| line |
true |
false |
branch |
|
238
|
4 |
0 |
if $seq |
|
241
|
1 |
3 |
$enzymes ? : |
|
277
|
6 |
10 |
if (@_) |
|
279
|
0 |
6 |
unless $seq->isa('Bio::PrimarySeqI') |
|
281
|
0 |
6 |
unless $seq->alphabet eq 'dna' |
|
310
|
2 |
0 |
if (@_) |
|
312
|
2 |
0 |
unless $self->{'_enzymes'} |
|
365
|
0 |
10 |
unless $self->seq |
|
368
|
3 |
7 |
if ($opt and uc $opt eq 'MULTIPLE') { } |
|
369
|
0 |
3 |
unless $ec |
|
424
|
0 |
8 |
unless $self->{'_cut'} |
|
425
|
0 |
8 |
unless $enz |
|
429
|
8 |
0 |
defined $self->{'_cut_positions'}{$enz} ? : |
|
452
|
3 |
15 |
unless $self->{'_cut'} |
|
453
|
0 |
18 |
unless $enz |
|
515
|
1 |
20 |
unless $self->{'_cut'} |
|
516
|
0 |
21 |
unless $enz |
|
525
|
13 |
8 |
if (ref $enz eq '' and exists $self->{'_cut_positions'}{$enz}) { } |
|
|
5 |
3 |
elsif ($enz->isa('Bio::Restriction::EnzymeI')) { } |
|
|
2 |
1 |
elsif ($enz->isa('Bio::Restriction::EnzymeCollection')) { } |
|
534
|
4 |
17 |
unless (defined $cut_positions[0]) |
|
545
|
4 |
0 |
defined $self->{'_frag_map_list'}{$enz} ? : |
|
551
|
50 |
22 |
if $i != $cuts[$#cuts] |
|
556
|
1 |
66 |
unless $stop |
|
562
|
0 |
17 |
if ($start > $stop) { } |
|
571
|
6 |
11 |
if ($self->{'_seq'}->is_circular) |
|
589
|
17 |
0 |
defined $self->{'_frag_map_list'}{$enz} ? : |
|
620
|
0 |
3 |
unless $enz |
|
623
|
1 |
2 |
if (&blessed($enz)) |
|
624
|
0 |
1 |
unless $enz->isa('Bio::Restriction::EnzymeI') |
|
628
|
0 |
3 |
unless $self->{'_cut'} |
|
632
|
0 |
9 |
$kb ? : |
|
637
|
0 |
3 |
$kb ? : |
|
638
|
1 |
2 |
if ($self->{'_seq'}->is_circular) |
|
643
|
0 |
3 |
$sort ? : |
|
666
|
0 |
4 |
unless defined $enz |
|
668
|
0 |
4 |
unless $self->{'_cut'} |
|
702
|
1 |
4 |
unless $self->{'_cut'} |
|
705
|
4 |
1 |
if (defined $a) { } |
|
706
|
0 |
4 |
unless $a =~ /^[+]?\d+$/ |
|
712
|
0 |
5 |
if $start > $self->{'maximum_cuts'} |
|
714
|
0 |
5 |
if (defined $z) { } |
|
|
4 |
1 |
elsif (defined $a) { } |
|
715
|
0 |
0 |
unless $z =~ /^[+]?\d+$/ and $z >= $a |
|
724
|
0 |
5 |
if $end > $self->{'maximum_cuts'} |
|
728
|
0 |
5 |
unless $self->{'maximum_cuts'} |
|
732
|
8 |
5 |
if defined $self->{'_number_of_cuts_by_cuts'}{$i} |
|
807
|
58 |
9517 |
if $enz->can('others') |
|
821
|
4286 |
5355 |
if ($self->{'_seq'}->is_circular) |
|
827
|
868 |
8773 |
unless ($enzyme->is_symmetric) |
|
834
|
432 |
436 |
if ($self->{'_seq'}->is_circular) |
|
841
|
1717 |
7858 |
if (defined $all_cuts[0]) { } |
|
847
|
565 |
2071 |
if $i != ${$self->{'_cut_positions'}{$enz->name};}[$#{$self->{'_cut_positions'}{$enz->name};}] |
|
866
|
24 |
9551 |
if ($number_of_cuts > $self->{'maximum_cuts'}) |
|
890
|
0 |
0 |
$comp ? : |
|
892
|
0 |
0 |
unless defined $site |
|
909
|
0 |
0 |
if ($site <= 0) { } |
|
|
0 |
0 |
elsif ($site >= $enz->seq->length) { } |
|
920
|
0 |
0 |
if ($enz->is_ambiguous) |
|
964
|
0 |
0 |
if ($new_left_cut == 0) { } |
|
|
0 |
0 |
elsif ($new_left_cut == $enz->seq->length) { } |
|
977
|
0 |
0 |
if ($enz->is_ambiguous) { } |
|
986
|
0 |
0 |
if $self->{'_seq'}->is_circular |
|
1027
|
0 |
0 |
if ($#cuts) { } |
|
1031
|
0 |
0 |
if ($i == 0) { } |
|
1085
|
0 |
0 |
$comp ? : |
|
1113
|
0 |
0 |
$comp ? : |
|
1114
|
0 |
0 |
if ($beforeseq eq '.') |
|
1115
|
0 |
0 |
if ($afterseq eq '.') |
|
1119
|
0 |
0 |
if $index_posn == -1 |
|
1156
|
0 |
15481 |
unless $_ |
|
|
298 |
14951 |
$enz->can('others') ? : |
|
1160
|
1370 |
14111 |
$comp ? : |
|
1163
|
5810 |
9671 |
if ($recog =~ /[^\w]/) { } |
|
1167
|
864 |
4946 |
unless ($enz->is_palindromic) |
|
1171
|
429 |
435 |
$comp ? : |
|
1184
|
1943 |
7728 |
unless ($enz->is_palindromic) |
|
1186
|
939 |
1004 |
$comp ? : |
|
1212
|
0 |
3 |
unless $self->{'_cut'} |
|
1219
|
15 |
0 |
if defined $self->{'_cut_positions'}{$enz->name} |
|
1228
|
0 |
3 |
if ($number_of_cuts > $self->{'maximum_cuts'}) |
|
1247
|
4718 |
0 |
length $target > 20 ? : |
|
1258
|
0 |
4718 |
unless $cut_positions |
|
1267
|
2 |
273 |
if ($cut == length $last) { } |
|
|
150 |
123 |
elsif ($cut < length $last) { } |