Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Ontology::InterProTerm - Implementation of InterProI term interface

SYNOPSIS

         my $term = Bio::Ontology::InterProTerm->new(
               -interpro_id => "IPR000001",
                         -name => "Kringle",
                         -definition => "Kringles are autonomous structural domains ...",
                         -ontology => "Domain"
                                                    );
         print $term->interpro_id(), "\n";
         print $term->name(), "\n";
         print $term->definition(), "\n";
         print $term->is_obsolete(), "\n";
         print $term->ontology->name(), "\n";

DESCRIPTION

       This is a simple extension of Bio::Ontology::Term for InterPro terms.

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 the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Dimitrov

       Email dimitrov@gnf.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000002",
                                                            -name => "Cdc20/Fizzy",
                                                            -definition => "The Cdc20/Fizzy region is almost always ...",
                                                            -ontology => "Domain"
                                                          );

        Function: Creates a new Bio::Ontology::InterProTerm.
        Example :
        Returns : A new Bio::Ontology::InterProTerm object.
        Args    :
         -interpro_id => the InterPro ID of the term. Has the form IPRdddddd, where dddddd is a zero-padded six digit number
         -name => the name of this InterPro term [scalar]
         -definition => the definition/abstract of this InterPro term [scalar]
         -ontology => ontology of InterPro terms [Bio::Ontology::OntologyI]
         -comment => a comment [scalar]

   init
        Title   : init
        Usage   : $term->init();
        Function: Initializes this InterProTerm to all "" and empty lists.
        Example :
        Returns :
        Args    :

   _check_interpro_id
        Title   : _check_interpro_id
        Usage   :
        Function: Performs simple check in order to validate that its argument has the form IPRdddddd, where dddddd is a zero-padded six digit number.
        Example :
        Returns : Returns its argument if valid, otherwise throws exception.
        Args    : String

   interpro_id
        Title   : interpro_id
        Usage   : $obj->interpro_id($newval)
        Function: Set/get for the interpro_id of this InterProTerm
        Example :
        Returns : value of interpro_id (a scalar)
        Args    : new value (a scalar, optional)

   short_name
        Title   : short_name
        Usage   : $obj->short_name($newval)
        Function: Set/get for the short name of this InterProTerm.
        Example :
        Returns : value of short_name (a scalar)
        Args    : new value (a scalar, optional)

   protein_count
        Title   : protein_count
        Usage   : $obj->protein_count($newval)
        Function: Set/get for the protein count of this InterProTerm.
        Example :
        Returns : value of protein_count (a scalar)
        Args    : new value (a scalar, optional)

   get_references
        Title   : get_references
        Usage   :
        Function: Get the references for this InterPro term.
        Example :
        Returns : An array of L<Bio::Annotation::Reference> objects
        Args    :

   add_reference
        Title   : add_reference
        Usage   :
        Function: Add one or more references to this InterPro term.
        Example :
        Returns :
        Args    : One or more L<Bio::Annotation::Reference> objects.

   remove_references
        Title   : remove_references
        Usage   :
        Function: Remove all references for this InterPro term.
        Example :
        Returns : The list of previous references as an array of
                  L<Bio::Annotation::Reference> objects.
        Args    :

   get_members
        Title   : get_members
        Usage   : @arr = get_members()
        Function: Get the list of member(s) for this object.
        Example :
        Returns : An array of Bio::Annotation::DBLink objects
        Args    :

   add_member
        Title   : add_member
        Usage   :
        Function: Add one or more member(s) to this object.
        Example :
        Returns :
        Args    : One or more Bio::Annotation::DBLink objects.

   remove_members
        Title   : remove_members
        Usage   :
        Function: Remove all members for this class.
        Example :
        Returns : The list of previous members as an array of
                  Bio::Annotation::DBLink objects.
        Args    :

   get_examples
        Title   : get_examples
        Usage   : @arr = get_examples()
        Function: Get the list of example(s) for this object.

                  This is an element of the InterPro xml schema.

        Example :
        Returns : An array of Bio::Annotation::DBLink objects
        Args    :

   add_example
        Title   : add_example
        Usage   :
        Function: Add one or more example(s) to this object.

                  This is an element of the InterPro xml schema.

        Example :
        Returns :
        Args    : One or more Bio::Annotation::DBLink objects.

   remove_examples
        Title   : remove_examples
        Usage   :
        Function: Remove all examples for this class.

                  This is an element of the InterPro xml schema.

        Example :
        Returns : The list of previous examples as an array of
                  Bio::Annotation::DBLink objects.
        Args    :

   get_external_documents
        Title   : get_external_documents
        Usage   : @arr = get_external_documents()
        Function: Get the list of external_document(s) for this object.

                  This is an element of the InterPro xml schema.

        Example :
        Returns : An array of Bio::Annotation::DBLink objects
        Args    :

   add_external_document
        Title   : add_external_document
        Usage   :
        Function: Add one or more external_document(s) to this object.

                  This is an element of the InterPro xml schema.

        Example :
        Returns :
        Args    : One or more Bio::Annotation::DBLink objects.

   remove_external_documents
        Title   : remove_external_documents
        Usage   :
        Function: Remove all external_documents for this class.

                  This is an element of the InterPro xml schema.

        Example :
        Returns : The list of previous external_documents as an array of
                  Bio::Annotation::DBLink objects.
        Args    :

   class_list
        Title   : class_list
        Usage   : $obj->class_list($newval)
        Function: Set/get for class list element of the InterPro xml schema
        Example :
        Returns : reference to an array of Bio::Annotation::DBLink objects
        Args    : reference to an array of Bio::Annotation::DBLink objects

   to_string
        Title   : to_string()
        Usage   : print $term->to_string();
        Function: to_string method for InterPro terms.
        Returns : A string representation of this InterPro term.
        Args    :

Deprecated methods

       These are here for backwards compatibility.

   secondary_ids
        Title   : secondary_ids
        Usage   : $obj->secondary_ids($newval)
        Function: This is deprecated. Use get_secondary_ids() or
                  add_secondary_id() instead.
        Example :
        Returns : reference to an array of strings
        Args    : reference to an array of strings