| line |
true |
false |
branch |
|
154
|
2 |
0 |
unless defined $exename |
|
156
|
0 |
2 |
if (defined $exe and -x $exe) |
|
159
|
2 |
0 |
unless (defined $self->{'_pathtoexe'}{$exename}) |
|
161
|
0 |
2 |
if -e $f and -x $f |
|
166
|
2 |
0 |
unless ($exe) |
|
167
|
0 |
2 |
if ($exe = $self->io->exists_exe($exename) and -x $exe) { } |
|
170
|
0 |
2 |
if $warn |
|
192
|
0 |
2 |
if $self->program_dir |
|
193
|
0 |
2 |
$^O =~ /mswin/i ? : |
|
209
|
0 |
2 |
if $ENV{'MAFFTDIR'} |
|
220
|
1 |
1 |
if $attr =~ /^-/ |
|
224
|
1 |
0 |
unless $self->output |
|
225
|
1 |
0 |
unless ($self->_version6) |
|
226
|
1 |
0 |
unless $self->method |
|
237
|
0 |
4 |
if ($self->_version6) |
|
238
|
0 |
0 |
if ($Bio::Tools::Run::Alignment::MAFFT::OK_FIELD6{$attr}) |
|
240
|
0 |
0 |
if @_ |
|
246
|
0 |
4 |
if $attr eq 'OUTFILE_NAME' |
|
247
|
0 |
4 |
unless $Bio::Tools::Run::Alignment::MAFFT::OK_FIELD{$attr} |
|
249
|
2 |
2 |
if @_ |
|
266
|
0 |
0 |
if (defined $value) |
|
287
|
1 |
0 |
unless $exe = $self->executable |
|
295
|
0 |
0 |
if (open my $NAME, "grep 'export version' $exe | ") { } |
|
297
|
0 |
0 |
if (/version.*?([\d.a-z]+)\s+/) |
|
354
|
0 |
0 |
unless ($infilename) |
|
386
|
0 |
0 |
if (not -e $outfile or -z $outfile) |
|
413
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
416
|
0 |
0 |
unless (-e $input) |
|
422
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
430
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
432
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
473
|
0 |
0 |
unless (defined($outfile = $self->outfile)) |
|
482
|
0 |
0 |
if ($self->_version6) { } |
|
485
|
0 |
0 |
unless defined $value |
|
492
|
0 |
0 |
unless defined $value |
|
497
|
0 |
0 |
unless ($self->no_param_checks) |
|
501
|
0 |
0 |
if (@set > 1) |
|
509
|
0 |
0 |
unless defined $value |
|
516
|
0 |
0 |
unless defined $method |
|
517
|
0 |
0 |
if (not $method =~ /(rough|nsi)$/ and defined $self->cycles) |
|
525
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
527
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
563
|
1 |
4 |
unless (defined $self->{'_version6'}) |
|
565
|
0 |
1 |
if ($version =~ /^v6/) { } |