Bio::Das::FeatureTypeI(3pm) User Contributed Perl Documentation Bio::Das::FeatureTypeI(3pm)
NAME
Bio::Das::FeatureTypeI - Simple interface to Sequence Ontology feature types
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.
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 one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bio.perl.org
Support
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 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 the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Lincoln Stein
Email lstein@cshl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
this is somehow FUBAR, implementation classes cannot successfully inherit from Bio::Das::FeatureTypeI
name
Title : name
Usage : $string = $term->name
Function: return the term for the type
Returns : a string
Args : none
Status : Public
accession
Title : accession
Usage : $string = $term->accession
Function: return the accession number for the term
Returns : a string
Args : none
Status : Public
definition
Title : definition
Usage : $string = $term->definition
Function: return the human-readable definition for the term
Returns : a string
Args : none
Status : Public
parents
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".
children
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".
relationship
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).
equals
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_descendent
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_parent
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().
match
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.
new
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_child
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_child
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.
perl v5.14.2 2012-03-02 Bio::Das::FeatureTypeI(3pm)