Bio::Das FeatureTypeI
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Summary
Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
  # Get a Bio::Das::FeatureTypeI object from somewhere
$term = $db->fetch....
# Get the name of the term $definition = $term->name; # Get the accession of the term $accession = $term->accession; # Get the definition of the term $definition = $term->definition; # Get the parents of the term, optionally filtered by relationship @parents = $term->parents($relationship); # Get the children of the term, optionally filtered by relationship @children = $term->children($relationship); # Given a parent and child, returns their relationship, or undef if # not directly related $relationship = $parent->relationship($child); # Return true if two terms are identical $match = $term1->equals($term2); # Return true if $term2 is a descendent of $term1, optionally # filtering by relationship ("isa" assumed) $match = $term1->is_descendent($term2,$relationship); # Return true if $term2 is a parent of $term1, optionally # filtering by relationship ("isa" assumed) $match = $term1->is_parent($term2,$relationship); # Return true if $term2 is equal to $term1 or if $term2 descends # from term 1 via the "isa" relationship $match = $term1->match($term2); # Create a new term de novo $term = Bio::Das::FeatureTypeI->new(-name => $name, -accession => $accession, -definition => $definition); # Add a child to a term $term1->add_child($term2,$relationship); # Delete a child from a term $term1->delete_child($term2);
Description
Bio::Das::FeatureTypeI is an interface to the Gene Ontology
Consortium's Sequence Ontology (SO). The SO, like other ontologies,
is a directed acyclic graph in which a child node may have multiple
parents. The relationship between parent and child is one of a list
of relationships. The SO currently recognizes two relationships "isa"
and "partof".
The intent of this interface is to interoperate with older software
that uses bare strings to represent feature types. For this reason,
the interface overloads the stringify ("") and string equals (eq)
operations.
Methods
nameDescriptionCode
accessionDescriptionCode
definitionDescriptionCode
parentsDescriptionCode
childrenDescriptionCode
relationshipDescriptionCode
equalsDescriptionCode
is_descendentDescriptionCode
is_parentDescriptionCode
matchDescriptionCode
newDescriptionCode
add_childDescriptionCode
delete_childDescriptionCode
Methods description
namecode    nextTop
 Title   : name
Usage : $string = $term->name
Function: return the term for the type
Returns : a string
Args : none
Status : Public
accessioncodeprevnextTop
 Title   : accession
Usage : $string = $term->accession
Function: return the accession number for the term
Returns : a string
Args : none
Status : Public
definitioncodeprevnextTop
 Title   : definition
Usage : $string = $term->definition
Function: return the human-readable definition for the term
Returns : a string
Args : none
Status : Public
parentscodeprevnextTop
 Title   : parents
Usage : @terms = $term->parents($relationship)
Function: return parent terms
Returns : list of Bio::Das::FeatureTypeI
Args : none
Status : Public
Returns the parents for the current term, empty if there are none. An
optional relationship argument will return those parents
that are related via the specified relationship type.
The relationship is one of "isa" or "partof".
childrencodeprevnextTop
 Title   : children
Usage : @terms = $term->children($relationship)
Function: return children terms
Returns : list of Bio::Das::FeatureTypeI
Args : none
Status : Public
Returns the children for the current term, empty if there are none. An
optional relationship argument will return those children
that are related via the specified relationship type.
The relationship is one of "isa" or "partof".
relationshipcodeprevnextTop
 Title   : relationship
Usage : $relationship = $parent->relationship($child)
Function: return the relationship between a parent and a child
Returns : one of "isa" or "partof"
Args : none
Status : Public
This method returns the relationship between a parent and one of its
immediate descendents. It can return "isa", "partof", or undef if
there is not a direct parent/child relationship (kissing cousins are
*not* recognized).
equalscodeprevnextTop
 Title   : equals
Usage : $boolean = $term1->equals($term2)
Function: return true if $term1 and $term2 are the same
Returns : boolean
Args : second term
Status : Public
The two terms must be identical. In practice, this means that if
term2 is a Bio::Das::FeatureI object, then its accession number must
match the first term's accession number. Otherwise, if term2 is a
bare string, then it must equal (in a case insensitive manner)
the name of term1.
NOTE TO IMPLEMENTORS: This method is defined in terms of other
methods, so does not need to be implemented.
is_descendentcodeprevnextTop
 Title   : is_descendent
Usage : $boolean = $term1->is_descendent($term2 [,$relationship])
Function: return true of $term2 is a descendent of $term1
Returns : boolean
Args : second term
Status : Public
This method returns true if $term2 descends from $term1. The
operation traverses the tree. The traversal can be limited to the
relationship type ("isa" or "partof") if desired. $term2 can be a
bare string, in which case the term names will be used as the basis
for term matching (see equals()).
NOTE TO IMPLEMENTORS: this method is defined as the inverse of
is_parent(). Do not implement it directly, but do implement
is_parent().
is_parentcodeprevnextTop
 Title   : is_parent
Usage : $boolean = $term1->is_parent($term2 [,$relationship])
Function: return true of $term2 is a parent of $term1
Returns : boolean
Args : second term
Status : Public
This method returns true if $term2 is a parent of $term1. The
operation traverses the tree. The traversal can be limited to the
relationship type ("isa" or "partof") if desired. $term2 can be a
bare string, in which case the term names will be used as the basis
for term matching (see equals()).
NOTE TO IMPLEMENTORS: Implementing this method will also implement
is_descendent().
matchcodeprevnextTop
 Title   : match
Usage : $boolean = $term1->match($term2)
Function: return true if $term1 equals $term2 or if $term2 is an "isa" descendent
Returns : boolean
Args : second term
Status : Public
This method combines equals() and is_descendent() in such a way that
the two terms will match if they are the same or if the second term is
an instance of the first one. This is also the basis of the operator
overloading of eq.
NOTE TO IMPLEMENTORS: This method is defined in terms of other methods
and does not need to be implemented.
newcodeprevnextTop
 Title   : new
Usage : $term = Bio::Das::FeatureTypeI->new(@args)
Function: create a new term
Returns : new term
Args : see below
Status : Public
This method creates a new Bio::Das::FeatureTypeI. Arguments:
  Argument    Description
-------- ------------
-name Name of this term -accession Accession number for the term -definition Definition of the term
add_childcodeprevnextTop
 Title   : add_child
Usage : $boolean = $term->add_child($term2,$relationship)
Function: add a child to a term
Returns : a boolean indicating success
Args : new child
Throws : a "cycle detected" exception
Status : Public
This method adds a new child to the indicated node. It may detect a
cycle in the DAG and throw a "cycle detected" exception.
delete_childcodeprevnextTop
 Title   : delete_child
Usage : $boolean = $term->delete_child($term2);
Function: delete a child of the term
Returns : a boolean indicating success
Args : child to be deleted
Throws : a "not a child" exception
Status : Public
This method deletes a new child from the indicated node. It will
throw an exception if the indicated child is not a direct descendent.
Methods code
namedescriptionprevnextTop
sub name {
 shift->throw_not_implemented
}
accessiondescriptionprevnextTop
sub accession {
 shift->throw_not_implemented
}
definitiondescriptionprevnextTop
sub definition {
 shift->throw_not_implemented
}
parentsdescriptionprevnextTop
sub parents {
 shift->throw_not_implemented;
}
childrendescriptionprevnextTop
sub children {
 shift->throw_not_implemented;
}
relationshipdescriptionprevnextTop
sub relationship {
 shift->throw_not_implemented
}
equalsdescriptionprevnextTop
sub equals {
  my $self = shift;
  my $term2 = shift;
  if ($term2->isa('Bio::Das::FeatureTypeI')) {
    return $self->accession eq $term2->accession;
  } else {
    return lc $self->name eq lc $term2;
  }
}
is_descendentdescriptionprevnextTop
sub is_descendent {
  my $self = shift;
  my ($term,$relationship) = @_;
  $self->throw("$term is not a Bio::Das::FeatureTypeI")
    unless $term->isa('Bio::Das::FeatureTypeI');
  $term->is_parent($self,$relationship);
}
is_parentdescriptionprevnextTop
sub is_parent {
 shift->throw_not_implemented
}
matchdescriptionprevnextTop
sub match {
  my $self  = shift;
  my $term2 = shift;
  return 1 if $self->equals($term2);
  return $self->is_descendent($term2,'isa');
}
newdescriptionprevnextTop
sub new {
 shift->throw_not_implemented
}
add_childdescriptionprevnextTop
sub add_child {
 shift->throw_not_implemented
}
delete_childdescriptionprevnextTop
sub delete_child {
 shift->throw_not_implemented
}
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@bio.perl.org
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/
AUTHOR - Lincoln SteinTop
Email lstein@cshl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _