/ 
bioperl-1.4
/ Bio::Phenotype::MeSH::Twig

NAME

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

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.)

SEE ALSO

Bio::Phenotype::MeSH::Term

FEEDBACK

Mailing Lists

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://bio.perl.org/MailList.html             - About the mailing lists

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:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR

Heikki Lehvaslaiho, heikki@ebi.ac.uk

APPENDIX

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

parent

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).

term

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).

add_child

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).

each_child

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    :

purge_children

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

add_sister

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).

each_sister

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    :

purge_sisters

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