| line |
true |
false |
branch |
|
156
|
0 |
3 |
if $ENV{'NJTREEDIR'} |
|
184
|
0 |
1 |
if defined $aln |
|
185
|
0 |
1 |
if defined $tree |
|
186
|
0 |
1 |
if defined $st |
|
187
|
0 |
1 |
if defined $exe |
|
207
|
0 |
0 |
unless ($self->save_tempfiles) |
|
211
|
0 |
0 |
unless $tree |
|
212
|
0 |
0 |
unless $aln |
|
213
|
0 |
0 |
unless ($aln) |
|
217
|
0 |
0 |
unless ($tree) |
|
223
|
0 |
0 |
if (not ref $aln and -e $aln) { } |
|
226
|
0 |
0 |
$self->save_tempfiles ? : |
|
239
|
0 |
0 |
if (not ref $tree and -e $tree) { } |
|
242
|
0 |
0 |
$self->save_tempfiles ? : |
|
275
|
0 |
0 |
unless defined $self->{'_prepared'} |
|
287
|
0 |
0 |
unless ($self->outfile_name) |
|
296
|
0 |
0 |
unless $njtree_executable and -e $njtree_executable and -x _ |
|
299
|
0 |
0 |
unless open RUN, "$commandstring |" |
|
305
|
0 |
0 |
if (grep {/^\[ /io;} @output or not $exit_status) |
|
313
|
0 |
0 |
if ($@) |
|
317
|
0 |
0 |
unless ($self->save_tempfiles) |
|
330
|
0 |
0 |
unless $Bio::Tools::Run::Phylo::Njtree::Best::OK_FIELD{$attr} |
|
332
|
0 |
0 |
if @_ |
|
349
|
0 |
0 |
if (defined $value) |
|
371
|
0 |
0 |
unless $exe = $self->executable |
|
395
|
0 |
0 |
if (defined $aln) |
|
396
|
0 |
0 |
if (-e $aln) { } |
|
|
0 |
0 |
elsif (not ref $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
425
|
0 |
0 |
if (defined $tree) |
|
426
|
0 |
0 |
unless (ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
451
|
0 |
0 |
unless ($aln) |
|
455
|
0 |
0 |
unless ($tree) |
|
470
|
0 |
0 |
unless defined $self->{'_treeids'}{$alnid} |
|
472
|
0 |
0 |
if (defined $self->{'_unmappedids'}) |
|
500
|
0 |
0 |
unless defined $value |
|
508
|
0 |
0 |
unless $value |
|
581
|
1 |
0 |
unless ($self->save_tempfiles) |