| line |
true |
false |
branch |
|
309
|
169 |
169 |
if ($class =~ /Bio::AlignIO::(\S+)/) { } |
|
319
|
8 |
161 |
unless ($format) |
|
320
|
8 |
0 |
if ($param{-'file'}) { } |
|
|
0 |
0 |
elsif ($param{-'fh'}) { } |
|
328
|
0 |
169 |
unless $format |
|
331
|
0 |
169 |
unless $class->_load_format_module($format) |
|
352
|
0 |
56 |
unless my $self = $class->new(@_) |
|
398
|
0 |
169 |
if defined $flat |
|
400
|
0 |
169 |
if defined $width |
|
424
|
0 |
169 |
if ($@) |
|
480
|
0 |
25 |
unless $_ = shift() |
|
481
|
2 |
23 |
if /\.aln$/i |
|
482
|
0 |
23 |
if /\.(water|needle)$/i |
|
483
|
1 |
22 |
if /\.metafasta$/ |
|
484
|
2 |
20 |
if /\.(fasta|fast|seq|fa|fsa|nt|aa)$/i |
|
485
|
2 |
18 |
if /\.maf/i |
|
486
|
1 |
17 |
if /\.(meg|mega)$/i |
|
487
|
0 |
17 |
if /\.meme$/i |
|
488
|
2 |
15 |
if /\.(msf|pileup|gcg)$/i |
|
489
|
1 |
14 |
if /\.(nexus|nex)$/i |
|
490
|
4 |
10 |
if /\.(pfam|pfm)$/i |
|
491
|
1 |
9 |
if /\.(phylip|phlp|phyl|phy|ph)$/i |
|
492
|
0 |
9 |
if /\.psi$/i |
|
493
|
0 |
9 |
if /\.stk$/i |
|
494
|
1 |
8 |
if /\.(selex|slx|selx|slex|sx)$/i |
|
495
|
0 |
8 |
if /\.xmfa$/i |
|
510
|
28 |
0 |
unless wantarray |
|
536
|
0 |
4 |
if @_ |
|
555
|
4 |
1181 |
if (defined $value) |
|
556
|
0 |
2 |
unless $value eq 'rna' or $value eq 'protein' or $value eq 'dna' |