| line |
true |
false |
branch |
|
353
|
0 |
0 |
unless $name || $enzyme and $site || $recog || $seq |
|
366
|
7 |
10156 |
if $enzyme |
|
367
|
10156 |
7 |
if $name |
|
377
|
2531 |
7632 |
if ($cut and $cut <= length $site) |
|
381
|
10163 |
0 |
if ($site) { } |
|
385
|
0 |
0 |
if $seq |
|
388
|
7495 |
2667 |
if ($recog) { } |
|
392
|
0 |
2667 |
if $seq |
|
393
|
2667 |
0 |
if $site |
|
400
|
7494 |
2668 |
if ($xln_sub) |
|
401
|
0 |
7494 |
unless ref $xln_sub eq 'CODE' |
|
413
|
2664 |
7498 |
if (defined $cut) { } |
|
|
457 |
7041 |
elsif (defined $pc_cut) { } |
|
414
|
0 |
2664 |
$xln_sub ? : |
|
417
|
456 |
1 |
$xln_sub ? : |
|
420
|
4 |
10158 |
if (defined $complementary_cut) { } |
|
|
457 |
9701 |
elsif (defined $pc_comp_cut) { } |
|
421
|
0 |
4 |
$xln_sub ? : |
|
424
|
456 |
1 |
$xln_sub ? : |
|
427
|
7207 |
2955 |
if $is_prototype |
|
428
|
9 |
10153 |
if $prototype |
|
429
|
7453 |
2709 |
if $isoschizomers |
|
430
|
0 |
10162 |
if $meth |
|
431
|
0 |
10162 |
if $microbe |
|
432
|
7453 |
2709 |
if $source |
|
433
|
7469 |
2693 |
if $vendors |
|
434
|
7469 |
2693 |
if $references |
|
435
|
0 |
10162 |
if $neo |
|
438
|
49 |
10113 |
if (defined $precut) |
|
442
|
49 |
0 |
$xln_sub ? : |
|
443
|
49 |
0 |
$xln_sub ? : |
|
476
|
10164 |
59883 |
if ($name) |
|
482
|
0 |
10164 |
if ($name =~ /(1+)$/) |
|
490
|
0 |
10164 |
unless ($name eq $old_name) |
|
532
|
10163 |
6 |
if ($site) |
|
534
|
1 |
10162 |
if $site =~ /[^ATGCMRWSYKVHDBN\^]/i |
|
545
|
4945 |
5217 |
if defined $first |
|
557
|
4945 |
5217 |
if (defined $first) |
|
590
|
4950 |
10162 |
if $self->{'_revcom_site'} |
|
594
|
9266 |
896 |
if ($self->is_palindromic) |
|
600
|
0 |
896 |
if $site =~ /[^ATGCMRWSYKVHDBN\^]/i |
|
603
|
16 |
880 |
if ($site =~ /\^/) { } |
|
678
|
8117 |
16177 |
if (defined $value) |
|
679
|
0 |
8117 |
unless $value =~ /[-+]?\d+/ |
|
684
|
5174 |
2943 |
if (not $self->{'_site'} =~ /\^/ and $value <= length $self->{'_site'}) |
|
691
|
7697 |
420 |
if $self->{'_site'} =~ /\^/ and $self->type eq 'II' |
|
732
|
13152 |
3279 |
if (defined $num) |
|
733
|
0 |
13152 |
unless $num =~ /[-+]?\d+/ |
|
788
|
0 |
7707 |
if ($value) |
|
791
|
0 |
0 |
unless $Bio::Restriction::Enzyme::TYPE{$value} |
|
799
|
0 |
7707 |
if $self->{'_seq'}->seq =~ /N*[^N]+N{6,8}[^N]/ and abs $self->cut > 50 |
|
802
|
10 |
7697 |
if $self->{'_seq'}->length == 3 |
|
804
|
0 |
5280 |
if length $self->string == 5 || length $self->string == 6 and not $self->palindromic and abs $self->cut > 20 |
|
861
|
15481 |
10162 |
unless $recog |
|
863
|
3887 |
6275 |
if $recog =~ /[^ATGC]/ |
|
883
|
2807 |
10162 |
unless ($recog) |
|
884
|
0 |
2807 |
unless $self->{'revcom_recog'} |
|
888
|
3887 |
6275 |
if $recog =~ /[^ATGC]/ |
|
996
|
26661 |
10162 |
if defined $self->{'_palindromic'} |
|
997
|
9266 |
896 |
if ($self->string eq $self->revcom) |
|
1026
|
4286 |
5355 |
if defined $self->{'_symmetric'} |
|
1027
|
4892 |
463 |
if ($self->is_palindromic) |
|
1030
|
27 |
436 |
if ($self->cut == length($self->string) - $self->complementary_cut) |
|
1067
|
32 |
513 |
unless ($self->{'_cut'} and $self->{'_rc_cut'}) |
|
1070
|
287 |
226 |
if ($self->{'_cut'} < $self->{'_rc_cut'}) { } |
|
|
116 |
110 |
elsif ($self->{'_cut'} == $self->{'_rc_cut'}) { } |
|
|
110 |
0 |
elsif ($self->{'_cut'} > $self->{'_rc_cut'}) { } |
|
1125
|
0 |
5 |
if $self->overhang eq 'blunt' |
|
1127
|
0 |
5 |
unless ($self->{'_cut'} and $self->{'_rc_cut'}) |
|
1131
|
0 |
0 |
unless ($self->{'_cut'} and $self->{'_rc_cut'}) |
|
1139
|
0 |
5 |
if ($self->{'_cut'} < 0 or $self->{'_rc_cut'} < 0 or $self->{'_cut'} > $self->seq->length or $self->{'_rc_cut'} > $self->seq->length) |
|
1145
|
0 |
0 |
if ($self->{'_cut'} > $self->{'_rc_cut'}) { } |
|
|
0 |
0 |
elsif ($self->{'_cut'} < $self->{'_rc_cut'}) { } |
|
1154
|
0 |
5 |
if ($self->{'_cut'} > $self->{'_rc_cut'}) { } |
|
|
5 |
0 |
elsif ($self->{'_cut'} < $self->{'_rc_cut'}) { } |
|
1185
|
0 |
1 |
unless $re->isa('Bio::Restriction::Enzyme') |
|
1191
|
0 |
1 |
if $self->overhang_seq =~ /N/ or $re->overhang_seq =~ /N/ |
|
1194
|
1 |
0 |
if $self->overhang_seq eq $re->overhang_seq and $self->overhang eq $re->overhang |
|
1213
|
0 |
1 |
$self->string =~ /[^AGCT]/ ? : |
|
1238
|
7210 |
3 |
if (defined $value) |
|
1241
|
2 |
1 |
if (defined $self->{'_is_prototype'}) { } |
|
1265
|
0 |
0 |
if (defined $value) |
|
1268
|
0 |
0 |
if (defined $self->{'_is_neoschizomer'}) { } |
|
1299
|
10 |
2 |
if @_ |
|
1300
|
10 |
2 |
if $self->{'_is_prototype'} |
|
1325
|
7454 |
2 |
if @_ |
|
1330
|
7456 |
0 |
if ($self->{'_isoschizomers'}) |
|
1429
|
1 |
1 |
if ($microbe) |
|
1451
|
7454 |
1 |
if ($source) |
|
1475
|
7470 |
2 |
if @_ |
|
1476
|
7472 |
0 |
if ($self->{'_vendors'}) |
|
1537
|
7470 |
2 |
if @_ |
|
1580
|
0 |
0 |
unless $@ |
|
1582
|
0 |
0 |
unless ($this) |
|
1585
|
0 |
0 |
if (not ref $self->{$k}) { } |
|
1595
|
0 |
0 |
if (not ref $this) { } |
|
|
0 |
0 |
elsif (ref $this eq 'ARRAY') { } |
|
|
0 |
0 |
elsif (ref $this eq 'HASH') { } |
|
1604
|
0 |
0 |
if $this->isa('Bio::Restriction::EnzymeI') |
|
1605
|
0 |
0 |
if $this->can('clone') |
|
1608
|
0 |
0 |
if (not ref $this->{$k}) { } |
|
1622
|
52 |
1449 |
unless (defined $this) |
|
1630
|
475 |
974 |
if (ref $_) |
|
1631
|
2 |
473 |
if $visited->{$this} |
|
1634
|
974 |
473 |
unless (ref $_) |
|
1639
|
108 |
365 |
if (ref($_) =~ /^Bio::/) |
|
1644
|
1088 |
108 |
defined $_->{$attr} ? : |
|
1648
|
311 |
54 |
if (ref $_ eq 'ARRAY') |
|
1652
|
309 |
0 |
defined $elt ? : |
|
1656
|
54 |
0 |
if (ref $_ eq 'HASH') |
|
1661
|
0 |
0 |
defined $_->{'key'} ? : |
|
1666
|
0 |
0 |
if (ref $_ eq 'SCALAR') |