| line |
!l |
l&&!r |
l&&r |
condition |
|
449
|
0 |
0 |
0 |
not ref $aln and -e $aln |
|
477
|
0 |
0 |
0 |
not ref $tree and -e $tree |
|
534
|
0 |
0 |
0 |
$codemlexe and -e $codemlexe |
|
|
0 |
0 |
0 |
$codemlexe and -e $codemlexe and -x _ |
|
598
|
0 |
0 |
0 |
ref $aln && $aln->isa('Bio::Align::AlignI') |
|
630
|
0 |
0 |
0 |
ref $tree and $tree->isa('Bio::Tree::TreeI') |
|
681
|
8 |
0 |
0 |
defined $self->{'no_param_checks'} and $self->{'no_param_checks'} == 1 |
|
686
|
3 |
0 |
5 |
ref($Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param}) =~ /ARRAY/i and scalar @{$Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param};} > 0 |
|
718
|
28 |
0 |
0 |
defined $self->{'_codemlparams'}{$param} and $keepold |