comparison variant_effect_predictor/Bio/Ontology/Term.pm @ 0:1f6dce3d34e0

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# $Id: Term.pm,v 1.8.2.3 2003/05/27 22:00:52 lapp Exp $
#
# BioPerl module for Bio::Ontology::Term
#
# Cared for by Christian M. Zmasek <[e-mail]> or <[e-mail]>
#
# (c) Christian M. Zmasek, [e-mail], 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


=head1 NAME

Term - interface for ontology terms

=head1 SYNOPSIS

#get Bio::Ontology::TermI somehow.

  print $term->identifier(), "\n";
  print $term->name(), "\n";
  print $term->definition(), "\n";
  print $term->is_obsolete(), "\n";
  print $term->comment(), "\n";

  foreach my $synonym ( $term->each_synonym() ) {
      print $synonym, "\n";
  }

=head1 DESCRIPTION

This is "dumb" interface for ontology terms providing basic methods
(it provides no functionality related to graphs). It implements the
L<Bio::Ontology::TermI> interface.

This class also implements L<Bio::IdentifiableI> and
L<Bio::DescribableI>.

=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 one
of the Bioperl mailing lists.  Your participation is much appreciated.

  [e-mail]             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists

=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 email
or the web:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR

Christian M. Zmasek

Email: [e-mail]  or  [e-mail]

WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/

Address:

  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121

=head1 APPENDIX

The rest of the documentation details each of the object
methods.

=cut


# Let the code begin...

package Bio::Ontology::Term;
use vars qw( @ISA );
use strict;
use Bio::Root::Object;
use Bio::Ontology::TermI;
use Bio::Ontology::Ontology;
use Bio::Ontology::OntologyStore;
use Bio::IdentifiableI;
use Bio::DescribableI;

use constant TRUE    => 1;
use constant FALSE   => 0;

@ISA = qw( Bio::Root::Root
           Bio::Ontology::TermI
           Bio::IdentifiableI
           Bio::DescribableI
         );



=head2 new

 Title   : new
 Usage   : $term = Bio::Ontology::Term->new( -identifier  => "16847",
                                             -name        => "1-aminocyclopropane-1-carboxylate synthase",
                                             -definition  => "Catalysis of ...",
                                             -is_obsolete => 0,
                                             -comment     => "" );
 Function: Creates a new Bio::Ontology::Term.
 Returns : A new Bio::Ontology::Term object.
 Args    : -identifier            => the identifier of this term [scalar]
           -name                  => the name of this term [scalar]
           -definition            => the definition of this term [scalar]
           -ontology              => the ontology this term lives in
                                     (a L<Bio::Ontology::OntologyI> object)
           -version               => version information [scalar]
           -is_obsolete           => the obsoleteness of this term [0 or 1]
           -comment               => a comment [scalar]

=cut

sub new {

    my( $class,@args ) = @_;

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

    my ( $identifier,
         $name,
         $definition,
         $category,
	 $ont,
         $version,
         $is_obsolete,
         $comment,
	 $dblinks)
	= $self->_rearrange( [ qw( IDENTIFIER
				   NAME
				   DEFINITION
				   CATEGORY
                                   ONTOLOGY
				   VERSION
				   IS_OBSOLETE
				   COMMENT
                                   DBLINKS
                                 ) ], @args );

    $self->init();

    $identifier            && $self->identifier( $identifier );
    $name                  && $self->name( $name );
    $definition            && $self->definition( $definition );
    $category              && $self->category( $category );
    $ont                   && $self->ontology( $ont );
    defined($version)      && $self->version( $version );
    defined($is_obsolete)  && $self->is_obsolete( $is_obsolete );
    $comment               && $self->comment( $comment  );
    ref($dblinks)          && $self->add_dblink(@$dblinks);

    return $self;

} # new



sub init {

    my $self = shift;

    $self->identifier(undef);
    $self->name(undef);
    $self->comment(undef);
    $self->definition(undef);
    $self->ontology(undef);
    $self->is_obsolete(0);
    $self->remove_synonyms();
    $self->remove_dblinks();
    $self->remove_secondary_ids();

} # init



=head2 identifier

 Title   : identifier
 Usage   : $term->identifier( "0003947" );
           or
           print $term->identifier();
 Function: Set/get for the identifier of this Term.
 Returns : The identifier [scalar].
 Args    : The identifier [scalar] (optional).

=cut

sub identifier {
    my $self = shift;

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




=head2 name

 Title   : name
 Usage   : $term->name( "N-acetylgalactosaminyltransferase" );
           or
           print $term->name();
 Function: Set/get for the name of this Term.
 Returns : The name [scalar].
 Args    : The name [scalar] (optional).

=cut

sub name {
    my $self = shift;

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





=head2 definition

 Title   : definition
 Usage   : $term->definition( "Catalysis of ..." );
           or
           print $term->definition();
 Function: Set/get for the definition of this Term.
 Returns : The definition [scalar].
 Args    : The definition [scalar] (optional).

=cut

sub definition {
    my $self = shift;

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


=head2 ontology

 Title   : ontology
 Usage   : $ont = $term->ontology();
           or
           $term->ontology( $ont );
 Function: Get the ontology this term is in.

           Note that with the ontology in hand you can query for all
           related terms etc. See L<Bio::Ontology::OntologyI>.

 Returns : The ontology of this Term as a L<Bio::Ontology::OntologyI>
           implementing object.
 Args    : On set, the  ontology of this Term as a L<Bio::Ontology::OntologyI>
           implementing object or a string representing its name.

=cut

sub ontology {
    my $self = shift;
    my $ont;

    if(@_) {
	$ont = shift;
	if($ont) {
	    $ont = Bio::Ontology::Ontology->new(-name => $ont) if ! ref($ont);
	    if(! $ont->isa("Bio::Ontology::OntologyI")) {
		$self->throw(ref($ont)." does not implement ".
			     "Bio::Ontology::OntologyI. Bummer.");
	    }
	}
	return $self->{"_ontology"} = $ont;
    }
    return $self->{"_ontology"};
} # ontology


=head2 version

 Title   : version
 Usage   : $term->version( "1.00" );
           or
           print $term->version();
 Function: Set/get for version information.
 Returns : The version [scalar].
 Args    : The version [scalar] (optional).

=cut

sub version {
    my $self = shift;

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



=head2 is_obsolete

 Title   : is_obsolete
 Usage   : $term->is_obsolete( 1 );
           or
           if ( $term->is_obsolete() )
 Function: Set/get for the obsoleteness of this Term.
 Returns : the obsoleteness [0 or 1].
 Args    : the obsoleteness [0 or 1] (optional).

=cut

sub is_obsolete{
    my $self = shift;

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





=head2 comment

 Title   : comment
 Usage   : $term->comment( "Consider the term ..." );
           or
           print $term->comment();
 Function: Set/get for an arbitrary comment about this Term.
 Returns : A comment.
 Args    : A comment (optional).

=cut

sub comment{
    my $self = shift;

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




=head2 get_synonyms

 Title   : get_synonyms
 Usage   : @aliases = $term->get_synonyms;
 Function: Returns a list of aliases of this Term.
 Returns : A list of aliases [array of [scalar]].
 Args    :

=cut

sub get_synonyms {
    my $self = shift;

    return @{ $self->{ "_synonyms" } } if exists($self->{ "_synonyms" });
    return ();
} # get_synonyms


=head2 add_synonym

 Title   : add_synonym
 Usage   : $term->add_synonym( @asynonyms );
           or
           $term->add_synonym( $synonym );
 Function: Pushes one or more synonyms into the list of synonyms.
 Returns :
 Args    : One synonym [scalar] or a list of synonyms [array of [scalar]].

=cut

sub add_synonym {
    my ( $self, @values ) = @_;

    return unless( @values );

    # avoid duplicates
    foreach my $syn (@values) {
	next if grep { $_ eq $syn; } @{$self->{ "_synonyms" }};
	push( @{ $self->{ "_synonyms" } }, $syn );
    }

} # add_synonym


=head2 remove_synonyms

 Title   : remove_synonyms()
 Usage   : $term->remove_synonyms();
 Function: Deletes (and returns) the synonyms of this Term.
 Returns : A list of synonyms [array of [scalar]].
 Args    :

=cut

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

    my @a = $self->get_synonyms();
    $self->{ "_synonyms" } = [];
    return @a;

} # remove_synonyms

=head2 get_dblinks

 Title   : get_dblinks()
 Usage   : @ds = $term->get_dblinks();
 Function: Returns a list of each dblinks of this GO term.
 Returns : A list of dblinks [array of [scalars]].
 Args    :

=cut

sub get_dblinks {
    my $self = shift;

    return @{$self->{ "_dblinks" }} if exists($self->{ "_dblinks" });
    return ();
} # get_dblinks


=head2 add_dblink

 Title   : add_dblink
 Usage   : $term->add_dblink( @dbls );
           or
           $term->add_dblink( $dbl );
 Function: Pushes one or more dblinks onto the list of dblinks.
 Returns :
 Args    : One  dblink [scalar] or a list of
            dblinks [array of [scalars]].

=cut

sub add_dblink {
    my ( $self, @values ) = @_;

    return unless( @values );

    # avoid duplicates
    foreach my $dbl (@values) {
	next if grep { $_ eq $dbl; } @{$self->{ "_dblinks" }};
	push( @{ $self->{ "_dblinks" } }, $dbl );
    }

} # add_dblink


=head2 remove_dblinks

 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    :

=cut

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

    my @a = $self->get_dblinks();
    $self->{ "_dblinks" } = [];
    return @a;

} # remove_dblinks

=head2 get_secondary_ids

 Title   : get_secondary_ids
 Usage   : @ids = $term->get_secondary_ids();
 Function: Returns a list of secondary identifiers of this Term.

           Secondary identifiers mostly originate from merging terms,
           or possibly also from splitting terms.

 Returns : A list of secondary identifiers [array of [scalar]]
 Args    :

=cut

sub get_secondary_ids {
    my $self = shift;

    return @{$self->{"_secondary_ids"}} if exists($self->{"_secondary_ids"});
    return ();
} # get_secondary_ids


=head2 add_secondary_id

 Title   : add_secondary_id
 Usage   : $term->add_secondary_id( @ids );
           or
           $term->add_secondary_id( $id );
 Function: Adds one or more secondary identifiers to this term.
 Returns :
 Args    : One or more secondary identifiers [scalars]

=cut

sub add_secondary_id {
    my $self = shift;

    return unless @_;

    # avoid duplicates
    foreach my $id (@_) {
	next if grep { $_ eq $id; } @{$self->{ "_secondary_ids" }};
	push( @{ $self->{ "_secondary_ids" } }, $id );
    }

} # add_secondary_id


=head2 remove_secondary_ids

 Title   : remove_secondary_ids
 Usage   : $term->remove_secondary_ids();
 Function: Deletes (and returns) the secondary identifiers of this Term.
 Returns : The previous list of secondary identifiers [array of [scalars]]
 Args    :

=cut

sub remove_secondary_ids {
    my $self = shift;

    my @a = $self->get_secondary_ids();
    $self->{ "_secondary_ids" } = [];
    return @a;

} # remove_secondary_ids


# Title   :_is_true_or_false
# Function: Checks whether the argument is TRUE or FALSE.
# Returns :
# Args    : The value to be checked.
sub _is_true_or_false {
    my ( $self, $value ) = @_;
    unless ( $value !~ /\D/ && ( $value == TRUE || $value == FALSE ) ) {
        $self->throw( "Found [" . $value
        . "] where " . TRUE . " or " . FALSE . " expected" );
    }
} # _is_true_or_false

=head1 Methods implementing L<Bio::IdentifiableI> and L<Bio::DescribableI>

=cut

=head2 object_id

 Title   : object_id
 Usage   : $string    = $obj->object_id()
 Function: a string which represents the stable primary identifier
           in this namespace of this object.

           This is a synonym for identifier().

 Returns : A scalar

=cut

sub object_id {
    return shift->identifier(@_);
}

=head2 authority

 Title   : authority
 Usage   : $authority    = $obj->authority()
 Function: a string which represents the organisation which
           granted the namespace, written as the DNS name for
           organisation (eg, wormbase.org)

           This forwards to ontology()->authority(). Note that you
           cannot set the authority before having set the ontology or
           the namespace (which will set the ontology).

 Returns : A scalar
 Args    : on set, the new value (a scalar)

=cut

sub authority {
    my $self = shift;
    my $ont = $self->ontology();

    return $ont->authority(@_) if $ont;
    $self->throw("cannot manipulate authority prior to ".
		 "setting the namespace or ontology") if @_;
    return undef;
}


=head2 namespace

 Title   : namespace
 Usage   : $string    = $obj->namespace()
 Function: A string representing the name space this identifier
           is valid in, often the database name or the name
           describing the collection.

           This forwards to ontology() (set mode) and
           ontology()->name() (get mode). I.e., setting the namespace
           will set the ontology to one matching that name in the
           ontology store, or to one newly created.

 Returns : A scalar
 Args    : on set, the new value (a scalar)

=cut

sub namespace {
    my $self = shift;

    $self->ontology(@_) if(@_);
    my $ont = $self->ontology();
    return defined($ont) ? $ont->name() : undef;
}

=head2 display_name

 Title   : display_name
 Usage   : $string    = $obj->display_name()
 Function: A string which is what should be displayed to the user.

           The definition in L<Bio::DescribableI> states that the
           string should not contain spaces. As this isn't very
           sensible for ontology terms, we relax this here. The
           implementation just forwards to name().

 Returns : A scalar
 Args    : on set, the new value (a scalar)

=cut

sub display_name {
    return shift->name(@_);
}


=head2 description

 Title   : description
 Usage   : $string    = $obj->description()
 Function: A text string suitable for displaying to the user a
           description. This string is likely to have spaces, but
           should not have any newlines or formatting - just plain
           text.

           This forwards to definition(). The caveat is that the text
           will often be longer for ontology term definitions than the
           255 characters stated in the definition in
           L<Bio::DescribableI>.

 Returns : A scalar
 Args    : on set, the new value (a scalar)

=cut

sub description {
    return shift->definition(@_);
}

#################################################################
# aliases or forwards to maintain backward compatibility
#################################################################

=head1  Deprecated methods

Used for looking up the methods that supercedes them.

=cut

=head2 category

 Title   : category
 Usage   :
 Function: This method is deprecated. Use ontology() instead.
 Example :
 Returns :
 Args    :


=cut

sub category {
    my $self = shift;

    $self->warn("TermI::category is deprecated and being phased out. ".
		"Use TermI::ontology instead.");

    # called in set mode?
    if(@_) {
	# yes; what is incompatible with ontology() is if we were given
	# a TermI object
	my $arg = shift;
	$arg = $arg->name() if ref($arg) && $arg->isa("Bio::Ontology::TermI");
	return $self->ontology($arg,@_);
    } else {
	# No, called in get mode. This is always incompatible with ontology()
	# since category is supposed to return a TermI.
	my $ont = $self->ontology();
	my $term;
	if(defined($ont)) {
	    $term = Bio::Ontology::Term->new(-name => $ont->name(),
					     -identifier =>$ont->identifier());
	}
	return $term;
    }
} # category

*each_synonym = \&get_synonyms;
*add_synonyms = \&add_synonym;
*each_dblink = \&get_dblinks;
*add_dblinks = \&add_dblink;

1;