| blib/lib/Bio/GeneDesign.pm | |||
|---|---|---|---|
| Criterion | Covered | Total | % |
| condition | 34 | 150 | 22.6 |
| line | !l | l&&!r | l&&r | condition |
|---|---|---|---|---|
| 714 | 0 | 7 | 0 | $table_path and not -e $table_path |
| 776 | 0 | 7 | 0 | $rscu_path and not -e $rscu_path |
| 1090 | 3 | 0 | 0 | $set_name and not $set_path |
| 1325 | 2 | 0 | 2 | $esab ne $base and $lagcheck eq $esab |
| 1997 | 0 | 0 | 0 | $olilenmax and $olilen |
| 0 | 0 | 0 | $olilenmax and $olilen and $olilenmax < $olilen | |
| 2091 | 0 | 0 | 0 | $seq1 and $seq2 |
| 2161 | 0 | 0 | 0 | $outformat and $flag |
| 2204 | 30000 | 0 | 0 | $rstop and not $$self{'codontable'} |
| 2208 | 0 | 30000 | 0 | $rgc and $rgc < 0 || $rgc > 100 |
| line | l | !l | condition |
|---|---|---|---|
| 327 | 0 | 4 | $salt || 0.05 |
| 328 | 0 | 4 | $conc || 1e-07 |
| 381 | 3 | 1 | $swit || 0 |
| 558 | 4 | 0 | $frame || 1 |
| 1401 | 2 | 1 | $re || 0 |
| 1538 | 20001 | 0 | $algorithm || 'balanced' |
| 1734 | 0 | 0 | $temp || 60 |
| 1755 | 0 | 0 | $length || 5 |
| 1774 | 0 | 0 | $length || 5 |
| 1818 | 0 | 0 | $$self{'tmp_path'} || './' |
| 1819 | 0 | 0 | $mismatches || 1 |
| 1820 | 0 | 0 | $revcom || 1 |
| 1872 | 0 | 0 | $$self{'tmp_path'} || './' |
| 1873 | 0 | 0 | $percent || 75 |
| 1874 | 0 | 0 | $revcom || 1 |
| 1914 | 0 | 0 | $tarbblen || 1000 |
| 1915 | 0 | 0 | $maxbblen || 1023 |
| 1916 | 0 | 0 | $minbblen || 200 |
| 1925 | 0 | 0 | $tarbblap || 40 |
| 1927 | 0 | 0 | $algorithm || 'overlap' |
| 1990 | 0 | 0 | $olilen || 180 |
| 1991 | 0 | 0 | $olilenmin || 45 |
| 1992 | 0 | 0 | $olilenmax || 200 |
| 1993 | 0 | 0 | $laptemp || 70 |
| 1994 | 0 | 0 | $tmtol || 0.5 |
| 1995 | 0 | 0 | $verbose || undef |
| 2000 | 0 | 0 | $algorithm || 'JGI' |
| 2088 | 0 | 0 | $window || 10 |
| 2089 | 0 | 0 | $stringency || 10 |
| 2207 | 20000 | 10000 | $rgc || 50 |
| 2274 | 0 | 0 | $chars || '0' |
| 2330 | 20047 | 20012 | $enz_allowed || 0 |
| 2358 | 20016 | 20011 | $enz_allowed || 0 |
| line | l | !l&&r | !l&&!r | condition |
|---|---|---|---|---|
| 647 | 0 | 0 | 0 | $seek->isa('Bio::Seq') or $seek->isa('Bio::SeqFeatureI') |
| 0 | 0 | 0 | $seek->isa('Bio::Seq') or $seek->isa('Bio::SeqFeatureI') or $seek->isa('Bio::GeneDesign::RestrictionEnzyme') | |
| 1047 | 0 | 0 | 0 | $name eq '.' or $name eq '..' |
| 1090 | 0 | 3 | 0 | $set_name || $set_path |
| 1130 | 0 | 3 | 0 | $set_name || basename($set_path) |
| 1300 | 0 | 0 | 10 | $seq->isa('Bio::Seq') or $seq->isa('Bio::SeqFeatureI') |
| 0 | 10 | 0 | $seq->isa('Bio::Seq') or $seq->isa('Bio::SeqFeatureI') or $seq->isa('Bio::GeneDesign::RestrictionEnzyme') | |
| 1405 | 0 | 3 | 0 | $peptide || $self->translate(-'sequence', $str) |
| 1487 | 0 | 0 | 9 | abs $frame > 4 or abs $frame < 0 |
| 1543 | 20001 | 0 | 0 | &$subref($$self{'reversecodontable'}, $$self{'rscutable'}, $str) || $self->throw("Can't reverse translate with $algorithm? $!") |
| 1598 | 20003 | 0 | 0 | &$subref($$self{'codontable'}, $$self{'reversecodontable'}, $$self{'rscutable'}, $str) || $self->throw("Can't run $algorithm? $!") |
| 1647 | 2 | 0 | 1 | $rem->isa('Bio::Seq') or $rem->isa('Bio::SeqFeatureI') |
| 1918 | 0 | 0 | 0 | $tarbblen < $minbblen or $tarbblen > $maxbblen |
| 1922 | 0 | 0 | 0 | $maxbblen < $minbblen or $maxbblen < 0 |
| 0 | 0 | 0 | $maxbblen < $minbblen or $maxbblen < 0 or $minbblen < 0 | |
| 2123 | 1 | 0 | 0 | 'Bio::SeqIO'->new(-'file', $path) || $self->throw("Can't parse $path!") |
| 2208 | 0 | 0 | 30000 | $rgc < 0 || $rgc > 100 |
| 2211 | 0 | 0 | 30000 | not $rlen or $rlen < 1 |