| line |
true |
false |
branch |
|
162
|
0 |
3 |
if $ENV{'SIMPROTDIR'} |
|
191
|
0 |
1 |
if defined $tree |
|
192
|
0 |
1 |
if defined $st |
|
193
|
0 |
1 |
if defined $exe |
|
196
|
0 |
1 |
if (defined $params) |
|
197
|
0 |
0 |
if (not ref($params) =~ /HASH/i) { } |
|
219
|
0 |
0 |
unless (defined $self->{'no_param_checks'} and $self->{'no_param_checks'} == 1) |
|
220
|
0 |
0 |
unless (defined $Bio::Tools::Run::Simprot::VALIDVALUES{$param}) |
|
224
|
0 |
0 |
if (ref($Bio::Tools::Run::Simprot::VALIDVALUES{$param}) =~ /ARRAY/i and scalar @{$Bio::Tools::Run::Simprot::VALIDVALUES{$param};} > 0) |
|
227
|
0 |
0 |
unless (grep {$value eq $_;} @{$Bio::Tools::Run::Simprot::VALIDVALUES{$param};}) |
|
254
|
1 |
0 |
unless defined $keepold |
|
258
|
0 |
11 |
if defined $self->{'_simprotparams'}{$param} and $keepold |
|
259
|
1 |
10 |
if (ref($val) =~ /ARRAY/i) { } |
|
302
|
0 |
0 |
unless ($self->save_tempfiles) |
|
306
|
0 |
0 |
unless $tree |
|
307
|
0 |
0 |
unless ($tree) |
|
314
|
0 |
0 |
if (not ref $tree and -e $tree) { } |
|
317
|
0 |
0 |
$self->save_tempfiles ? : |
|
354
|
0 |
0 |
unless defined $self->{'_prepared'} |
|
377
|
0 |
0 |
unless $simprot_executable and -e $simprot_executable and -x _ |
|
380
|
0 |
0 |
unless open RUN, "$commandstring |" |
|
386
|
0 |
0 |
if (grep {/^\[ /io;} @output or not $exit_status) |
|
394
|
0 |
0 |
if ($@) |
|
398
|
0 |
0 |
unless ($self->save_tempfiles) |
|
418
|
0 |
0 |
if (defined $value) |
|
440
|
0 |
0 |
unless $exe = $self->executable |
|
464
|
0 |
0 |
if (defined $aln) |
|
465
|
0 |
0 |
if (-e $aln) { } |
|
|
0 |
0 |
elsif (not ref $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
494
|
0 |
0 |
if (defined $tree) |
|
495
|
0 |
0 |
unless (ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
568
|
1 |
0 |
unless ($self->save_tempfiles) |