Branch Coverage

Bio/LiveSeq/Transcript.pm
Criterion Covered Total %
branch 69 204 33.8


line true false branch
70 0 6 unless (@exons)
84 0 6 unless (_checkexons(\@exons))
119 1642 0 if ($exon->obj_valid) { }
125 0 306 if ($#exons != $#newexons)
153 0 23 if (defined $howmany) { }
154 0 0 unless ($howmany > 0)
158 19 4 unless ($self->{'seq'}->alphabet eq 'rna')
161 19 0 if ($self->gene) { }
164 19 0 if (CORE::length $str > 0) { }
182 0 4 if ($howmany) { }
185 4 0 if ($strand == 1) { }
207 0 1 if (defined $howmany) { }
208 0 0 unless ($howmany > 0)
212 1 0 unless ($self->{'seq'}->alphabet eq 'rna')
213 1 0 if ($self->gene) { }
216 1 0 if (CORE::length $str > 0) { }
232 0 0 if ($howmany) { }
234 0 0 if ($labelbefore < 1)
235 0 0 if ($strand == 1) { }
244 0 0 if ($strand == 1) { }
262 0 23 unless ($position)
268 3 20 unless (defined $firstlabel)
274 10 13 if ($position < 1)
279 0 23 if ($arraypos < 0) { }
0 23 elsif ($arraypos >= $length) { }
297 0 16 unless ($self->{'seq'}->valid($label))
301 1 15 unless (defined $firstlabel)
304 0 16 if ($label == $firstlabel)
311 16 0 if ($self->valid($label)) { }
314 0 16 if ($position <= 0)
318 0 0 if ($self->follows($end, $label)) { }
0 0 elsif ($self->follows($label, $start)) { }
376 0 0 if ($start)
377 0 0 unless ($self->valid($start))
382 0 0 if ($end)
383 0 0 if ($end == $start) { }
386 0 0 unless ($self->valid($end))
389 0 0 unless ($self->follows($start, $end) == 1)
403 12 0 unless (defined $unsecuremode and $unsecuremode eq 'unsecuremoderequested')
406 12 0 if ($start) { }
407 0 12 unless ($self->valid($start))
413 6 6 if ($end) { }
414 0 6 if ($end == $start) { }
419 0 6 unless ($self->valid($end))
422 0 6 unless ($self->follows($start, $end) == 1)
434 12 44 if (not defined $startexon and $exon->valid($start))
437 10 46 if ($exon->valid($end))
440 12 44 if (not defined $seq and defined $startexon)
441 5 7 if (defined $endexon and $endexon eq $startexon) { }
442 1 4 if ($length) { }
455 7 44 if ($startexon and $exon ne $startexon)
456 5 2 if (defined $endexon) { }
2 0 elsif (defined $startexon) { }
463 2 0 if ($length)
464 2 0 if ($seq and CORE::length $seq >= $length)
470 6 6 if ($length) { }
487 1 6 if ($exon->valid($label))
499 0 0 if (defined $pos1) { }
500 0 0 if ($pos1 == 0)
503 0 0 if (defined $pos2 and $pos1 > $pos2)
507 0 0 unless ($self->valid($startlabel))
510 0 0 if ($startlabel < 1)
516 0 0 if (defined $pos2) { }
517 0 0 if ($pos2 == 0)
521 0 0 if (defined $pos1 and $pos1 > $pos2)
525 0 0 unless ($self->valid($endlabel))
528 0 0 if ($endlabel < 1)
532 0 0 unless (defined $length)
543 0 0 if (defined $length)
544 0 0 if ($length < 1)
553 0 0 if (defined $pos1) { }
556 0 0 if ($pos1 == 0) { }
0 0 elsif ($pos1 < 0) { }
561 0 0 if (defined $pos2 and $pos1 > $pos2)
567 0 0 if (defined $pos2) { }
570 0 0 if ($pos2 == 0) { }
0 0 elsif ($pos2 < 0) { }
575 0 0 if (defined $pos1 and $pos1 > $pos2)
580 0 0 if ($endcount > $seqlength)
589 0 0 if ($offset < 0) { }
0 0 elsif ($offset >= $seqlength) { }
597 0 0 if (CORE::length $str < $length)
598 0 0 if $self->verbose > 0
635 55 59871 if ($label == $checkme)
652 0 6 unless (ref $firstexon eq 'Bio::LiveSeq::Exon')
661 0 28 unless (ref $exon eq 'Bio::LiveSeq::Exon')
665 0 28 if ($exon->strand != $strand)
670 0 28 unless ($exon->{'seq'}->follows($prevend, $thisstart, $strand))
706 0 0 if ($startexon == 0 and $exon->valid($startlabel))
709 0 0 if ($endexon == 0 and $exon->valid($endlabel))
712 0 0 if ($startexon and $endexon)
719 0 0 if ($startexon eq $endexon) { }
720 0 0 if ($startexon->start eq $startlabel and $startexon->end eq $endlabel) { }
0 0 elsif ($startexon->start eq $startlabel) { }
0 0 elsif ($startexon->end eq $endlabel) { }
724 0 0 unless ($exon eq $startexon)
743 0 0 if ($exon eq $startexon) { }
0 0 elsif ($exon eq $endexon) { }
752 0 0 if ($notmiddle)
775 1 45 if (defined $value)
778 4 42 if (exists $self->{'translation_table'}) { }
809 7 9440 if ($inputlabel == $label)