Branch Coverage

Bio/Variation/AAChange.pm
Criterion Covered Total %
branch 87 140 62.1


line true false branch
152 4 92 if $aa eq '*'
154 96 0 if defined $2
204 17 2 if $start
205 12 7 if $end
206 12 7 if $length
207 0 19 if $strand
208 0 19 if $primary
209 0 19 if $source
210 0 19 if $frame
211 0 19 if $score
212 0 19 if $gff_string
214 0 19 if $allele_ori
215 0 19 if $allele_mut
216 0 19 if $upstreamseq
217 0 19 if $dnstreamseq
219 0 19 if $label
220 0 19 if $status
221 12 7 if $proof
222 0 19 if $region
223 0 19 if $region_value
224 0 19 if $region_dist
225 0 19 if $numbering
226 12 7 if $mut_number
227 0 19 if $ismutation
245 18 48 if (defined $value)
246 0 18 if (not $value->isa('Bio::Variation::RNAChange')) { }
254 0 66 if (not exists $self->{'RNAChange'}) { }
286 15 0 if $self->allele_ori and $self->allele_ori->seq
287 14 1 if $self->allele_mut and $self->allele_mut->seq
289 0 15 if ($self->start == 1) { }
0 15 elsif ($o and substr($o, 0, 1) eq '*') { }
0 15 elsif ($o and $m and $o eq $m) { }
2 13 elsif ($m and $m eq '*') { }
0 13 elsif ($o and $m and $o eq $m) { }
1 12 elsif (not $m or $o and $m and length $o > length $m and substr($m, -1, 1) ne '*') { }
1 11 elsif (not $o or $o and $m and length $o < length $m and substr($m, -1, 1) ne '*') { }
8 3 elsif ($o and $m and $o ne $m and length $o == 1 and length $m == 1) { }
290 0 0 if ($o and substr($o, 0, 1) ne substr($m, 0, 1)) { }
0 0 elsif ($o and $m and $o eq $m) { }
299 0 0 if ($m and substr($o, 0, 1) ne substr($m, 0, 1)) { }
0 0 elsif ($m and $o eq $m) { }
319 0 0 if ($o and $m and not $o =~ /$m/ and not $o =~ /$m/)
327 1 0 if ($o and $m and not $o =~ /$m/ and not $o =~ /$m/)
335 8 0 if (defined $value)
336 2 6 $value < 0 ? :
361 9 0 if $self->allele_ori and $self->allele_ori->seq
362 9 0 if $self->allele_mut and $self->allele_mut->seq
363 0 9 unless $o and $m and length $o == 1 and length $m == 1
364 0 9 unless $o =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i and $m =~ /[ARNDCQEGHILKMFPSTWYVBZX*]/i
389 0 19 if (defined $value) { }
394 19 0 if $self->allele_ori and $self->allele_ori->seq
397 19 0 if $o
401 17 2 if ($self->isMutation) { }
407 2 17 if $sep eq '|'
411 19 1 if $allele->seq
416 19 1 if $m
417 0 20 if ($self->RNAChange->label =~ /initiation codon/ and ($o and $m and $o ne $m)) { }
15 5 elsif (length $o == 1 and length $m == 1) { }
2 3 elsif ($self->RNAChange->label =~ /deletion/) { }
2 1 elsif ($self->RNAChange->label =~ /insertion/) { }
1 0 elsif ($self->RNAChange->label =~ /complex/) { }
0 0 elsif ($self->label =~ /truncation/) { }
427 1 1 if ($aamutterm eq '*')
431 1 1 if ($self->RNAChange and $self->RNAChange->label =~ /inframe/)
437 1 1 if ($aamutterm eq '*' and length($m) - 1 != 0)
441 1 1 if ($self->RNAChange->label =~ /inframe/)
447 1 0 if ($diff >= 0) { }
452 1 0 if ($aamutterm eq '*' and length($m) - 1 != 0)
456 0 1 if ($self->RNAChange->label =~ /inframe/)
458 0 0 if ($diff >= 0) { }