| line |
true |
false |
branch |
|
27
|
0 |
1 |
$^O =~ /mswin/i ? : |
|
28
|
0 |
1 |
if (defined $ENV{'PAMLDIR'}) |
|
29
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
143
|
0 |
3 |
if $ENV{'PAMLDIR'} |
|
157
|
0 |
1 |
if defined $aln |
|
158
|
0 |
1 |
if defined $tree |
|
159
|
0 |
1 |
if defined $st |
|
160
|
0 |
1 |
if defined $exe |
|
163
|
1 |
0 |
if (defined $params) |
|
164
|
0 |
1 |
if (not ref($params) =~ /HASH/i) { } |
|
177
|
1 |
0 |
unless ($self->save_tempfiles) |
|
181
|
1 |
0 |
unless $tree |
|
182
|
1 |
0 |
unless $aln |
|
183
|
0 |
1 |
unless ($aln) |
|
189
|
0 |
1 |
if (not ref $aln and -e $aln) { } |
|
192
|
0 |
1 |
$self->save_tempfiles ? : |
|
195
|
1 |
0 |
$Bio::Tools::Run::Phylo::PAML::Codeml::MINNAMELEN > $aln->maxdisplayname_length ? : |
|
210
|
0 |
1 |
unless open CODEML, ">$codeml_ctl" |
|
215
|
0 |
1 |
if ($tree) |
|
217
|
0 |
0 |
if (not ref $tree and -e $tree) { } |
|
220
|
0 |
0 |
$self->save_tempfiles ? : |
|
235
|
1 |
27 |
if $param eq 'outfile' |
|
262
|
0 |
0 |
unless $codemlexe and -e $codemlexe and -x _ |
|
264
|
0 |
0 |
if ($self->{'_branchLengths'}) { } |
|
265
|
0 |
0 |
unless open $run, "echo $self->{'_branchLengths'} | $codemlexe |" |
|
267
|
0 |
0 |
unless open $run, "$codemlexe |" |
|
272
|
0 |
0 |
if (grep {/\berr(or)?: /io;} @output or not $exit_status) |
|
281
|
0 |
0 |
if ($@) |
|
292
|
0 |
0 |
if (defined $value) |
|
303
|
1 |
1 |
if (defined $aln) |
|
304
|
0 |
1 |
if (-e $aln) { } |
|
|
0 |
1 |
elsif (not ref $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
319
|
0 |
1 |
if (defined $tree) |
|
320
|
0 |
0 |
unless (ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
324
|
0 |
0 |
if (defined $params{'_branchLengths'}) |
|
326
|
0 |
0 |
unless ($ubl =~ /^(0|1|2)$/) |
|
346
|
8 |
0 |
unless (defined $self->{'no_param_checks'} and $self->{'no_param_checks'} == 1) |
|
347
|
0 |
8 |
unless (defined $Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param}) |
|
351
|
5 |
3 |
if (ref($Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param}) =~ /ARRAY/i and scalar @{$Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param};} > 0) |
|
354
|
0 |
5 |
unless (grep {$value eq $_;} @{$Bio::Tools::Run::Phylo::PAML::Codeml::VALIDVALUES{$param};}) |
|
367
|
1 |
0 |
unless defined $keepold |
|
371
|
0 |
28 |
if defined $self->{'_codemlparams'}{$param} and $keepold |
|
372
|
21 |
7 |
if (ref($val) =~ /ARRAY/i) { } |
|
385
|
0 |
0 |
if (defined $value) |
|
396
|
0 |
2 |
if (@_) |
|
399
|
0 |
2 |
unless (defined $self->{'_codemlparams'}{'outfile'}) |
|
410
|
1 |
0 |
unless ($self->save_tempfiles) |