| line |
true |
false |
branch |
|
207
|
6 |
14989 |
if (defined $id and defined $given_id) |
|
208
|
0 |
6 |
if ($id ne $given_id) |
|
212
|
11740 |
3255 |
if (defined $given_id) |
|
215
|
13980 |
1015 |
if defined $id |
|
216
|
651 |
14344 |
if $acc |
|
217
|
229 |
14766 |
if defined $pid |
|
220
|
11775 |
3220 |
if $alphabet |
|
226
|
1 |
14994 |
if ($ref_to_seq) { } |
|
229
|
14268 |
726 |
if (defined $seq) |
|
235
|
916 |
14077 |
if $desc |
|
236
|
27 |
14966 |
if $description |
|
237
|
491 |
14502 |
if $ns |
|
238
|
84 |
14909 |
if $auth |
|
241
|
288 |
14705 |
if defined $v |
|
242
|
0 |
14993 |
if defined $oid |
|
243
|
18 |
14975 |
if defined $is_circular |
|
267
|
141004 |
27452 |
if (scalar @args == 0) |
|
272
|
27452 |
0 |
if (@args) |
|
286
|
27281 |
172 |
if (not $self->{'_direct'} and defined $$seq_str_ref) |
|
295
|
12798 |
14652 |
if $is_changed_seq |
|
296
|
27448 |
2 |
unless exists $self->{'_freeze_length'} |
|
302
|
18 |
27432 |
if ($alphabet) { } |
|
|
15780 |
11652 |
elsif ($is_changed_seq or not defined $self->alphabet) { } |
|
335
|
8 |
23090 |
if (defined $seqstr and not $seqstr =~ /^[$MATCHPATTERN]*$/) |
|
337
|
3 |
5 |
if ($throw) |
|
380
|
2 |
10037 |
if (defined $replace) |
|
381
|
1 |
1 |
unless $self->validate_seq($replace) |
|
385
|
52 |
9986 |
if (ref $start and $start->isa('Bio::LocationI')) { } |
|
|
9986 |
0 |
elsif (defined $start and defined $end) { } |
|
392
|
44 |
8 |
if ($loc->isa('Bio::Location::SplitLocationI')) |
|
395
|
18 |
26 |
defined $loc->guide_strand ? : |
|
396
|
9 |
35 |
$guide_strand == -1 ? : |
|
401
|
9 |
43 |
$order == -1 ? : |
|
407
|
1 |
119 |
if $nogap |
|
411
|
101 |
19 |
defined $subloc->strand ? : |
|
412
|
59 |
61 |
if ($strand < 0) |
|
419
|
0 |
9986 |
if ($start > $end) |
|
423
|
0 |
9986 |
if ($start <= 0) |
|
431
|
1 |
9985 |
if (defined $replace) { } |
|
438
|
1 |
9985 |
if ($end > $self->length) |
|
439
|
1 |
0 |
if ($self->is_circular) { } |
|
444
|
0 |
1 |
if (defined $replace) { } |
|
457
|
3 |
9983 |
if $nogap |
|
496
|
5 |
30689 |
if (defined $val) |
|
498
|
1 |
4 |
if ($len and $len != $val) |
|
534
|
14090 |
9770 |
if (defined $value) |
|
566
|
654 |
246 |
if (defined $acc) { } |
|
570
|
38 |
208 |
unless defined $acc |
|
595
|
447 |
58 |
if (@_) |
|
598
|
21 |
484 |
unless (defined $self->{'primary_id'}) |
|
624
|
27920 |
26972 |
if (defined $value) |
|
626
|
0 |
27920 |
unless ($valid_type{$value}) |
|
653
|
1257 |
454 |
if @_ |
|
704
|
26 |
143362 |
if @_ |
|
745
|
292 |
3290 |
if (defined $value) |
|
766
|
86 |
5 |
if (defined $value) |
|
787
|
493 |
34 |
if (defined $value) |
|
903
|
15853 |
2 |
if $alphabet |
|
912
|
15845 |
3007 |
unless defined $nowarnonempty |
|
920
|
2 |
18850 |
if ($total == 0) |
|
921
|
1 |
1 |
unless ($nowarnonempty) |
|
928
|
18850 |
2 |
unless (defined $alphabet) |
|
929
|
1762 |
17088 |
if ($str =~ /[EFIJLOPQXZ]/i) { } |
|
940
|
16081 |
1007 |
if ($str =~ tr/ACGKMNS-UWacgkmns-uw// / $total > 0.7) { } |
|
941
|
53 |
16028 |
if ($str =~ /U/i) { } |