| line |
true |
false |
branch |
|
203
|
1 |
0 |
unless $self->informat |
|
204
|
1 |
0 |
unless $self->_READMETHOD |
|
225
|
0 |
0 |
unless $self->can($program) |
|
245
|
0 |
0 |
unless (defined $self->o) |
|
248
|
0 |
0 |
unless ($self->outformat) |
|
272
|
0 |
0 |
unless (defined $self->hmm) |
|
293
|
0 |
0 |
if $hmm |
|
294
|
0 |
0 |
unless $self->hmm |
|
312
|
0 |
0 |
if $hmm |
|
313
|
0 |
0 |
unless $self->hmm |
|
315
|
0 |
0 |
unless (defined $self->o) |
|
368
|
0 |
0 |
unless @things |
|
371
|
0 |
0 |
if (ref $things[0] and $things[0]->isa('Bio::PrimarySeqI')) { } |
|
|
0 |
0 |
elsif (ref $things[0] and $things[0]->isa('Bio::Align::AlignI')) { } |
|
|
0 |
0 |
elsif (-e $things[0]) { } |
|
401
|
0 |
0 |
if ($file =~ / /) |
|
407
|
0 |
0 |
if ($str =~ / /) |
|
412
|
0 |
0 |
if $file |
|
419
|
0 |
0 |
if ($progname =~ /align|build|emit/) { } |
|
|
0 |
0 |
elsif ($progname =~ /pfam|search/i) { } |
|
421
|
0 |
0 |
if ($outfile or $progname eq 'hmmbuild') { } |
|
422
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
423
|
0 |
0 |
if $self->quiet |
|
425
|
0 |
0 |
if ($progname eq 'hmmbuild') { } |
|
427
|
0 |
0 |
$status ? : |
|
430
|
0 |
0 |
if system $str |
|
435
|
0 |
0 |
unless open my $fh, "$str |" |
|
440
|
0 |
0 |
unless open my $fh, "$str |" |
|
447
|
0 |
0 |
if ($progname eq 'hmmalign') { } |
|
|
0 |
0 |
elsif ($progname eq 'hmmemit') { } |
|
|
0 |
0 |
elsif ($progname =~ /calibrate/) { } |
|
458
|
0 |
0 |
$^O =~ /mswin/i ? : |
|
459
|
0 |
0 |
if $self->quiet |
|
461
|
0 |
0 |
$status ? : |
|
481
|
0 |
0 |
if (/align/) |
|
484
|
0 |
0 |
if (/build/) |
|
487
|
0 |
0 |
if (/calibrate/) |
|
490
|
0 |
0 |
if (/emit/) |
|
493
|
0 |
0 |
if (/pfam/) |
|
496
|
0 |
0 |
if (/search/) |
|
507
|
0 |
0 |
if ($hmm =~ / /) |
|
527
|
1 |
6 |
if (@_) |
|
547
|
0 |
3 |
if $ENV{'HMMERDIR'} |