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
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[email protected]
Support
Please direct usage questions or support issues to the mailing list: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 [email protected]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.