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://github.com/bioperl/bioperl-live/issues
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.