s .= "-- Aliases:\n";
    $s .= $self->_array_to_string( $self->get_synonyms() );
    
    return $s;
    
} # to_string
# Title : _check_go_id
# Function: Checks whether the argument is [GO:nnnnnnn].
# If "GO:" is not present, it adds it.
# Returns : The canonical GO id.
# Args : The value to be checked.
}
_check_go_iddescriptionprevnextTop
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;
} # _check_go_id
# Title : _array_to_string
# Function:
# Returns :
# Args :
}
_array_to_stringdescriptionprevnextTop
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;
    
} # _array_to_string
#################################################################
# aliases or forwards to maintain backward compatibility
#################################################################
*each_secondary_GO_id =\& get_secondary_GO_ids; *add_secondary_GO_ids =\& add_secondary_GO_id; 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 one
of 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
Support Top
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
the bugs and their resolution. Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
  Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121
APPENDIXTop
The rest of the documentation details each of the object
methods.