Raw content of Bio::OntologyIO::InterProParser
<![CDATA[# $GNF: projects/gi/symgene/src/perl/seqproc/Bio/OntologyIO/InterProParser.pm,v 1.5 2003/02/07 22:05:58 pdimitro Exp $
#
# BioPerl module for InterProParser
#
# Cared for by Peter Dimitrov <dimitrov@gnf.org>
#
# Copyright Peter Dimitrov
# (c) Peter Dimitrov, dimitrov@gnf.org, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
InterProParser - Parser for InterPro xml files.
=head1 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' );
=head1 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.
=head1 FEEDBACK
=head2 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/MailList.shtml - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Peter Dimitrov
Email dimitrov@gnf.org
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::OntologyIO::InterProParser;
use vars qw(@ISA);
use strict;
#use Carp;
use XML::Parser::PerlSAX;
use Bio::Ontology::SimpleOntologyEngine;
use Bio::Ontology::TermFactory;
use Bio::OntologyIO;
use Bio::OntologyIO::Handlers::InterProHandler;
@ISA = qw( Bio::OntologyIO );
=head2 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.
=cut
# in reality we let OntologyIO handle the first pass initialization
# and instead override _initialize().
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());
}
=head2 parse
Title : parse
Usage :
Function: Performs the actual parsing.
Example : $ipp->parse();
Returns :
Args :
=cut
sub parse{
my $self = shift;
my $ret = $self->{_parser}->parse( Source => {
SystemId => $self->file() } );
$self->_is_parsed(1);
return $ret;
}
=head2 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 L<Bio::Ontology::OntologyEngineI>
compliant object.
Args :
=cut
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;
}
=head2 _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)
=cut
sub _is_parsed{
my $self = shift;
return $self->{'_is_parsed'} = shift if @_;
return $self->{'_is_parsed'};
}
=head2 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 = $interpro_parser->secondary_accessions_map;
Returns : Reference to a hash that maps InterPro identifier to an
array reference of secondary accessions following the InterPro
xml schema.
Args : Empty hash reference
=cut
sub secondary_accessions_map{
my ($self) = @_;
return $self->{_interpro_handler}->{secondary_accessions_map};
}
1;
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