| line |
true |
false |
branch |
|
116
|
0 |
768 |
if ($object) { } |
|
118
|
0 |
0 |
unless $object->isa('Bio::GeneDesign::RestrictionEnzyme') |
|
126
|
0 |
768 |
unless $id |
|
129
|
0 |
768 |
unless $cutseq |
|
145
|
567 |
201 |
if ($cutseq =~ /$IIPreg/) { } |
|
|
33 |
168 |
elsif ($cutseq =~ /$IIBreg/) { } |
|
|
168 |
0 |
elsif ($cutseq =~ /$IIAreg/) { } |
|
152
|
123 |
444 |
if ($lef == $rig) { } |
|
159
|
126 |
318 |
if $inlef > 0.5 * length($recseq) |
|
161
|
54 |
390 |
if ($mattersbit and $mattersbit =~ /$Bio::GeneDesign::RestrictionEnzyme::ambnt/ and length($mattersbit) % 2 == 0) { } |
|
|
384 |
6 |
elsif ($mattersbit and $mattersbit eq _complement($mattersbit, 1)) { } |
|
|
6 |
0 |
elsif ($mattersbit) { } |
|
198
|
438 |
330 |
if ($lef < $rig) { } |
|
|
195 |
135 |
elsif ($lef > $rig) { } |
|
|
135 |
0 |
elsif ($lef == $rig) { } |
|
214
|
60 |
708 |
if abs $lef - $rig == 1 |
|
217
|
765 |
3 |
if $temp |
|
218
|
630 |
138 |
if ($tempin) |
|
225
|
768 |
0 |
if $score |
|
228
|
177 |
591 |
if $staract |
|
230
|
54 |
714 |
if (exists $methtrans{$methdam}) { } |
|
239
|
105 |
663 |
if (exists $methtrans{$methdcm}) { } |
|
248
|
390 |
378 |
if (exists $methtrans{$methcpg}) { } |
|
257
|
765 |
3 |
if ($vendors) |
|
262
|
2991 |
0 |
if exists $RE_vendors{$v} |
|
263
|
0 |
2991 |
unless exists $RE_vendors{$v} |
|
268
|
768 |
0 |
if $buffers |
|
271
|
0 |
768 |
if $start |
|
273
|
0 |
768 |
if $exclude |
|
340
|
0 |
0 |
if ($self->{'class'} eq 'IIP') { } |
|
|
0 |
0 |
elsif ($self->{'class'} eq 'IIA') { } |
|
342
|
0 |
0 |
if $self->{'cutseq'} =~ /$IIPreg/ |
|
343
|
0 |
0 |
if $rig < $lef |
|
349
|
0 |
0 |
if $self->{'cutseq'} =~ /$IIAreg/ |
|
350
|
0 |
0 |
if $rig < $lef |
|
351
|
0 |
0 |
if ($strand == 1) { } |
|
360
|
0 |
0 |
$strand == 1 ? : |
|
379
|
0 |
0 |
$self->{'staract'} ? : |
|
381
|
0 |
0 |
if $self->{'methcpg'} eq 'blocked' |
|
382
|
0 |
0 |
if $self->{'methdam'} eq 'blocked' |
|
383
|
0 |
0 |
if $self->{'methdcm'} eq 'blocked' |
|
384
|
0 |
0 |
if $self->{'methcpg'} eq 'inhibited' |
|
385
|
0 |
0 |
if $self->{'methdam'} eq 'inhibited' |
|
386
|
0 |
0 |
if $self->{'methdcm'} eq 'inhibited' |
|
390
|
0 |
0 |
if $self->{'buffers'}{$_} |
|
394
|
0 |
0 |
$self->{'tempin'} ? : |
|
398
|
0 |
0 |
if $self->{'start'} |
|
418
|
0 |
0 |
unless $buddy->isa('Bio::GeneDesign::RestrictionEnzyme') |
|
428
|
0 |
0 |
if ($skey eq 'Other' and $sval and $bval and "$sval" eq "$bval") { } |
|
|
0 |
0 |
elsif ($sval and $bval and "$sval" == 100 and "$bval" == 100) { } |
|
437
|
0 |
0 |
$bool ? : |
|
450
|
0 |
0 |
unless $buddy->isa('Bio::GeneDesign::RestrictionEnzyme') |
|
461
|
0 |
0 |
if ($skey eq 'Other' and $sval and $bval and $sval == $bval) { } |
|
|
0 |
0 |
elsif ($sval and $bval and $sval >= $level and $bval >= $level) { } |
|
470
|
0 |
0 |
if $answers{$b} <=> $answers{$a} |
|
471
|
0 |
0 |
scalar @keys ? : |
|
498
|
0 |
0 |
$jad > 0 ? : |
|
523
|
0 |
0 |
unless $req |
|
528
|
0 |
0 |
if ($regex =~ /\[ X \]/x) |
|
534
|
0 |
0 |
if $req == 1 and $self->{'recseq'} =~ /$regex/ |
|
535
|
0 |
0 |
if $req == 0 and not $self->{'recseq'} =~ /$regex/ |
|
553
|
0 |
0 |
if $self->{'score'} > $score |
|
573
|
0 |
0 |
unless (exists $RE_vendors{$vend}) |
|
578
|
0 |
0 |
if exists $self->{'vendors'}{$vend} |
|
580
|
0 |
0 |
$flag == 0 ? : |
|
602
|
0 |
0 |
if not exists $rebuff->{$buff} or $rebuff->{$buff} < $val |
|
625
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent') |
|
633
|
0 |
0 |
unless exists $sensehsh{$self->{'methdcm'}} |
|
654
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent') |
|
662
|
0 |
0 |
unless exists $sensehsh{$self->{'methdam'}} |
|
683
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent') |
|
691
|
0 |
0 |
unless exists $sensehsh{$self->{'methcpg'}} |
|
708
|
0 |
0 |
unless $star |
|
709
|
0 |
0 |
if $star and not $self->{'staract'} or not $star and $self->{'staract'} |
|
729
|
0 |
0 |
if (not $temp =~ /\d/x or $temp <= 0) |
|
735
|
0 |
0 |
unless exists $temps{$self->{'temp'}} |
|
752
|
0 |
0 |
if (not $temp =~ /\d/x or $temp <= 0) { } |
|
758
|
0 |
0 |
if $self->{'tempin'} > $temp |
|
777
|
0 |
0 |
if ($ambig ne 'nonNonly' and $ambig ne 'ATCGonly') { } |
|
784
|
0 |
0 |
if $ambig eq 'nonNonly' |
|
785
|
0 |
0 |
if $ambig eq 'ATCGonly' |
|
786
|
0 |
0 |
unless $self->{'recseq'} =~ /$ambregex/ |
|
807
|
0 |
0 |
if ($len =~ /\D/x or $len <= 0) |
|
814
|
0 |
0 |
unless exists $lens{length $self->{'recseq'}} |
|
837
|
0 |
0 |
if ($pal ne 'pal' and $pal ne 'pnon' and $pal ne 'nonpal') |
|
844
|
0 |
0 |
unless exists $pals{$self->{'palindromy'}} |
|
868
|
0 |
0 |
if ($stick ne '5' and $stick ne '3' and $stick ne '1' and $stick ne 'b') |
|
875
|
0 |
0 |
if $self->{'onebpoverhang'} and not exists $sticks{'1'} |
|
878
|
0 |
0 |
unless exists $sticks{$type} |
|
920
|
0 |
0 |
if (defined $value) |
|
940
|
0 |
0 |
if (defined $value) |
|
1227
|
768 |
0 |
if (defined $value) |
|
1229
|
0 |
768 |
unless ref $value eq 'ARRAY' |
|
1275
|
0 |
0 |
if (defined $value) |