BioPerl
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Bio/OntologyIO.pm view on Meta::CPAN
sub term_factory{
my $self = shift;
return $self->{'term_factory'} = shift if @_;
return $self->{'term_factory'};
}
=head1 Private Methods
Some of these are actually 'protected' in OO speak, which means you
may or will want to utilize them in a derived ontology parser, but
you should not call them from outside.
=cut
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL OntologyIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self, $format) = @_;
my $module = "Bio::OntologyIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
END
}
return $ok;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub _map_format {
my $self = shift;
my $format = shift;
my $mod;
if($format) {
$mod = $format_driver_map{lc($format)};
$mod = lc($format) unless $mod;
} else {
$self->throw("unable to guess ontology format, specify -format");
}
return $mod;
}
sub unescape {
my( $self, $ref ) = @_;
$ref =~ s/<\\;/\</g;
$ref =~ s/>\\;/\>/g;
$ref =~ s/&pct\\;/\%/g;
$ref =~ s/\\n/\n/g;
$ref =~ s/\\t/\t/g;
return $ref;
}
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