| line |
true |
false |
branch |
|
228
|
0 |
0 |
if ($a =~ /^\d+$/) |
|
232
|
0 |
0 |
if ($a =~ /^\d+$/ and $a >= 0 and $a <= 100) |
|
266
|
0 |
3 |
if $ENV{'MOLPHYDIR'} |
|
299
|
0 |
1 |
if defined $aln |
|
300
|
0 |
1 |
if defined $tree |
|
301
|
0 |
1 |
if defined $st |
|
302
|
0 |
1 |
if defined $exe |
|
303
|
1 |
0 |
if (defined $flags) |
|
304
|
0 |
1 |
if (not ref($flags) =~ /HASH/i) { } |
|
308
|
1 |
2 |
if ($type =~ /other/i) { } |
|
318
|
0 |
1 |
if (defined $params) |
|
319
|
0 |
0 |
if (not ref($flags) =~ /HASH/i) { } |
|
344
|
0 |
0 |
unless ($self->save_tempfiles) |
|
349
|
0 |
0 |
unless ($align) |
|
353
|
0 |
0 |
if ($align->get_seq_by_pos(1)->alphabet ne 'protein') |
|
362
|
0 |
0 |
unless (defined $flags{'search'}) |
|
369
|
0 |
0 |
if ($t eq 'others') { } |
|
372
|
0 |
0 |
if $flags{$t} eq 'u' |
|
381
|
0 |
0 |
$self->save_tempfiles ? : |
|
385
|
0 |
0 |
$Bio::Tools::Run::Phylo::Molphy::ProtML::MINNAMELEN > $align->maxdisplayname_length ? : |
|
397
|
0 |
0 |
if ($tree and defined $flags{'search'} eq 'u') |
|
398
|
0 |
0 |
$self->save_tempfiles ? : |
|
410
|
0 |
0 |
unless (open PROTML, "$cmdstring |") |
|
433
|
0 |
0 |
if (defined $aln) |
|
434
|
0 |
0 |
unless (ref $aln and $aln->isa('Bio::Align::AlignI')) |
|
459
|
0 |
0 |
if (defined $tree) |
|
460
|
0 |
0 |
unless (ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
510
|
0 |
4 |
unless (defined $type and defined $param) |
|
516
|
0 |
4 |
unless ($Bio::Tools::Run::Phylo::Molphy::ProtML::VALIDFLAGS{$type}) |
|
525
|
0 |
4 |
unless ($self->no_param_checks or defined $Bio::Tools::Run::Phylo::Molphy::ProtML::VALIDFLAGS{$type}{$param}) |
|
529
|
2 |
2 |
if ($type eq 'others') { } |
|
576
|
0 |
0 |
unless ($self->no_param_checks or defined $Bio::Tools::Run::Phylo::Molphy::ProtML::VALIDVALUES{$param}) |
|
582
|
0 |
0 |
if ($paramflag) { } |
|
667
|
1 |
0 |
unless ($self->save_tempfiles) |