| line |
true |
false |
branch |
|
88
|
1 |
0 |
if $args{'-type'}
|
|
149
|
0 |
0 |
if (@_) { }
|
|
152
|
0 |
0 |
unless $self->{'_rate'}
|
|
153
|
0 |
0 |
unless ($self->{'_rate'}[$src])
|
|
287
|
0 |
0 |
unless $self->{'_pi'}
|
|
288
|
0 |
0 |
if (@_) { }
|
|
327
|
0 |
1 |
unless ref $q eq 'ARRAY'
|
|
328
|
0 |
1 |
unless scalar @{$q;} == 4
|
|
330
|
0 |
4 |
unless scalar @{$row;} == 4
|
|
447
|
0 |
1 |
if ($pinvar <= 0 or $pinvar >= 1)
|
|
470
|
0 |
1 |
unless ref $pi eq 'ARRAY'
|
|
474
|
0 |
1 |
unless abs 1 - $total < $epsilon
|
|
528
|
0 |
0 |
if (&looks_like_class('Statistics::R')) { }
|
|
538
|
0 |
0 |
if $timeout
|
|
542
|
0 |
0 |
if (!$R->get('package') eq 'TRUE')
|
|
553
|
0 |
0 |
if ($tree) { }
|
|
562
|
0 |
0 |
if (not $current_tree or scalar @{$current_tree->get_terminals;} < 3) { }
|
|
605
|
0 |
0 |
if ($modeltype =~ /JC/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /F81/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /GTR/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /HKY/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /K80/) { }
|
|
638
|
0 |
0 |
if ($modeltype =~ /\+G/)
|
|
652
|
0 |
0 |
if ($modeltype =~ /\+I/)
|
|
663
|
0 |
0 |
if ($@)
|
|
692
|
0 |
1 |
if ($args{'-format'} =~ /paup/i)
|
|
695
|
0 |
1 |
if ($args{'-format'} =~ /phyml/i)
|
|
698
|
0 |
1 |
if ($args{'-format'} =~ /mrbayes/i)
|
|
701
|
1 |
0 |
if ($args{'-format'} =~ /garli/i)
|
|
710
|
1 |
0 |
if (my $pinvar = $self->get_pinvar)
|
|
713
|
1 |
0 |
if (my $ncat = $self->get_ncat)
|
|
716
|
1 |
0 |
if (my $alpha = $self->get_alpha)
|
|
726
|
0 |
0 |
if ($self->get_pinvar and $self->get_alpha) { }
|
|
|
0 |
0 |
elsif ($self->get_pinvar) { }
|
|
|
0 |
0 |
elsif ($self->get_alpha) { }
|
|
728
|
0 |
0 |
if ($self->get_ncat)
|
|
737
|
0 |
0 |
if ($self->get_ncat)
|
|
742
|
0 |
0 |
if ($self->get_kappa and $self->get_nst == 2)
|
|
754
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G') and $self->get_pi('T'))
|
|
766
|
0 |
0 |
if ($self->get_alpha)
|
|
769
|
0 |
0 |
if ($self->get_pinvar)
|
|
779
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G') and $self->get_pi('T'))
|
|
791
|
0 |
0 |
if ($self->get_nst == 2 and defined(my $kappa = $self->get_kappa))
|
|
794
|
0 |
0 |
if ($self->get_pinvar)
|
|
797
|
0 |
0 |
if ($self->get_ncat)
|
|
799
|
0 |
0 |
if $self->get_median
|
|
801
|
0 |
0 |
if ($self->get_alpha)
|
|
811
|
0 |
0 |
if ($nst == 2 and defined(my $kappa = $self->get_kappa))
|
|
814
|
0 |
0 |
if ($nst == 6)
|
|
823
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G'))
|
|
830
|
0 |
0 |
if ($self->get_alpha)
|
|
833
|
0 |
0 |
if ($self->get_ncat)
|
|
835
|
0 |
0 |
$self->get_median ? :
|
|
837
|
0 |
0 |
if ($self->get_pinvar)
|