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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 47);
use_ok('Bio::Tools::Phylo::Phylip::ProtDist');
}
my $inputfilename= test_input_file('phylipdist.out');
my $tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
my $phy = $tool->next_matrix;
is(@{$phy->names}, 5);
is $phy->get_entry('Alpha','Beta'), '4.23419';
is $phy->get_entry('Gamma','Alpha'),'3.63330';
my @column = $phy->get_column('Alpha');
is $column[0], '0.00000';
is $column[1], '4.23419';
is $column[2], '3.63330';
is $column[3], '6.20865';
is $column[4], '3.45431';
my @row = $phy->get_row('Gamma');
is $row[0], '3.63330';
is $row[1], '3.49289';
is $row[2], '0.00000';
is $row[3], '3.68733';
is $row[4], '5.84929';
my @diag = $phy->get_diagonal;
is $diag[0], '0.00000';
is $diag[1], '0.00000';
is $diag[2], '0.00000';
is $diag[3], '0.00000';
is $diag[4], '0.00000';
my $matrix =<<END;
5
Alpha 0.00000 4.23419 3.63330 6.20865 3.45431
Beta 4.23419 0.00000 3.49289 3.36540 4.29179
Gamma 3.63330 3.49289 0.00000 3.68733 5.84929
Delta 6.20865 3.36540 3.68733 0.00000 4.43345
Epsilon 3.45431 4.29179 5.84929 4.43345 0.00000
END
;
is $phy->print_matrix , $matrix;
# now parse Phylip 3.6 output
$inputfilename= test_input_file('phylipdist-36.out');
$tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
$phy = $tool->next_matrix;
is(@{$phy->names}, 39);
is $phy->get_entry('CBG01299','CBG00435'), '4.7793';
is $phy->get_entry('CBG22788','CBG22521'),'5.3195';
is $phy->get_entry('CBG01466', 'CBG01473'), '3.3944';
@row = $phy->get_row('CBG01473');
is(scalar @row, 39);
@column = $phy->get_column('CBG01300');
is $column[0], '0.0817';
is $column[1], '0.0000';
is $column[2], '0.0950';
is $column[3], '0.3111';
is $column[37], '4.7190';
is $column[38], '4.7592';
@row = $phy->get_row('CBG17433');
is $row[0], '4.8451';
is $row[1], '4.5982';
is $row[2], '4.0620';
is $row[3], '5.9673';
is $row[4], '4.6224';
is $row[5], '5.1993';
is $row[6], '5.4427';
is $row[7], '4.2783';
@diag = $phy->get_diagonal;
is $diag[0], '0.0000';
is $diag[1], '0.0000';
is $diag[2], '0.0000';
is $diag[3], '0.0000';
is $diag[4], '0.0000';
is $diag[5], '0.0000';
is $diag[37], '0.0000';
is $diag[38], '0.0000';
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