Summary

Bio::Phenotype::MeSH::Twig - Context for a MeSH term

Package variables

Inherit

Bio::Root::Root

Synopsis

  use Bio::Phenotype::MeSH::Twig
  # create a twig object
  my $twig = Bio::Phenotype::MeSH::Twig->new();

  # the term has only one parent in any twig
  $twig->parent('Fats');

  # a twig makeas sense only in the context of a term
  # which is a  Bio::Phenotype::MeSH::Term object

  # a term can have many twigs i.e. it can appear in many places in
  # the hierarchy
  #
  $ term->add_twig($twig);

  # adding the twig into a term adds a link into into it 
  $twig->term eq $term;

  # a twig can know about other terms under the parant node
  $twig->add_sister('Bread', 'Candy', 'Cereals');
  print join ( ', ', $twig->each_sister()), "\n";

  # a twig can know about other terms under this term
  $twig->add_child('Butter', 'Margarine');
  print join ( ', ', $twig->each_child()), "\n";

Description

This class represents the immediate surrounding of a MeSH term. It
keeps track on nodes names above the current node ('parent') other
nodes at the same level ('sisters') and nodes under it ('children').
Note that these are name strings, not objects.
Each twig can be associated with only one term, but term can have
multiple twigs. (Twigs can be though to be roles for a term.)

Methods

Methods description

 Title   : parent
 Usage   : $obj->parent( "r1" );
           or
           print $obj->parent();
 Function: Set/get for the parent.
 Returns : A parent [scalar].
 Args    : A parent [scalar] (optional).

 Title   : term
 Usage   : $obj->term( "r1" );
           or
           print $obj->term();
 Function: Set/get for the term.
 Returns : A term [scalar].
 Args    : A term [scalar] (optional).

 Title   : add_child
 Usage   : $obj->add_child( @children );
           or
           $obj->add_child( $child );
 Function: Pushes one or more child term names [scalars, most likely Strings]
           into the list of children.
 Returns : 
 Args    : scalar(s).

 Title   : each_child()
 Usage   : @gs = $obj->each_child();
 Function: Returns a list of gene symbols [scalars, most likely Strings]
           associated with this phenotype.
 Returns : A list of scalars.
 Args    :

 Usage   : $obj->purge_child();
 Function: Deletes  the list of children associated with this term.
 Returns : A list of scalars.
 Args    :

 Title   : add_sister
 Usage   : $obj->add_sister( @sisters );
           or
           $obj->add_sister( $sister );
 Function: Pushes one or more sister term names [scalars, most likely Strings]
           into the list of sisters.
 Returns : 
 Args    : scalar(s).

 Title   : each_sister()
 Usage   : @gs = $obj->each_sister();
 Function: Returns a list of gene symbols [scalars, most likely Strings]
           associated with this phenotype.
 Returns : A list of scalars.
 Args    :

 Usage   : $obj->purge_sister();
 Function: Deletes  the list of sisters associated with this term.
 Returns : A list of scalars.
 Args    :

Methods code

sub new {

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

    my ($term, $parent ) = $self->_rearrange
        ( [ qw(
               TERM
               PARENT
              ) ],
          @args );

    $self->{"_children"} = [];
    $self->{"_sisters"} = [];

    $term && $self->term($term );
    $parent  && $self->parent($parent );
    return $self;

}

sub parent {

    my ( $self, $value ) = @_;
    $self->{ "_parent" } = $value if defined $value;
    return $self->{ "_parent" };

}

sub term {

    my ( $self, $value ) = @_;
    if (defined $value) {
        $self->throw ("Not a MeSH term [$value]")
            unless $value->isa('Bio::Phenotype::MeSH::Term');
        $self->{ "_term" } = $value
    }
    return $self->{ "_term" };

}

sub add_child {

    my ( $self, @values ) = @_;
    push( @{ $self->{ "_children" } }, @values );
    return scalar @values;

}

sub each_child {

    my ( $self ) = shift;
    return @{ $self->{ "_children" } };

}

sub purge_children {

    my ( $self ) = @_;
    $self->{ "_children" } = [];

}

sub add_sister {

    my ( $self, @values ) = @_;
    push( @{ $self->{ "_sisters" } }, @values );
    return scalar @values;

}

sub each_sister {

    my ( $self ) = shift;
    return @{ $self->{ "_sisters" } };

}

sub purge_sisters {

    my ( $self ) = @_;
    $self->{'_sisters'} = [];

}

General documentation

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 lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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:

  http://bugzilla.open-bio.org/

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _