Bio::Ontology OntologyEngineI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
OntologyEngineI - DESCRIPTION of Interface
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Carp
Inherit
Bio::Root::Root
Synopsis
Give standard usage here
Description
Describe the interface here
Methods
add_termDescriptionCode
add_relationshipDescriptionCode
get_relationshipsDescriptionCode
get_relationship_typesDescriptionCode
get_child_termsDescriptionCode
get_descendant_termsDescriptionCode
get_parent_termsDescriptionCode
get_ancestor_termsDescriptionCode
get_leaf_termsDescriptionCode
get_root_terms()
No description
Code
Methods description
add_termcode    nextTop
 Title   : add_term
 Usage   : add_term(TermI term): TermI
 Function:
 Example :
 Returns : 
 Args    :
add_relationshipcodeprevnextTop
 Title   : add_relationship
 Usage   : add_relationship(RelationshipI relationship)
  add_relatioship(TermI parent, TermI child, TermI relationship_type)
 Function:
 Example :
 Returns : 
 Args    :
get_relationshipscodeprevnextTop
 Title   : get_relationships
 Usage   : get_relationships([TermI term]): RelationshipI[]
 Function:
 Example :
 Returns : 
 Args    :
get_relationship_typescodeprevnextTop
 Title   : get_relationship_types
 Usage   : get_relationship_types(): TermI[]
 Function:
 Example :
 Returns :
 Args    :
get_child_termscodeprevnextTop
 Title   : get_child_terms
 Usage   : get_child_terms(TermI term, TermI[] rel_types): TermI[]
 Function:
 Example :

 Returns :
 Args    :
get_descendant_termscodeprevnextTop
 Title   : get_descendant_terms
 Usage   : get_descendant_terms(TermI term, TermI[] rel_types): TermI[]
 Function:
 Example :
 Returns : 
 Args    :
get_parent_termscodeprevnextTop
 Title   : get_parent_terms
 Usage   : get_parent_terms(TermI term, TermI[] rel_types): TermI[]
 Function:
 Example :
 Returns : 
 Args    :
get_ancestor_termscodeprevnextTop
 Title   : get_ancestor_terms
 Usage   : get_ancestor_terms(TermI term, TermI[] rel_types): TermI[]
 Function:
 Example :
 Returns : 
 Args    :
get_leaf_termscodeprevnextTop
 Title   : get_leaf_terms
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :
Methods code
add_termdescriptionprevnextTop
sub add_term {
  my ($self) = @_;

  $self->throw("Abstract method add_term implementing class did not provide method");
}
add_relationshipdescriptionprevnextTop
sub add_relationship {
  my ($self, $relationship) = @_;

  $self->throw("Abstract method add_relationship implementing class did not provide method");
}
get_relationshipsdescriptionprevnextTop
sub get_relationships {
  my ($self) = @_;

  $self->throw("Abstract method get_relationships implementing class did not provide method");
}
get_relationship_typesdescriptionprevnextTop
sub get_relationship_types {
  my ($self) = @_;

  $self->throw("Abstract method get_relationship_types implementing class did not provide method");
}
get_child_termsdescriptionprevnextTop
sub get_child_terms {
  my ($self) = @_;

  $self->throw("Abstract method get_child_terms implementing class did not provide method");
}
get_descendant_termsdescriptionprevnextTop
sub get_descendant_terms {
  my ($self) = @_;

  $self->throw("Abstract method get_descendant_terms implementing class did not provide method");
}
get_parent_termsdescriptionprevnextTop
sub get_parent_terms {
  my ($self) = @_;

  $self->throw("Abstract method get_parent_terms implementing class did not provide method");
}
get_ancestor_termsdescriptionprevnextTop
sub get_ancestor_terms {
  my ($self) = @_;

  $self->throw("Abstract method get_ancestor_terms implementing class did not provide method");
}
get_leaf_termsdescriptionprevnextTop
sub get_leaf_terms {
  my ($self) = @_;

  $self->throw("Abstract method get_leaf_terms implementing class did not provide method");
}
get_root_terms()descriptionprevnextTop
sub get_root_terms() {
  my ($self) = @_;

  $self->throw("Abstract method get_root_terms() implementing class did not provide method");
}
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/
AUTHOR - Peter DimitrovTop
Email dimitrov@gnf.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
get_root_terms()Top
 Title   : get_root_terms()
 Usage   : get_root_terms()
 Function:
 Example :
 Returns : 
 Args    :