Bio::OntologyIO InterProParser
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Summary
InterProParser - Parser for InterPro xml files.
Package variables
No package variables defined.
Included modules
Bio::Ontology::SimpleOntologyEngine
Bio::Ontology::TermFactory
Bio::OntologyIO
Bio::OntologyIO::Handlers::InterProHandler
XML::Parser::PerlSAX
Inherit
Bio::OntologyIO
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.
Methods
_initialize
No description
Code
_is_parsedDescriptionCode
next_ontologyDescriptionCode
parseDescriptionCode
secondary_accessions_mapDescriptionCode
Methods description
_is_parsedcode    nextTop
 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)
next_ontologycodeprevnextTop
 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    :
parsecodeprevnextTop
 Title   : parse
 Usage   :
 Function: Performs the actual parsing.
 Example : $ipp->parse();
 Returns : 
 Args    :
secondary_accessions_mapcodeprevnextTop
 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
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my $self = shift;

    $self->SUPER::_initialize(@_);

    my ($eng,$eng_type,$name) =
	$self->_rearrange([qw(ENGINE
			      ONTOLOGY_ENGINE
			      ONTOLOGY_NAME)
			   ], @_);

    my $ip_h = Bio::OntologyIO::Handlers::InterProHandler->new(
			                             -ontology_name => $name);

    if(! $eng) {
	if(lc($eng_type) eq 'simple') {
	    $eng = Bio::Ontology::SimpleOntologyEngine->new();
	} else {
	    $self->throw("ontology engine type '$eng_type' ".
			 "not implemented yet");
	}
    }
    if($eng->isa("Bio::Ontology::OntologyI")) {
	$ip_h->ontology($eng);
	$eng = $eng->engine() if $eng->can('engine');
    }
    $self->{_ontology_engine} = $eng;
    $ip_h->ontology_engine($eng);

    $self->{_parser} = XML::Parser::PerlSAX->new( Handler => $ip_h );
    $self->{_interpro_handler} = $ip_h;

    # default term object factory
    $self->term_factory(Bio::Ontology::TermFactory->new(
				   -type => "Bio::Ontology::InterProTerm"))
	unless $self->term_factory();
    $ip_h->term_factory($self->term_factory());
}
_is_parseddescriptionprevnextTop
sub _is_parsed {
    my $self = shift;

    return $self->{'_is_parsed'} = shift if @_;
    return $self->{'_is_parsed'};
}
next_ontologydescriptionprevnextTop
sub next_ontology {
  my $self = shift;

  $self->parse() unless $self->_is_parsed();
  # there is only one ontology in an InterPro source file
  if(exists($self->{'_ontology_engine'})) {
      my $ont = $self->{_interpro_handler}->ontology();
      delete $self->{_ontology_engine};
      return $ont;
  }
  return undef;
}
parsedescriptionprevnextTop
sub parse {
   my $self = shift;

   my $ret = $self->{_parser}->parse( Source => {
       SystemId => $self->file() } );
   $self->_is_parsed(1);
   return $ret;
}
secondary_accessions_mapdescriptionprevnextTop
sub secondary_accessions_map {
  my ($self) = @_;

  return $self->{_interpro_handler}->{secondary_accessions_map};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Peter DimitrovTop
Email dimitrov@gnf.org
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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.