| line |
true |
false |
branch |
|
192
|
0 |
3 |
if $ENV{'MSAPROBSDIR'} |
|
210
|
0 |
0 |
unless $exe = $self->executable |
|
214
|
0 |
0 |
if $version = $1 |
|
239
|
1 |
0 |
unless $arg =~ /^-/ |
|
241
|
0 |
1 |
unless $Bio::Tools::Run::Alignment::MSAProbs::OK_FIELD{$field} |
|
303
|
0 |
0 |
if (defined $input) { } |
|
|
0 |
0 |
elsif (defined $self->infile) { } |
|
310
|
0 |
0 |
unless ($infilename) |
|
333
|
0 |
0 |
if (defined $value) |
|
529
|
0 |
0 |
unless (-s $outfile) |
|
534
|
0 |
0 |
if ($self->clustalw) |
|
564
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
566
|
0 |
0 |
unless -s $input and -r $input |
|
569
|
0 |
0 |
unless open IN, $input |
|
572
|
0 |
0 |
unless $header =~ /^\s+$/ |
|
574
|
0 |
0 |
unless $header =~ /^>\s*\S+/ |
|
587
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
609
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
611
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
617
|
0 |
0 |
if ($string =~ tr/\-.~//) |
|
650
|
0 |
0 |
unless (defined $self->outfile) |
|
659
|
0 |
0 |
unless defined $value |
|
668
|
0 |
0 |
unless $value |
|
676
|
0 |
0 |
if ($self->clustalw or not $self->outfile) { } |
|
684
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
685
|
0 |
0 |
if $self->verbose > 0 |
|
687
|
0 |
0 |
if $self->quiet and $self->verbose < 1 |
|
706
|
0 |
0 |
if @_ |
|
722
|
0 |
0 |
unless $firstline =~ /^\s*$/ |
|
733
|
0 |
0 |
if -s $outfile |