Provided by: libbio-perl-perl_1.7.6-3_all bug

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.