| line |
true |
false |
branch |
|
387
|
419 |
422 |
if ($class =~ /Bio::SeqIO::(\S+)/) { } |
|
395
|
3 |
26 |
unless (defined $params{-'file'} or defined $params{-'fh'} or defined $params{-'string'}) |
|
399
|
1 |
2 |
if exists $params{'-file'} |
|
401
|
1 |
1 |
if exists $params{'-fh'} |
|
403
|
0 |
1 |
if exists $params{'-string'} |
|
409
|
27 |
393 |
unless ($format) |
|
410
|
24 |
3 |
if ($params{-'file'}) { } |
|
|
1 |
2 |
elsif ($params{-'fh'}) { } |
|
|
1 |
1 |
elsif ($params{-'string'}) { } |
|
425
|
2 |
417 |
unless $format |
|
429
|
55 |
362 |
if ($format =~ /-/) |
|
434
|
0 |
417 |
unless $class->_load_format_module($format) |
|
457
|
0 |
0 |
unless my $self = $class->new(@_) |
|
498
|
435 |
0 |
unless $locfact |
|
500
|
435 |
0 |
unless $objbuilder |
|
507
|
0 |
435 |
if $seqfact |
|
510
|
0 |
435 |
if $alphabet |
|
594
|
2 |
78 |
if (defined $value) |
|
596
|
2 |
0 |
unless ($valid_alphabet_cache{$value}) |
|
604
|
0 |
2 |
if ($@) |
|
634
|
0 |
417 |
if ($@) |
|
664
|
218 |
0 |
if $s1 and not $s1 =~ /-$/ and $s2 |
|
665
|
218 |
298 |
$s1 ? : |
|
|
516 |
0 |
$s2 ? : |
|
702
|
0 |
24 |
unless $_ = shift() |
|
704
|
0 |
24 |
if /\.ab[i1]$/i |
|
705
|
1 |
23 |
if /\.ace$/i |
|
706
|
0 |
23 |
if /\.alf$/i |
|
707
|
0 |
23 |
if /\.(bsm|bsml)$/i |
|
708
|
0 |
23 |
if /\.ctf$/i |
|
709
|
1 |
22 |
if /\.(embl|ebl|emb|dat)$/i |
|
710
|
0 |
22 |
if /\.asn$/i |
|
711
|
0 |
22 |
if /\.exp$/i |
|
712
|
7 |
15 |
if /\.(fasta|fast|fas|seq|fa|fsa|nt|aa|fna|faa)$/i |
|
713
|
2 |
13 |
if /\.fastq$/i |
|
714
|
1 |
12 |
if /\.gcg$/i |
|
715
|
4 |
8 |
if /\.(gb|gbank|genbank|gbk|gbs)$/i |
|
716
|
0 |
8 |
if /\.(phd|phred)$/i |
|
717
|
1 |
7 |
if /\.pir$/i |
|
718
|
0 |
7 |
if /\.pln$/i |
|
719
|
0 |
7 |
if /\.qual$/i |
|
720
|
0 |
7 |
if /\.txt$/i |
|
721
|
0 |
7 |
if /\.scf$/i |
|
725
|
0 |
7 |
if /\.(xdna|xdgn|xrna|xprt)$/i |
|
726
|
1 |
6 |
if /\.(swiss|sp)$/i |
|
727
|
0 |
6 |
if /\.ztr$/i |
|
745
|
0 |
0 |
unless wantarray |
|
770
|
412 |
1148 |
if (defined $obj) |
|
771
|
0 |
412 |
unless (ref $obj and $obj->isa('Bio::Factory::SequenceFactoryI')) |
|
776
|
410 |
0 |
if ($builder and $builder->can('sequence_factory') and not $builder->sequence_factory) |
|
820
|
435 |
617 |
if (defined $obj) |
|
821
|
0 |
435 |
unless (ref $obj and $obj->isa('Bio::Factory::ObjectBuilderI')) |
|
844
|
435 |
8980 |
if (defined $obj) |
|
845
|
0 |
435 |
unless (ref $obj and $obj->isa('Bio::Factory::LocationFactoryI')) |