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lib/Bio/PrimerDesigner.pm  view on Meta::CPAN

sub list_params {

=pod

=head2 list_params

Lists input options for primer3 or epcr, depending on the context

=cut

    my $self = shift;
    my $designer = $self->program or return $self->error;
    return $designer->list_params;
}

# -------------------------------------------------------------------
sub method {

=pod

=head2 method

Gets/sets method of accessing primer3 or epcr binaries.

=cut

    my $self    = shift;

    if ( my $arg = lc shift ) {
        return $self->error("Invalid argument for method: '$arg'")
            unless $arg eq 'local' || $arg eq 'remote';

        if ( !$self->os_is_unix && $arg eq 'local' ) {
            return $self->error("Local method doesn't work on Windows");
        }

        $self->{'method'} = $arg;
    }

    unless ( defined $self->{'method'} ) {
        $self->{'method'} = $self->os_is_unix ? $DEFAULT{'method'} : 'remote';
    }

    return $self->{'method'};
}

# -------------------------------------------------------------------
sub os_is_unix {

=pod

=head2 os_is_unix

Returns 1 if it looks like the operating system is a Unix variant, 
otherwise returns 0.

=cut

    my $self = shift;

    # technically, this should be 'os_is_not_windows'
    unless ( defined $self->{'os_is_unix'} ) {
        #$self->{'os_is_unix'} = ( $^O =~ /(n[iu]x|darwin)/ ) ? 1 : 0;
	$self->{'os_is_unix'} = ( $^O !~ /^MSWin/i ) ? 1 : 0;
    }

    return $self->{'os_is_unix'};
}

# -------------------------------------------------------------------
sub primer3_example {

=head2 primer3_example

Runs a sample design job for primers.  Returns an
Bio::PrimerDesigner::Results object.

=cut

    my $self = shift;
    my $pcr  = Bio::PrimerDesigner::primer3->new;
    return $pcr->example || $self->error( $pcr->error );
}

# -------------------------------------------------------------------
sub program {

=pod

=head2 program

Gets/sets which program to use.

=cut

    my $self    = shift;
    my $program = shift || $EMPTY_STR;
    my $reset   = 0; 

    if ( $program ) {
        return $self->error("Invalid argument for program: '$program'")
            unless $DESIGNER{ $program };
        $reset = 1;
    }

    if ( $reset || !defined $self->{'program'} ) {
        $program ||= $DEFAULT{'program'};
        my $class  = $DESIGNER{ $program };
        $self->{'program'} = $class->new or 
            return $self->error( $class->error );
    }

    return $self->{'program'};
}

# -------------------------------------------------------------------
sub run {

=pod

=head2 run