Bio::OntologyIO InterProParser
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Summary
Bio::OntologyIO::InterProParser - Parser for InterPro xml files.
Package variables
No package variables defined.
Included modules
Bio::Ontology::SimpleOntologyEngine
Bio::Ontology::TermFactory
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
parseDescriptionCode
next_ontologyDescriptionCode
_is_parsedDescriptionCode
secondary_accessions_mapDescriptionCode
Methods description
parsecode    nextTop
 Title   : parse
Usage :
Function: Performs the actual parsing.
Example : $ipp->parse();
Returns :
Args :
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 :
See Bio::Ontology::OntologyEngineI.
_is_parsedcodeprevnextTop
 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_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) {
	$eng_type = 'simple' unless $eng_type;
	if(lc($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());
}
parsedescriptionprevnextTop
sub parse {
   my $self = shift;

   my $ret;
   if ($self->file()) {
         $ret = $self->{_parser}->parse( Source => {
	                SystemId => $self->file() } );
   } elsif ($self->_fh()) {
        $ret = $self->{_parser}->parse( Source => {
                ByteStream => $self->_fh() } );
   } else {
        $ret = undef;
        $self->throw("Only filenames and filehandles are understood here.\n");
   }

   $self->_is_parsed(1);
   return $ret;
}
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;
}
_is_parseddescriptionprevnextTop
sub _is_parsed {
    my $self = shift;

    return $self->{'_is_parsed'} = shift if @_;
    return $self->{'_is_parsed'};
}
secondary_accessions_mapdescriptionprevnextTop
sub secondary_accessions_map {
  my ($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/wiki/Mailing_lists - About the mailing lists
Support Top
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 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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Peter DimitrovTop
Email dimitrov@gnf.org
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.