| line |
true |
false |
branch |
|
187
|
0 |
5 |
if ($min_intron) |
|
190
|
0 |
5 |
if ($cigar and $vulgar) |
|
222
|
6 |
369 |
if (/^\s*Query:\s+(\S+)\s*(.+)?/) { } |
|
|
5 |
364 |
elsif (/^Target:\s+(\S+)\s*(.+)?/) { } |
|
|
4 |
360 |
elsif (s/^vulgar:\s+(\S+)\s+ # query sequence id
(\d+)\s+(\d+)\s+([\-\+\.])\s+ # query start-end-strand
(\S+)\s+ # target sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand
(-?\d+)\s+ # score
//ox) { } |
|
|
2 |
358 |
elsif (s/^cigar:\s+(\S+)\s+ # query sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # query start-end-strand
(\S+)\s+ # target sequence id
(\d+)\s+(\d+)\s+([\-\+])\s+ # target start-end-strand
(-?\d+)\s+ # score
//ox) { } |
|
223
|
0 |
6 |
if ($seentop) |
|
230
|
4 |
2 |
if defined $desc |
|
244
|
3 |
2 |
if defined $desc |
|
258
|
0 |
4 |
if $self->cigar or $self->{'_seencigar'} |
|
264
|
0 |
4 |
unless ($self->within_element('result')) |
|
269
|
1 |
3 |
unless ($self->within_element('hit')) |
|
293
|
0 |
4 |
if ($qstrand eq '-') { } |
|
301
|
0 |
4 |
if ($hstrand eq '-') { } |
|
320
|
20 |
40 |
if ($state eq 'M') { } |
|
321
|
4 |
16 |
if ($laststate eq 'G') { } |
|
339
|
4 |
36 |
if $state eq 'G' |
|
371
|
0 |
2 |
if $self->vulgar or $self->{'_seenvulgar'} |
|
374
|
0 |
2 |
unless ($self->within_element('result')) |
|
379
|
0 |
2 |
unless ($self->within_element('hit')) |
|
396
|
2 |
0 |
if ($qstrand eq '-') { } |
|
401
|
0 |
2 |
if ($hstrand eq '-') { } |
|
418
|
0 |
10 |
if ($state eq 'I') { } |
|
|
4 |
6 |
elsif ($state eq 'D') { } |
|
421
|
4 |
0 |
if ($len >= $Bio::SearchIO::exonerate::MIN_INTRON) |
|
542
|
0 |
4 |
if $seentop |
|
562
|
34 |
237 |
if ($type) |
|
563
|
34 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
568
|
6 |
28 |
if ($type eq 'result') |
|
593
|
34 |
237 |
if ($type = $Bio::SearchIO::exonerate::MODEMAP{$nm}) { } |
|
|
237 |
0 |
elsif ($Bio::SearchIO::exonerate::MAPPING{$nm}) { } |
|
594
|
34 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
603
|
0 |
237 |
if (ref($Bio::SearchIO::exonerate::MAPPING{$nm}) =~ /hash/i) { } |
|
614
|
6 |
265 |
if defined $type and $type eq 'result' |
|
650
|
22 |
215 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/ |
|
672
|
0 |
12 |
if not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
674
|
11 |
6 |
if ($_ eq $name) |
|
697
|
0 |
0 |
unless defined $self->{'_elements'}[0] |
|
742
|
0 |
0 |
unless (defined $self->writer) |
|
769
|
5 |
2 |
if @_ |
|
770
|
0 |
7 |
if (@_) |
|
771
|
0 |
0 |
if ($_[0] and $self->{'_cigar'}) |
|
793
|
5 |
4 |
if @_ |
|
794
|
0 |
9 |
if (@_) |
|
795
|
0 |
0 |
if ($_[0] and $self->{'_vulgar'}) |