| line |
true |
false |
branch |
|
40
|
0 |
61 |
if (scalar @_ == 1) { }
|
|
41
|
0 |
0 |
unless ref $_[0] eq 'HASH'
|
|
49
|
4 |
57 |
if exists $a{'delim'} and not defined $a{'delim'}
|
|
51
|
4 |
57 |
if exists $a{'desc'} and not defined $a{'desc'}
|
|
67
|
1 |
0 |
if (defined $str and CORE::length $str > 0)
|
|
92
|
55 |
8 |
if ref $seq eq 'ARRAY'
|
|
159
|
28 |
192 |
$self->desc ? :
|
|
171
|
0 |
1 |
$self->desc ? :
|
|
204
|
0 |
1 |
if ($str =~ /[EFIJLOPQXZ]/i) { }
|
|
214
|
1 |
0 |
if ($str =~ tr/ACGNTUacgntu// / $total > 0.7) { }
|
|
215
|
0 |
1 |
if ($str =~ /U/i) { }
|
|
243
|
0 |
0 |
if &blessed($range) and $range->isa('Bio::Gonzales::Feat')
|
|
253
|
0 |
0 |
if ($c->{'attach_details'})
|
|
256
|
0 |
0 |
$strand > 0 ? :
|
|
|
0 |
0 |
$strand < 0 ? :
|
|
257
|
0 |
0 |
if @rest > 0
|
|
260
|
0 |
0 |
unless ($keep_original_id)
|
|
262
|
0 |
0 |
$strand > 0 ? :
|
|
|
0 |
0 |
$strand < 0 ? :
|
|
|
0 |
0 |
if defined $strand
|
|
264
|
0 |
0 |
if @rest > 0
|
|
287
|
0 |
0 |
if defined $c and ref $c ne 'HASH'
|
|
290
|
0 |
0 |
if ($c->{'relaxed_range'})
|
|
298
|
0 |
0 |
unless $b and $e
|
|
306
|
0 |
0 |
if $b eq '^'
|
|
307
|
0 |
0 |
if $b eq '$'
|
|
309
|
0 |
0 |
if $e eq '^'
|
|
310
|
0 |
0 |
if $e eq '$'
|
|
312
|
0 |
0 |
if $b > $e and $b > 0 and $e > 0
|
|
315
|
0 |
0 |
if ($b < 0)
|
|
316
|
0 |
0 |
$c->{'wrap'} ? :
|
|
318
|
0 |
0 |
if ($e < 0)
|
|
319
|
0 |
0 |
$c->{'wrap'} ? :
|
|
327
|
0 |
0 |
if ($strand and $strand < 0)
|
|
328
|
0 |
0 |
if ($c->{'relaxed_revcom'}) { }
|
|
331
|
0 |
0 |
if $seq =~ /[^AGCTN]/i
|
|
338
|
0 |
0 |
wantarray ? :
|
|
345
|
0 |
1 |
if ($alphabet eq 'protein')
|
|
348
|
0 |
1 |
if ($alphabet ne 'dna' and $alphabet ne 'rna')
|
|
354
|
0 |
1 |
if ($alphabet eq 'rna')
|
|
363
|
0 |
1 |
if ($alphabet eq 'rna')
|