| line |
true |
false |
branch |
|
93
|
0 |
5 |
unless $self->SUPER::_initialize(@args) |
|
110
|
0 |
17 |
unless my $entry = $self->_readline |
|
112
|
2 |
15 |
if $entry =~ /^\s+$/ |
|
114
|
0 |
15 |
unless $entry =~ /\s*ID\s+\S+/ |
|
116
|
0 |
15 |
unless my($id, $offset, $alphabet) = $entry =~ /\s*ID +([^:]+)..(\d+)[^\)]*.\[?([cg])?/ |
|
122
|
15 |
0 |
if ($alphabet) |
|
123
|
4 |
11 |
if ($alphabet eq 'g') { } |
|
|
11 |
0 |
elsif ($alphabet eq 'c') { } |
|
149
|
1 |
16 |
if ($change_number and $change_number > 1) { } |
|
151
|
1 |
0 |
if $mut |
|
164
|
12 |
4 |
unless defined $end |
|
166
|
2 |
14 |
if defined $sep and $sep eq '^' |
|
168
|
14 |
2 |
if $change =~ />/ |
|
181
|
14 |
2 |
if $ori |
|
184
|
14 |
2 |
if $mut |
|
186
|
14 |
2 |
if ($ismut) |
|
190
|
4 |
12 |
if defined $region |
|
191
|
2 |
14 |
if defined $region_value |
|
192
|
4 |
12 |
if defined $region_dist |
|
222
|
1 |
16 |
if ($change_number and $change_number > 1) { } |
|
224
|
1 |
0 |
if $mut |
|
229
|
12 |
4 |
unless defined $end |
|
231
|
2 |
14 |
if defined $sep and $sep eq '^' |
|
233
|
14 |
2 |
if $change =~ />/ |
|
249
|
14 |
2 |
if $ori |
|
252
|
14 |
2 |
if $mut |
|
254
|
14 |
2 |
if ($ismut) |
|
258
|
16 |
0 |
if defined $region |
|
259
|
0 |
16 |
if defined $region_value |
|
260
|
2 |
14 |
if defined $region_dist |
|
262
|
12 |
4 |
if $codon_table |
|
263
|
12 |
4 |
if $codon_pos |
|
266
|
18 |
17 |
if ($mut->isa('Bio::Variation::DNAMutation')) |
|
267
|
16 |
2 |
if ($mut->mut_number == $rnamut->mut_number) |
|
298
|
1 |
12 |
if ($change_number and $change_number > 1) { } |
|
300
|
1 |
0 |
if $mut |
|
304
|
11 |
1 |
unless defined $end |
|
306
|
0 |
12 |
if defined $sep and $sep eq '^' |
|
308
|
10 |
2 |
if $change =~ />/ |
|
319
|
12 |
0 |
if $ori |
|
322
|
11 |
1 |
if $mut |
|
324
|
10 |
2 |
if ($ismut) |
|
328
|
0 |
12 |
if $region |
|
331
|
14 |
27 |
if ($mut->isa('Bio::Variation::RNAChange')) |
|
332
|
12 |
2 |
if ($mut->mut_number == $aamut->mut_number) |
|
371
|
0 |
16 |
unless (defined $h[0]) |
|
387
|
2 |
14 |
if $h->sysname =~ /-/ |
|
389
|
12 |
4 |
if $h->trivname |
|
409
|
17 |
30 |
if ($mut->isa('Bio::Variation::DNAMutation')) { } |
|
|
17 |
13 |
elsif ($mut->isa('Bio::Variation::RNAChange')) { } |
|
|
13 |
0 |
elsif ($mut->isa('Bio::Variation::AAChange')) { } |
|
411
|
0 |
17 |
unless $mut->allele_ori |
|
413
|
15 |
2 |
if ($mut->isMutation) { } |
|
424
|
1 |
17 |
if ($change_number and $change_number != $count) |
|
436
|
18 |
0 |
if ($mut->proof) |
|
443
|
2 |
16 |
if ($mut->length > 1) { } |
|
|
2 |
14 |
elsif ($mut->length == 0) { } |
|
449
|
0 |
2 |
if $tmp_start == 0 |
|
455
|
4 |
14 |
if ($h->alphabet and $h->alphabet eq 'dna') |
|
457
|
0 |
4 |
if $tmp <= 0 |
|
458
|
1 |
3 |
if $mut->start < 1 |
|
461
|
0 |
4 |
if ($mut->length > 1) { } |
|
|
0 |
4 |
elsif ($mut->length == 0) { } |
|
462
|
0 |
0 |
if $mut->end < 1 |
|
467
|
0 |
0 |
if $tmp == 0 |
|
480
|
16 |
2 |
if $mut->allele_ori->seq |
|
482
|
16 |
2 |
if $mut->allele_mut->seq |
|
492
|
17 |
1 |
if ($mut->restriction_changes ne '') |
|
500
|
4 |
14 |
if ($mut->region) |
|
502
|
4 |
0 |
if $mut->region_value or $mut->region_dist |
|
503
|
2 |
2 |
if $mut->region_value |
|
504
|
4 |
0 |
if ($mut->region_dist) |
|
506
|
2 |
2 |
if $mut->region_dist > 1 |
|
512
|
0 |
18 |
if ($mut->CpG) |
|
524
|
0 |
17 |
unless $mut->allele_ori |
|
528
|
15 |
2 |
if ($mut->isMutation) { } |
|
538
|
1 |
17 |
if ($change_number and $change_number != $count) |
|
549
|
18 |
0 |
if ($mut->proof) |
|
555
|
2 |
16 |
if ($mut->length > 1) { } |
|
|
2 |
14 |
elsif ($mut->length == 0) { } |
|
562
|
0 |
2 |
if $tmp_start == 0 |
|
568
|
14 |
4 |
if ($h->alphabet and $h->alphabet eq 'rna') |
|
570
|
0 |
14 |
if $tmp <= 0 |
|
575
|
2 |
12 |
if ($mut->length > 1) { } |
|
|
2 |
10 |
elsif ($mut->length == 0) { } |
|
594
|
16 |
2 |
if $mut->allele_ori->seq |
|
596
|
16 |
2 |
if $mut->allele_mut->seq |
|
605
|
17 |
1 |
if ($mut->restriction_changes ne '') |
|
613
|
14 |
4 |
if ($mut->region eq 'coding') |
|
621
|
9 |
5 |
if ($mut->DNAMutation->label =~ /.*point/) { } |
|
631
|
18 |
0 |
if ($mut->region) |
|
633
|
2 |
16 |
if $mut->region_value or $mut->region_dist |
|
634
|
0 |
18 |
if $mut->region_value |
|
635
|
2 |
16 |
if ($mut->region_dist) |
|
637
|
1 |
1 |
if $mut->region_dist > 1 |
|
649
|
0 |
13 |
unless $mut->allele_ori |
|
651
|
11 |
2 |
if ($mut->isMutation) { } |
|
662
|
1 |
13 |
if ($change_number and $change_number != $count) |
|
673
|
14 |
0 |
if ($mut->proof) |
|
681
|
1 |
13 |
if ($mut->length > 1) |
|
688
|
14 |
0 |
if $mut->allele_ori->seq |
|
690
|
13 |
1 |
if $mut->allele_mut->seq |
|
696
|
0 |
14 |
if ($mut->region) |
|
698
|
0 |
0 |
if $mut->region_value or $mut->region_dist |
|
699
|
0 |
0 |
if $mut->region_value |
|
700
|
0 |
0 |
if ($mut->region_dist) |
|
702
|
0 |
0 |
if $mut->region_dist > 1 |