File Coverage

blib/lib/Bio/Phylo/Parsers/Abstract.pm

Criterion	Covered	Total	%
statement	81	123	65.8
branch	33	60	55.0
condition	3	12	25.0
subroutine	24	27	88.8
pod			n/a
total	141	222	63.5

package Bio::Phylo::Parsers::Abstract;
use strict;
use base 'Bio::Phylo::IO';
use IO::Handle;
use Bio::Phylo::Util::Exceptions 'throw';
use Bio::Phylo::Util::CONSTANT '/looks_like/';
use Bio::Phylo::Util::Logger ':simple';
use Bio::Phylo::Factory;

=head1 NAME

Bio::Phylo::Parsers::Abstract - Superclass for parsers used by Bio::Phylo::IO

=head1 DESCRIPTION

This package is subclassed by all other packages within Bio::Phylo::Parsers::.*.
There is no direct usage.

=cut

my $factory = Bio::Phylo::Factory->new;
my $logger  = Bio::Phylo::Util::Logger->new;

# argument is a file name, which we open
sub _open_file {
    my $file_name = shift;
    my $encoding  = shift || '';
    open my $handle, "<${encoding}", $file_name or throw 'FileError' => $!;
    return $handle;
}

# argument is a string, which, at perl version >5.8,
# we can treat as a handle by opening it by reference
sub _open_string {
    my $string_value = shift;
    my $encoding     = shift || '';
    open my $handle, "<${encoding}", \$string_value or throw 'FileError' => $!;
    return $handle;
}

# argument is a url,
sub _open_url {
    my $url = shift;
    my $encoding = shift || '';
    my $handle;

    # we need to use LWP::UserAgent to fetch the resource, but
    # we don't "use" it at the top of the module because that
    # would make it a required dependency
    eval { require LWP::UserAgent };
    if ($@) {
        throw 'ExtensionError' =>
            "Providing a -url argument requires\nsuccesful loading "
          . "of LWP::UserAgent.\nHowever, there was an error when "
          . "I\ntried that:\n"
          . $@;
    }

    # apparently it's installed, so let's instantiate a client
    my $ua = LWP::UserAgent->new;
    $ua->timeout(10);
    $ua->env_proxy;

    # fetch the resource, get an HTTP::Response object
    my $response = $ua->get($url);

    # i.e. 200, or 304 (unchanged cache)
    if ( $response->is_success or $response->status_line =~ /304/ ) {

        # content is a string, so we create a handle in the same way
        # as when the argument was a string
        $handle = _open_string( $response->content, $encoding );
    }
    else {
        throw 'NetworkError' => $response->status_line;
    }
    return $handle;
}

# deal with all possible data sources, return
# a handle to whatever it is or throw an exception
sub _open_handle {
    my %args = @_;
    my $handle;
    if ( $args{'-handle'} ) {
        binmode $args{'-handle'}, ":utf8";
        $handle = $args{'-handle'};
    }
    elsif ( $args{'-file'} ) {
        $handle = _open_file( $args{'-file'}, $args{'-encoding'} );
    }
    elsif ( $args{'-string'} ) {
        $handle = _open_string( $args{'-string'}, $args{'-encoding'} );
    }
    elsif ( $args{'-url'} ) {
        $handle = _open_url( $args{'-url'}, $args{'-encoding'} );
    }
    else {
        throw 'BadArgs' => 'No data source provided!';
    }

    # check to see if the data source contains anything
    #if ( eof $handle ) {
    #    throw 'NoData' => "Source is empty!";
    #}
    return $handle;
}

# open a Bio::Phylo::Project if asked (if the -as_project flag
# was provided.) If the user has supplied one (the -project flag)
# simply return that or undefined otherwise.
sub _open_project {
    my ( $fac, %args ) = @_;
    if ( $args{'-project'} ) {
        return $args{'-project'};
    }
    elsif ( $args{'-as_project'} ) {
        return $fac->create_project;
    }
    else {
        return undef;
    }
}

# this constructor is called by the Bio::Phylo::IO::parse
# subroutine
sub _new {
    my $class = shift;
    my %args  = looks_like_hash @_;

    # we need to guess the format
    if ( $class eq __PACKAGE__ ) {
        if ( my $format = _guess_format(_open_handle(%args)) ) {
            $class = 'Bio::Phylo::Parsers::' . ucfirst($format);
            return looks_like_class($class)->_new(%args);
        }
        else {
            throw 'BadArgs' => "No format specified and unable to guess!";
        }
    }

    # factory is either user supplied or a private static
    my $fac = $args{'-factory'} || $factory;

    # values of these object fields will be accessed
    # by child classes through the appropriate protected
    # getters
    return bless {
        '_fac'      => $fac,
        '_handle'   => _open_handle(%args),
        '_proj'     => _open_project( $fac, %args ),
        '_args'     => \%args, # for child-specific arguments
        '_encoding' => $args{'-encoding'},
        '_handlers' => $args{'-handlers'},
        '_flush'    => $args{'-flush'},
    }, $class;
}

# child classes can override this to specify
# that their return value is a single scalar
# (e.g. a tree block, as is the case for newick),
# instead of an array of blocks
sub _return_is_scalar { 0 }

# this is called by Bio::Phylo::IO::parse, and
# in turn it calls the _parse method of whatever
# the concrete child instance is.
sub _process {
    my $self = shift;
    if ( $self->_return_is_scalar ) {
        my $result = $self->_parse;
        if ( my $p = $self->_project ) {
        	if ( my $meta = $self->_project_meta ) {
        		$p->add_meta($_) for @{ $meta };
        	}
            return $p->insert($result);
        }
        else {
            return $result;
        }
    }
    else {
        my @result = $self->_parse;
        if ( my $p = $self->_project ) {
        	if ( my $meta = $self->_project_meta ) {
        		$p->add_meta($_) for @{ $meta };
        	}
            return $p->insert(@result);
        }
        else {
            return [@result];
        }
    }
}

# once this is called, the handle will have read to
# the end of the stream, so it needs to be rewound
# if we want to read from the top
sub _string {
    my $self   = shift;
    my $handle = $self->_handle;
    my $string = do { local $/; <$handle> };
    return $string;
}
sub _project_meta {};
sub _logger   { $logger }
sub _project  { shift->{'_proj'} }
sub _handle   { shift->{'_handle'} }
sub _factory  { shift->{'_fac'} }
sub _args     { shift->{'_args'} }
sub _encoding { shift->{'_encoding'} }
sub _flush    { shift->{'_flush'} }
sub _handlers {
    my ( $self, $type ) = @_;
    if ( my $h = $self->{'_handlers'} ) {
        return defined $type ? $h->{$type} : $h;
    }
}

sub _guess_format {
    my $handle = shift;
    my $line = $handle->getline;
    my $format;
    if ( $line =~ /^#nexus/i ) {
        $format = 'nexus';
    }
    elsif ( $line =~ /^<[^>]*nexml/ ) {
        $format = 'nexml';
    }
    elsif ( $line =~ /^<[^>]*phyloxml/ ) {
        $format = 'phyloxml';
    }
    elsif ( $line =~ /^\s*\d+\s+\d+\s*$/ ) {
        $format = 'phylip';
    }
    elsif ( $line =~ /^>/ ) {
        $format = 'fasta';
    }
    elsif ( $line =~ /^\@/ ) {
        $format = 'fastq';
    }
    elsif ( $line =~ /^\s*\(/ ) {
        $format = 'newick';
        if ( $line =~ /{/ ) {
            $format = 'figtree';
        }
    }
    elsif ( $line =~ /<\? xml/ ) {
        $line = $handle;
        if ( $line =~ /^<[^>]*nexml/ ) {
            $format = 'nexml';
        }
        elsif ( $line =~ /^<[^>]*phyloxml/ ) {
            $format = 'phyloxml';
        }
    }
    seek( $handle, 0, 0 );
    return $format;
}

# podinherit_insert_token

=head1 SEE ALSO

There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo>
for any user or developer questions and discussions.

=over

=item L<Bio::Phylo::IO>

The parsers are called by the L<Bio::Phylo::IO> object.
Look there for examples.

=item L<Bio::Phylo::Manual>

Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>.

=back

=head1 CITATION

If you use Bio::Phylo in published research, please cite it:

B<Rutger A Vos>, B<Jason Caravas>, B<Klaas Hartmann>, B<Mark A Jensen>
and B<Chase Miller>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I<BMC Bioinformatics> B<12>:63.
L<http://dx.doi.org/10.1186/1471-2105-12-63>

=cut

1;