File Coverage

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

Criterion	Covered	Total	%
statement	19	19	100.0
branch			n/a
condition	4	4	100.0
subroutine	3	3	100.0
pod			n/a
total	26	26	100.0

package Bio::Phylo::Parsers::Table;
use strict;
use base 'Bio::Phylo::Parsers::Abstract';

=head1 NAME

Bio::Phylo::Parsers::Table - Parser used by Bio::Phylo::IO, no serviceable parts inside

=head1 DESCRIPTION

This module is used to import data and taxa from plain text files or strings.
The following additional argument must be used in the call
to L:

 -type => (one of [DNA|RNA|STANDARD|PROTEIN|NUCLEOTIDE|CONTINUOUS])

In addition, these arguments may be used to indicate line separators (default
is "\n") and field separators (default is "\t"):

 -fieldsep => '\t',
 -linesep  => '\n'

=cut

sub _parse {
    my $self = shift;
    my $fh   = $self->_handle;
    my $fac  = $self->_factory;
    my $type = $self->_args->{'-type'};
    local $/ = $self->_args->{'-linesep'} || "\n";
    my $sep    = $self->_args->{'-fieldsep'} || "\t";
    my $regex  = qr/$sep/;
    my $matrix = $fac->create_matrix( '-type' => $type );
    while (<$fh>) {
        chomp;
        my ( $name, @char ) = split $regex, $_;
        $matrix->insert(
            $fac->create_datum(
                '-type' => $type,
                '-name' => $name,
                '-char' => \@char,
            )
        );
    }
    return $matrix;
}

# podinherit_insert_token

=head1 SEE ALSO

There is a mailing list at L
for any user or developer questions and discussions.

=over

=item L

The table parser is called by the L object.
Look there to learn how to parse tab- (or otherwise) delimited matrices.

=item L

Also see the manual: L and L

=back

=head1 CITATION

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

B, B, B, B
and B, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I B<12>:63.
L

=cut

1;