| line |
true |
false |
branch |
|
156
|
0 |
1 |
if $self->msf |
|
157
|
0 |
1 |
if $self->clw or $self->clwstrict |
|
159
|
0 |
1 |
if (defined $self->out) |
|
206
|
0 |
0 |
if (defined $value) |
|
226
|
0 |
0 |
unless $exe = $self->executable |
|
277
|
0 |
0 |
if (defined $input) { } |
|
|
0 |
0 |
elsif (defined $self->in) { } |
|
286
|
0 |
0 |
unless ($infilename) |
|
320
|
0 |
0 |
if ($self->version ne '3.52') |
|
324
|
0 |
0 |
if (defined $alnfilename) { } |
|
325
|
0 |
0 |
unless (ref $alnfilename) |
|
329
|
0 |
0 |
unless (-e $infilename) |
|
332
|
0 |
0 |
unless open IN, $infilename |
|
335
|
0 |
0 |
unless $header =~ /^\s+$/ |
|
338
|
0 |
0 |
unless ($header =~ /^>\s*\S+/) |
|
347
|
0 |
0 |
unless ($infilename) |
|
351
|
0 |
0 |
if (defined $seqsfilename) { } |
|
352
|
0 |
0 |
unless (ref $seqsfilename) |
|
356
|
0 |
0 |
unless (-e $infilename) |
|
359
|
0 |
0 |
unless open IN, $infilename |
|
362
|
0 |
0 |
unless $header =~ /^\s+$/ |
|
365
|
0 |
0 |
unless ($header =~ /^>\s*\S+/) |
|
374
|
0 |
0 |
unless ($infilename) |
|
398
|
1 |
0 |
if @_ |
|
419
|
0 |
0 |
if ($self->{'_profile'}) { } |
|
432
|
0 |
0 |
if (not -e $outfile or -z $outfile) |
|
459
|
0 |
0 |
if (not ref $input) { } |
|
|
0 |
0 |
elsif (ref($input) =~ /ARRAY/i) { } |
|
463
|
0 |
0 |
unless (-e $input) |
|
466
|
0 |
0 |
unless open IN, $infilename |
|
469
|
0 |
0 |
unless $header =~ /^\s+$/ |
|
472
|
0 |
0 |
unless ($header =~ /^>\s*\S+/) |
|
482
|
0 |
0 |
if (not ref $input->[0]) { } |
|
|
0 |
0 |
elsif ($input->[0]->isa('Bio::PrimarySeqI')) { } |
|
495
|
0 |
0 |
unless ref $seq and $seq->isa('Bio::PrimarySeqI') |
|
497
|
0 |
0 |
if (not defined $seq->display_id or $seq->display_id =~ /^\s+$/) |
|
542
|
0 |
0 |
unless defined $value |
|
549
|
0 |
0 |
unless $value |
|
556
|
0 |
0 |
unless ($self->outfile_name) |
|
564
|
0 |
0 |
if ($self->quiet or $self->verbose < 0) |
|
565
|
0 |
0 |
$^O =~ /mswin/i ? : |