| line |
true |
false |
branch |
|
70
|
0 |
6 |
unless (@exons) |
|
84
|
0 |
6 |
unless (_checkexons(\@exons)) |
|
119
|
0 |
1642 |
if (not $exon->obj_valid) { } |
|
125
|
0 |
306 |
if ($#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 (not 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 (not 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
|
42 |
4 |
if (not exists $self->{'translation_table'}) { } |
|
809
|
7 |
9440 |
if ($inputlabel == $label) |