Branch Coverage

blib/lib/Bio/GeneDesign.pm

Criterion	Covered	Total	%
branch	117	368	31.7

line	true	false	branch
63	0	9	unless substr($$self{'conf'}, -1, 1) eq '/'
66	9	0	unless substr($$self{'tmp_path'}, -1, 1) eq '/'
69	0	9	if ($$self{'graph'})
76	0	9	if ($$self{'EMBOSS'})
83	0	9	if ($self->BLAST)
91	0	9	if ($$self{'vmatch'})
323	0	4	unless $seq
326	1	3	$nnflag ? :
331	1	3	if ($nnflag)
378	0	4	unless $seq
417	0	2	unless $seq
459	0	6	unless $seq
464	2	4	if ($arrswit) { }
492	0	1	unless $seq
522	0	5	unless $seq
555	0	4	unless $seq
562	0	4	unless exists $ambtransswits{$frame}
591	0	1	unless $seq
633	0	2	unless $seq
636	0	2	unless $seek
645	0	2	if ($qref) { }
647	0	0	unless $seek->isa('Bio::Seq') or $seek->isa('Bio::SeqFeatureI') or $seek->isa('Bio::GeneDesign::RestrictionEnzyme')
652	0	0	if ($seek->isa('Bio::GeneDesign::RestrictionEnzyme')) { }
658	0	0	ref $seek->seq ? :
659	0	0	$revcom ? :
664	0	2	$revcom ? :
711	0	7	unless $orgname
714	0	7	if $table_path and not -e $table_path
717	0	7	unless ($table_path)
720	0	0	unless (-e $table_path)
773	0	7	unless $orgname
776	0	7	if $rscu_path and not -e $rscu_path
779	0	7	unless ($rscu_path)
782	0	0	unless (-e $rscu_path)
821	0	7	unless $orgname
865	0	3	unless $$self{'codontable'}
868	0	3	unless $input
877	0	3	if exists $$cod_count{'XXX'}
904	0	1	unless $$self{'codontable'}
907	0	1	unless $seqobjs
946	0	0	unless $$self{'codontable'}
949	0	0	unless $seqobjs
1001	0	0	unless $$self{'codontable'}
1004	0	0	unless $seqobjs
1007	0	0	unless ref $comments eq 'ARRAY'
1042	0	0	unless opendir my $ENZDIR, $epath
1047	0	0	if $name eq '.' or $name eq '..'
1090	0	3	if (not $set_name || $set_path) { }
	0	3	elsif ($set_name and not $set_path) { }
	3	0	elsif ($set_path) { }
1098	0	0	unless -e $set_path
1104	0	0	unless (exists $$self{'all_enzymes'}{$id})
1116	0	3	unless -e $set_path
1122	0	87	unless (exists $$self{'all_enzymes'}{$id})
1153	0	0	unless $enzes
1155	0	0	unless $$self{'enzyme_set'}
1160	0	0	if ($ref eq 'ARRAY') { }
1172	0	0	if ($eref)
1174	0	0	unless $enz->isa('Bio::GeneDesign::RestrictionEnzyme')
1180	0	0	if (exists $$self{'enzyme_set'}{$eid})
1216	0	0	unless $enzes
1218	0	0	unless $$self{'enzyme_set'}
1223	0	0	if ($ref eq 'ARRAY') { }
1233	0	0	unless $enz->isa('Bio::GeneDesign::RestrictionEnzyme')
1237	0	0	if exists $$self{'enzyme_set'}{$enz->id}
1253	0	1	unless $$self{'enzyme_set'}
1256	0	1	unless $seq
1288	0	2	unless $list
1298	10	0	if ($ref)
1300	0	10	unless $seq->isa('Bio::Seq') or $seq->isa('Bio::SeqFeatureI') or $seq->isa('Bio::GeneDesign::RestrictionEnzyme')
1306	0	10	ref $seq->seq ? :
1310	4	6	if ($pep) { }
1312	0	4	unless $$self{'codontable'}
1325	2	2	if ($esab ne $base and $lagcheck eq $esab)
1338	3	3	if ($esab ne $base)
1368	0	2	unless $seq
1371	0	2	unless $tree
1374	0	2	unless $tree->isa('Bio::GeneDesign::PrefixTree')
1395	0	3	unless $$self{'codontable'}
1398	0	3	unless $seq
1413	2	1	$re ? :
1426	0	1	unless $$self{'codontable'}
1429	0	1	unless $seq
1454	0	0	unless $$self{'codontable'}
1457	0	0	unless $codold
1460	0	0	unless $codnew
1477	0	9	unless $$self{'codontable'}
1480	0	9	unless $seq
1485	6	3	$frame ? :
1487	0	9	if abs $frame > 4 or abs $frame < 0
1491	6	3	if (ref $seq) { }
1494	0	6	$newobj->desc ? :
1520	0	20001	unless $$self{'codontable'}
1523	0	20001	unless $$self{'rscutable'}
1526	0	20001	unless $pep
1533	0	20001	if (scalar @baddies)
1546	20001	0	if (ref $pep) { }
1549	0	20001	$newobj->desc ? :
1575	0	20003	unless $$self{'codontable'}
1578	0	20003	unless $$self{'rscutable'}
1581	0	20003	unless $seq
1585	0	20003	unless $algorithm
1591	0	20003	unless length($str) % 3 == 0
1603	20003	0	if (ref $seq) { }
1606	0	20003	$newobj->desc ? :
1629	0	3	unless $$self{'codontable'}
1632	0	3	unless $$self{'rscutable'}
1635	0	3	unless $seq
1638	0	3	unless $rem
1645	3	0	if (ref $rem) { }
1647	2	1	if ($rem->isa('Bio::Seq') or $rem->isa('Bio::SeqFeatureI')) { }
	1	0	elsif ($rem->isa('Bio::GeneDesign::RestrictionEnzyme')) { }
1649	0	2	ref $rem->seq ? :
1676	3	0	if (ref $seq) { }
1679	0	3	$newobj->desc ? :
1702	0	0	unless $$self{'codontable'}
1705	0	0	unless $$self{'rscutable'}
1708	0	0	unless $seq
1733	0	0	unless $seq
1754	0	0	unless $seq
1772	0	0	unless $seqs
1790	0	0	unless $self->vmatch
1800	0	0	unless $seqobj
1803	0	0	unless $seqobj->isa('Bio::Seq')
1806	0	0	unless $seqobj->alphabet eq 'dna'
1809	0	0	unless $parent
1812	0	0	unless $parent->isa('Bio::Seq')
1815	0	0	unless $parent->alphabet eq 'dna'
1838	0	0	unless $self->BLAST
1848	0	0	unless $seqobjs
1851	0	0	unless ref $seqobjs eq 'ARRAY'
1856	0	0	unless $seqobj->isa('Bio::Seq')
1859	0	0	unless $seqobj->alphabet eq 'dna'
1863	0	0	unless $parent
1866	0	0	unless $parent->isa('Bio::Seq')
1869	0	0	unless $parent->alphabet eq 'dna'
1908	0	0	unless $chobj
1911	0	0	unless $chobj->isa('Bio::Seq')
1918	0	0	if $tarbblen < $minbblen or $tarbblen > $maxbblen
1922	0	0	if $maxbblen < $minbblen or $maxbblen < 0 or $minbblen < 0
1935	0	0	unless ($req)
1951	0	0	if ($e = 'Bio::GeneDesign::Exception::UnBBable'->caught)
1984	0	0	unless $bbobj
1987	0	0	unless $bbobj->isa('Bio::SeqFeatureI')
1997	0	0	if $olilenmax and $olilen and $olilenmax < $olilen
2008	0	0	unless ($req)
2023	0	0	if ($e = 'Bio::GeneDesign::Exception::UnOLable'->caught)
2038	0	0	unless $$self{'graph'}
2044	0	0	unless $$self{'codontable'}
2047	0	0	unless $$self{'rscutable'}
2050	0	0	unless $seqobjs
2053	0	0	unless ref $seqobjs eq 'ARRAY'
2058	0	0	unless $seqobj->isa('Bio::Seq')
2061	0	0	unless $seqobj->alphabet eq 'dna'
2082	0	0	unless $$self{'graph'}
2091	0	0	unless $seq1 and $seq2
2096	0	0	unless $seqobj->isa('Bio::Seq')
2099	0	0	unless $seqobj->alphabet eq 'dna'
2121	0	1	unless -e $path
2127	1	0	if substr($suffix, 0, 1) eq '.'
2128	0	1	if $suffix eq 'fa'
2150	0	0	$outpath ? :
2151	0	0	unless substr($outpath, -1, 1) =~ m[[ / ]]x
2152	0	0	unless -e $outpath
2154	0	0	$outformat ? :
2161	0	0	unless $outformat and $flag
2166	0	0	if ($outformat eq 'genbank')
2183	0	0	unless open my $OUTFH, '>', $path
2204	0	30000	if $rstop and not $$self{'codontable'}
2208	0	30000	if $rgc and $rgc < 0 || $rgc > 100
2211	0	30000	if (not $rlen or $rlen < 1) { }
	30000	0	elsif ($rlen == 1) { }
2217	30000	0	$rgc ? :
2230	0	3	unless $seq
2237	0	3	if (ref $seq) { }
2240	0	0	$newobj->desc ? :
2315	0	0	if (substr($path, -1, 1) ne '/')
2331	3	40056	ref $seqarg eq 'ARRAY' ? :
2337	40027	32	if ($ref)
2340	0	40027	if $bit < 1
2341	0	40027	ref $seq->seq ? :
2345	3	40056	if $type eq 'ARRAY'
2357	0	40027	unless $ref
2362	20016	20011	if ($enz_allowed)