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

NAME

       Bio::OntologyIO::InterProParser - Parser for InterPro xml files.

SYNOPSIS

           # don't use this module directly - use Bio::OntologyIO with instead
           my $ipp = Bio::OntologyIO->new( -format  => 'interpro',
                                           -file    => 't/data/interpro.xml',
                                           -ontology_engine => 'simple' );

DESCRIPTION

         Use InterProParser to parse InterPro files in xml format. Typical
         use is the interpro.xml file published by EBI. The xml records
         should follow the format described in interpro.dtd, although the dtd
         file is not needed, and the XML file will not be validated against it.

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   :
        Function: Initializes objects needed for parsing.
        Example : $ipp = Bio::OntologyIO::InterProParser->new(
                                         -file => 't/data/interpro.xml',
                                         -ontology_engine => 'simple' )

        Returns : Object of class Bio::OntologyIO::InterProParser.
        Args    :

         -file            - file name
         -ontology_engine - type of ontology engine. Should satisfy the
                            OntologyEngine interface requirements. Currently
                            the only option is 'simple'. In the future
                            Graph.pm based engine will be added to the
                            choices.

   parse
        Title   : parse
        Usage   :
        Function: Performs the actual parsing.
        Example : $ipp->parse();
        Returns :
        Args    :

   next_ontology
        Title   : next_ontology
        Usage   : $ipp->next_ontology()
        Function: Parses the input file and returns the next InterPro ontology
                  available.

                  Usually there will be only one ontology returned from an
                  InterPro XML input.

        Example : $ipp->next_ontology();
        Returns : Returns the ontology as a Bio::Ontology::OntologyEngineI
                  compliant object.
        Args    :

       See Bio::Ontology::OntologyEngineI.

   _is_parsed
        Title   : _is_parsed
        Usage   : $obj->_is_parsed($newval)
        Function:
        Example :
        Returns : value of _is_parsed (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   secondary_accessions_map
        Title   : secondary_accessions_map
        Usage   : $obj->secondary_accessions_map()
        Function: This method is merely for convenience, and one should
                  normally use the InterProTerm secondary_ids method to
                  access the secondary accessions.
        Example : $map = $interpro_parser->secondary_accessions_map;
        Returns : Reference to a hash that maps InterPro identifier to an
                  array reference of secondary accessions following the
                  InterPro xml schema.
        Args    : Empty hash reference