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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
use vars qw($NTESTS);
$NTESTS = 46;
plan tests => $NTESTS;
}
use Bio::Tools::Phylo::Phylip::ProtDist;
END {
for ( $Test::ntest..$NTESTS ) {
skip("Error in ProtDist.pm",1);
}
}
my $inputfilename= Bio::Root::IO->catfile("t","data","phylipdist.out");
my $tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
my $phy = $tool->next_matrix;
ok(@{$phy->names}, 5);
ok $phy->get_entry('Alpha','Beta'), '4.23419';
ok $phy->get_entry('Gamma','Alpha'),'3.63330';
my @column = $phy->get_column('Alpha');
ok $column[0] = '0.00000';
ok $column[1] = '4.23419';
ok $column[2] = '3.63330';
ok $column[3] = '6.20865';
ok $column[4] = '3.45431';
my @row = $phy->get_row('Gamma');
ok $row[0] = '3.63330';
ok $row[1] = '3.49289';
ok $row[2] = '0.00000';
ok $row[3] = '3.68733';
ok $row[4] = '5.84929';
my @diag = $phy->get_diagonal;
ok $diag[0] = '0.00000';
ok $diag[1] = '0.00000';
ok $diag[2] = '0.00000';
ok $diag[3] = '0.00000';
ok $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
;
ok $phy->print_matrix , $matrix;
# now parse Phylip 3.6 output
$inputfilename= Bio::Root::IO->catfile("t","data","phylipdist-36.out");
$tool= Bio::Tools::Phylo::Phylip::ProtDist->new(-file => $inputfilename);
$phy = $tool->next_matrix;
ok(@{$phy->names}, 39);
ok $phy->get_entry('CBG01299','CBG00435'), '4.7793';
ok $phy->get_entry('CBG22788','CBG22521'),'5.3195';
ok $phy->get_entry('CBG01466', 'CBG01473'), '3.3944';
@row = $phy->get_row('CBG01473');
ok(scalar @row, 39);
@column = $phy->get_column('CBG01300');
ok $column[0] = '0.0817';
ok $column[1] = '0.0000';
ok $column[2] = '0.0950';
ok $column[3] = '0.3111';
ok $column[37] = '4.7190';
ok $column[38] = '4.7592';
@row = $phy->get_row('CBG17433');
ok $row[0] = '4.8451';
ok $row[1] = '4.5982';
ok $row[2] = '4.0620';
ok $row[3] = '5.9673';
ok $row[4] = '4.6224';
ok $row[5] = '5.1993';
ok $row[6] = '5.4427';
ok $row[7] = '4.2783';
@diag = $phy->get_diagonal;
ok $diag[0] = '0.00000';
ok $diag[1] = '0.00000';
ok $diag[2] = '0.00000';
ok $diag[3] = '0.00000';
ok $diag[4] = '0.00000';
ok $diag[5] = '0.00000';
ok $diag[37] = '0.00000';
ok $diag[38] = '0.00000';
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