| 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
|
|
297
|
0 |
0 |
if (ref $$self{$key} eq 'ARRAY') { }
|
|
|
0 |
0 |
elsif (ref $$self{$key} eq 'HASH') { }
|
|
351
|
0 |
0 |
if ($$self{'class'} eq 'IIP') { }
|
|
|
0 |
0 |
elsif ($$self{'class'} eq 'IIA') { }
|
|
353
|
0 |
0 |
if $$self{'cutseq'} =~ /$IIPreg/
|
|
354
|
0 |
0 |
if $rig < $lef
|
|
360
|
0 |
0 |
if $$self{'cutseq'} =~ /$IIAreg/
|
|
361
|
0 |
0 |
if $rig < $lef
|
|
362
|
0 |
0 |
if ($strand == 1) { }
|
|
371
|
0 |
0 |
$strand == 1 ? :
|
|
390
|
0 |
0 |
$$self{'staract'} ? :
|
|
392
|
0 |
0 |
if $$self{'methcpg'} eq 'blocked'
|
|
393
|
0 |
0 |
if $$self{'methdam'} eq 'blocked'
|
|
394
|
0 |
0 |
if $$self{'methdcm'} eq 'blocked'
|
|
395
|
0 |
0 |
if $$self{'methcpg'} eq 'inhibited'
|
|
396
|
0 |
0 |
if $$self{'methdam'} eq 'inhibited'
|
|
397
|
0 |
0 |
if $$self{'methdcm'} eq 'inhibited'
|
|
401
|
0 |
0 |
if $$self{'buffers'}{$_}
|
|
405
|
0 |
0 |
$$self{'tempin'} ? :
|
|
409
|
0 |
0 |
if $$self{'start'}
|
|
429
|
0 |
0 |
unless $buddy->isa('Bio::GeneDesign::RestrictionEnzyme')
|
|
439
|
0 |
0 |
if ($skey eq 'Other' and $sval and $bval and "$sval" eq "$bval") { }
|
|
|
0 |
0 |
elsif ($sval and $bval and "$sval" == 100 and "$bval" == 100) { }
|
|
448
|
0 |
0 |
$bool ? :
|
|
461
|
0 |
0 |
unless $buddy->isa('Bio::GeneDesign::RestrictionEnzyme')
|
|
472
|
0 |
0 |
if ($skey eq 'Other' and $sval and $bval and $sval == $bval) { }
|
|
|
0 |
0 |
elsif ($sval and $bval and $sval >= $level and $bval >= $level) { }
|
|
481
|
0 |
0 |
if $answers{$b} <=> $answers{$a}
|
|
482
|
0 |
0 |
scalar @keys ? :
|
|
509
|
0 |
0 |
$jad > 0 ? :
|
|
534
|
0 |
0 |
unless $req
|
|
539
|
0 |
0 |
if ($regex =~ /\[ X \]/x)
|
|
545
|
0 |
0 |
if $req == 1 and $$self{'recseq'} =~ /$regex/
|
|
546
|
0 |
0 |
if $req == 0 and not $$self{'recseq'} =~ /$regex/
|
|
564
|
0 |
0 |
if $$self{'score'} > $score
|
|
584
|
0 |
0 |
unless (exists $RE_vendors{$vend})
|
|
589
|
0 |
0 |
if exists $$self{'vendors'}{$vend}
|
|
591
|
0 |
0 |
$flag == 0 ? :
|
|
613
|
0 |
0 |
if not exists $$rebuff{$buff} or $$rebuff{$buff} < $val
|
|
636
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent')
|
|
644
|
0 |
0 |
unless exists $sensehsh{$$self{'methdcm'}}
|
|
665
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent')
|
|
673
|
0 |
0 |
unless exists $sensehsh{$$self{'methdam'}}
|
|
694
|
0 |
0 |
if ($sense ne 'blocked' and $sense ne 'inhibited' and $sense ne 'indifferent')
|
|
702
|
0 |
0 |
unless exists $sensehsh{$$self{'methcpg'}}
|
|
719
|
0 |
0 |
unless $star
|
|
720
|
0 |
0 |
if $star and not $$self{'staract'} or not $star and $$self{'staract'}
|
|
740
|
0 |
0 |
if (not $temp =~ /\d/x or $temp <= 0)
|
|
746
|
0 |
0 |
unless exists $temps{$$self{'temp'}}
|
|
763
|
0 |
0 |
if (not $temp =~ /\d/x or $temp <= 0) { }
|
|
769
|
0 |
0 |
if $$self{'tempin'} > $temp
|
|
788
|
0 |
0 |
if ($ambig ne 'nonNonly' and $ambig ne 'ATCGonly') { }
|
|
795
|
0 |
0 |
if $ambig eq 'nonNonly'
|
|
796
|
0 |
0 |
if $ambig eq 'ATCGonly'
|
|
797
|
0 |
0 |
unless $$self{'recseq'} =~ /$ambregex/
|
|
818
|
0 |
0 |
if ($len =~ /\D/x or $len <= 0)
|
|
825
|
0 |
0 |
unless exists $lens{length $$self{'recseq'}}
|
|
848
|
0 |
0 |
if ($pal ne 'pal' and $pal ne 'pnon' and $pal ne 'nonpal')
|
|
855
|
0 |
0 |
unless exists $pals{$$self{'palindromy'}}
|
|
879
|
0 |
0 |
if ($stick ne '5' and $stick ne '3' and $stick ne '1' and $stick ne 'b')
|
|
886
|
0 |
0 |
if $$self{'onebpoverhang'} and not exists $sticks{1}
|
|
889
|
0 |
0 |
unless exists $sticks{$type}
|
|
931
|
0 |
0 |
if (defined $value)
|
|
951
|
0 |
0 |
if (defined $value)
|
|
1238
|
768 |
0 |
if (defined $value)
|
|
1240
|
0 |
768 |
unless ref $value eq 'ARRAY'
|
|
1286
|
0 |
0 |
if (defined $value)
|