Branch Coverage

blib/lib/Bio/GeneDesign.pm

Criterion	Covered	Total	%
branch	117	318	36.7

line	true	false	branch
65	0	9	unless substr($self->{'conf'}, -1, 1) eq '/'
68	0	9	unless substr($self->{'tmp_path'}, -1, 1) eq '/'
71	0	9	if ($self->{'graph'} > 0)
78	0	9	if ($self->{'EMBOSS'})
85	0	9	if ($self->BLAST)
93	0	9	if ($self->{'vmatch'})
337	0	4	unless $seq
340	1	3	$nnflag ? :
345	1	3	if ($nnflag)
392	0	4	unless $seq
433	0	3	unless $seq
463	0	0	unless $seq
500	0	2	unless $seq
534	0	0	unless $seq
575	0	6	unless $seq
580	2	4	if ($arrswit) { }
608	0	1	unless $seq
638	0	5	unless $seq
671	0	4	unless $seq
679	0	4	unless exists $ambtransswits{$frame}
707	0	1	unless $seq
749	0	2	unless $seq
752	0	2	unless $seek
761	0	2	if ($qref) { }
763	0	0	unless $seek->isa('Bio::Seq') or $seek->isa('Bio::SeqFeatureI') or $seek->isa('Bio::GeneDesign::RestrictionEnzyme')
768	0	0	if ($seek->isa('Bio::GeneDesign::RestrictionEnzyme')) { }
774	0	0	ref $seek->seq ? :
775	0	0	$revcom ? :
780	0	2	$revcom ? :
839	0	7	unless $orgname
842	0	7	if $table_path and not -e $table_path
845	0	7	unless ($table_path)
848	0	0	if (-e $table_path and $orgname ne 'Standard') { }
904	0	7	unless $orgname
907	0	7	if $rscu_path and not -e $rscu_path
910	0	7	unless ($rscu_path)
913	0	0	unless (-e $rscu_path)
952	0	7	unless $orgname
997	0	3	unless $self->{'codontable'}
999	0	3	unless $input
1008	0	3	if exists $cod_count->{'XXX'}
1036	0	1	unless $self->{'codontable'}
1038	0	1	unless $seqobjs
1078	0	0	unless $self->{'codontable'}
1080	0	0	unless $seqobjs
1133	0	0	unless $self->{'codontable'}
1135	0	0	unless $seqobjs
1138	0	0	unless ref $comments eq 'ARRAY'
1173	0	0	unless opendir my $ENZDIR, $epath
1178	0	0	if $name eq '.' or $name eq '..'
1221	0	3	if (not $set_name || $set_path) { }
	0	3	elsif ($set_name and not $set_path) { }
	3	0	elsif ($set_path) { }
1229	0	0	unless (-e $set_path)
1240	0	0	unless (exists $self->{'all_enzymes'}{$id})
1252	0	3	unless -e $set_path
1258	0	87	unless (exists $self->{'all_enzymes'}{$id})
1289	0	0	unless $enzes
1292	0	0	unless $self->{'enzyme_set'}
1296	0	0	if ($ref eq 'ARRAY') { }
1308	0	0	if ($eref)
1310	0	0	unless $enz->isa('Bio::GeneDesign::RestrictionEnzyme')
1316	0	0	if (exists $self->{'enzyme_set'}{$eid})
1352	0	0	unless $enzes
1355	0	0	unless $self->{'enzyme_set'}
1359	0	0	if ($ref eq 'ARRAY') { }
1369	0	0	unless $enz->isa('Bio::GeneDesign::RestrictionEnzyme')
1373	0	0	if exists $self->{'enzyme_set'}{$enz->id}
1390	0	1	unless $self->{'enzyme_set'}
1392	0	1	unless $seq
1424	0	2	unless $list
1434	10	0	if ($ref)
1436	0	10	unless $seq->isa('Bio::Seq') or $seq->isa('Bio::SeqFeatureI') or $seq->isa('Bio::GeneDesign::RestrictionEnzyme')
1442	0	10	ref $seq->seq ? :
1446	4	6	if ($pep) { }
1449	0	4	unless $self->{'codontable'}
1461	2	2	if ($esab ne $base and $lagcheck eq $esab)
1474	3	3	if ($esab ne $base)
1504	0	2	unless $seq
1507	0	2	unless $tree
1510	0	2	unless $tree->isa('Bio::GeneDesign::PrefixTree')
1532	0	3	unless $self->{'codontable'}
1534	0	3	unless $seq
1549	2	1	$re ? :
1563	0	1	unless $self->{'codontable'}
1565	0	1	unless $seq
1591	0	0	unless $self->{'codontable'}
1593	0	0	unless $codold
1596	0	0	unless $codnew
1614	0	9	unless $self->{'codontable'}
1616	0	9	unless $seq
1621	6	3	$frame ? :
1623	0	9	if abs $frame > 4 or abs $frame < 0
1627	6	3	if (ref $seq) { }
1630	0	6	$newobj->desc ? :
1666	0	20001	unless $self->{'codontable'}
1669	0	20001	unless $self->{'rscutable'}
1671	0	20001	unless $pep
1678	0	20001	if (scalar @baddies)
1691	20001	0	if (ref $pep) { }
1694	0	20001	$newobj->desc ? :
1708	0	20001	unless $newobj->add_SeqFeature($CDS)
1740	0	20003	unless $self->{'codontable'}
1743	0	20003	unless $self->{'rscutable'}
1745	0	20003	unless $seq
1748	0	20003	unless $algorithm
1754	0	20003	unless length($str) % 3 == 0
1766	20003	0	if (ref $seq) { }
1769	0	20003	$newobj->desc ? :
1793	0	4	unless $self->{'codontable'}
1796	0	4	unless $self->{'rscutable'}
1798	0	4	unless $seq
1801	0	4	unless $rem
1808	4	0	if (ref $rem) { }
1810	3	1	if ($rem->isa('Bio::Seq') or $rem->isa('Bio::SeqFeatureI')) { }
	1	0	elsif ($rem->isa('Bio::GeneDesign::RestrictionEnzyme')) { }
1812	0	3	ref $rem->seq ? :
1839	4	0	if (ref $seq) { }
1842	0	4	$newobj->desc ? :
1866	0	0	unless $self->{'codontable'}
1869	0	0	unless $self->{'rscutable'}
1871	0	0	unless $seq
1884	0	0	if (ref $seq) { }
1887	0	0	$newobj->desc ? :
1912	0	0	unless $seq
1933	0	0	unless $seq
1951	0	0	unless $seqs
1972	0	0	unless ($pattern)
1990	0	0	unless $self->{'graph'}
1996	0	0	unless $self->{'codontable'}
1999	0	0	unless $self->{'rscutable'}
2001	0	0	unless $seqobjs
2004	0	0	unless ref $seqobjs eq 'ARRAY'
2009	0	0	unless $seqobj->isa('Bio::Seq')
2012	0	0	unless $seqobj->alphabet eq 'dna'
2034	0	0	unless $self->{'graph'}
2042	0	0	unless $seq1 and $seq2
2047	0	0	unless $seqobj->isa('Bio::Seq')
2050	0	0	unless $seqobj->alphabet eq 'dna'
2072	0	1	unless -e $path
2116	0	0	$outformat ? :
2117	0	0	unless _isa_BP_format($outformat)
2122	0	0	if $outformat eq 'genbank'
2142	0	30000	if $rstop and not $self->{'codontable'}
2145	0	30000	if $rgc and $rgc < 0 || $rgc > 100
2148	0	30000	if (not $rlen or $rlen < 1) { }
	30000	0	elsif ($rlen == 1) { }
2154	30000	0	$rgc ? :
2167	0	3	unless $seq
2174	0	3	if (ref $seq) { }
2177	0	0	$newobj->desc ? :
2252	0	0	if (substr($path, -1, 1) ne '/')
2268	3	40060	ref $seqarg eq 'ARRAY' ? :
2274	40028	35	if ($ref)
2277	0	40028	if $bit < 1
2278	0	40028	ref $seq->seq ? :
2282	3	40060	if $type eq 'ARRAY'
2294	0	40028	unless $ref
2299	20016	20012	if ($enz_allowed)