| line |
true |
false |
branch |
|
27
|
0 |
1 |
$^O =~ /mswin/i ? : |
|
28
|
0 |
1 |
if (defined $ENV{'PAMLDIR'}) |
|
69
|
0 |
0 |
if $ENV{'PAMLDIR'} |
|
79
|
0 |
0 |
if defined $aln |
|
80
|
0 |
0 |
if defined $st |
|
90
|
0 |
0 |
unless ($aln) |
|
96
|
0 |
0 |
if (not ref $aln and -e $aln) { } |
|
99
|
0 |
0 |
$self->save_tempfiles ? : |
|
102
|
0 |
0 |
$Bio::Tools::Run::Phylo::PAML::Yn00::MINNAMELEN > $aln->maxdisplayname_length ? : |
|
118
|
0 |
0 |
unless open YN, ">$yn_ctl" |
|
135
|
0 |
0 |
unless $ynexe |
|
140
|
0 |
0 |
if (grep {/\berr(or)?: /io;} @output or not $exit_status) |
|
149
|
0 |
0 |
if ($@) |
|
154
|
0 |
0 |
if ($self->verbose > 0) |
|
161
|
0 |
0 |
unless ($self->save_tempfiles) |
|
171
|
0 |
0 |
if (defined $value) |
|
181
|
0 |
0 |
if (defined $aln) |
|
182
|
0 |
0 |
unless (ref $aln and $aln->isa('Bio::Align::AlignI')) |
|
202
|
0 |
0 |
unless (defined $Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param}) |
|
206
|
0 |
0 |
if (ref($Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param}) =~ /ARRAY/i and scalar @{$Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param};} > 0) |
|
209
|
0 |
0 |
unless (grep {$value;} @{$Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param};}) |
|
221
|
0 |
0 |
unless defined $keepold |
|
225
|
0 |
0 |
if defined $self->{'_codemlparams'}{$param} and $keepold |
|
226
|
0 |
0 |
if (ref($val) =~ /ARRAY/i) { } |