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)