| line |
true |
false |
branch |
|
87
|
1 |
0 |
if $args{'-type'}
|
|
148
|
0 |
0 |
if (@_) { }
|
|
151
|
0 |
0 |
unless $self->{'_rate'}
|
|
152
|
0 |
0 |
unless ($self->{'_rate'}[$src])
|
|
286
|
0 |
0 |
unless $self->{'_pi'}
|
|
287
|
0 |
0 |
if (@_) { }
|
|
326
|
0 |
1 |
unless ref $q eq 'ARRAY'
|
|
327
|
0 |
1 |
unless scalar @{$q;} == 4
|
|
329
|
0 |
4 |
unless scalar @{$row;} == 4
|
|
446
|
0 |
1 |
if ($pinvar <= 0 or $pinvar >= 1)
|
|
469
|
0 |
1 |
unless ref $pi eq 'ARRAY'
|
|
473
|
0 |
1 |
unless abs 1 - $total < $epsilon
|
|
527
|
0 |
0 |
if (&looks_like_class('Statistics::R')) { }
|
|
537
|
0 |
0 |
if $timeout
|
|
541
|
0 |
0 |
if (!$R->get('package') eq 'TRUE')
|
|
552
|
0 |
0 |
if ($tree) { }
|
|
561
|
0 |
0 |
if (not $current_tree or scalar @{$current_tree->get_terminals;} < 3) { }
|
|
604
|
0 |
0 |
if ($modeltype =~ /JC/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /F81/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /GTR/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /HKY/) { }
|
|
|
0 |
0 |
elsif ($modeltype =~ /K80/) { }
|
|
637
|
0 |
0 |
if ($modeltype =~ /\+G/)
|
|
651
|
0 |
0 |
if ($modeltype =~ /\+I/)
|
|
662
|
0 |
0 |
if ($@)
|
|
691
|
0 |
1 |
if ($args{'-format'} =~ /paup/i)
|
|
694
|
0 |
1 |
if ($args{'-format'} =~ /phyml/i)
|
|
697
|
0 |
1 |
if ($args{'-format'} =~ /mrbayes/i)
|
|
700
|
1 |
0 |
if ($args{'-format'} =~ /garli/i)
|
|
709
|
1 |
0 |
if (my $pinvar = $self->get_pinvar)
|
|
712
|
1 |
0 |
if (my $ncat = $self->get_ncat)
|
|
715
|
1 |
0 |
if (my $alpha = $self->get_alpha)
|
|
725
|
0 |
0 |
if ($self->get_pinvar and $self->get_alpha) { }
|
|
|
0 |
0 |
elsif ($self->get_pinvar) { }
|
|
|
0 |
0 |
elsif ($self->get_alpha) { }
|
|
727
|
0 |
0 |
if ($self->get_ncat)
|
|
736
|
0 |
0 |
if ($self->get_ncat)
|
|
741
|
0 |
0 |
if ($self->get_kappa and $self->get_nst == 2)
|
|
753
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G') and $self->get_pi('T'))
|
|
765
|
0 |
0 |
if ($self->get_alpha)
|
|
768
|
0 |
0 |
if ($self->get_pinvar)
|
|
778
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G') and $self->get_pi('T'))
|
|
790
|
0 |
0 |
if ($self->get_nst == 2 and defined(my $kappa = $self->get_kappa))
|
|
793
|
0 |
0 |
if ($self->get_pinvar)
|
|
796
|
0 |
0 |
if ($self->get_ncat)
|
|
798
|
0 |
0 |
if $self->get_median
|
|
800
|
0 |
0 |
if ($self->get_alpha)
|
|
810
|
0 |
0 |
if ($nst == 2 and defined(my $kappa = $self->get_kappa))
|
|
813
|
0 |
0 |
if ($nst == 6)
|
|
822
|
0 |
0 |
if ($self->get_pi('A') and $self->get_pi('C') and $self->get_pi('G'))
|
|
829
|
0 |
0 |
if ($self->get_alpha)
|
|
832
|
0 |
0 |
if ($self->get_ncat)
|
|
834
|
0 |
0 |
$self->get_median ? :
|
|
836
|
0 |
0 |
if ($self->get_pinvar)
|