| line |
true |
false |
branch |
|
122
|
0 |
1 |
$^O =~ /mswin/i ? : |
|
123
|
0 |
1 |
if (defined $ENV{'PAMLDIR'}) |
|
182
|
0 |
0 |
if $ENV{'PAMLDIR'} |
|
203
|
0 |
0 |
if defined $aln |
|
204
|
0 |
0 |
if defined $st |
|
231
|
0 |
0 |
unless ($aln) |
|
237
|
0 |
0 |
if (not ref $aln and -e $aln) { } |
|
240
|
0 |
0 |
$self->save_tempfiles ? : |
|
243
|
0 |
0 |
$Bio::Tools::Run::Phylo::PAML::Yn00::MINNAMELEN > $aln->maxdisplayname_length ? : |
|
259
|
0 |
0 |
unless open YN, ">$yn_ctl" |
|
276
|
0 |
0 |
unless $ynexe |
|
281
|
0 |
0 |
if (grep {/\berr(or)?: /io;} @output or not $exit_status) |
|
290
|
0 |
0 |
if ($@) |
|
295
|
0 |
0 |
if ($self->verbose > 0) |
|
302
|
0 |
0 |
unless ($self->save_tempfiles) |
|
322
|
0 |
0 |
if (defined $value) |
|
344
|
0 |
0 |
if (defined $aln) |
|
345
|
0 |
0 |
unless (ref $aln and $aln->isa('Bio::Align::AlignI')) |
|
390
|
0 |
0 |
unless (defined $Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param}) |
|
394
|
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) |
|
397
|
0 |
0 |
unless (grep {$value;} @{$Bio::Tools::Run::Phylo::PAML::Yn00::VALIDVALUES{$param};}) |
|
421
|
0 |
0 |
unless defined $keepold |
|
425
|
0 |
0 |
if defined $self->{'_codemlparams'}{$param} and $keepold |
|
426
|
0 |
0 |
if (ref($val) =~ /ARRAY/i) { } |