| line |
true |
false |
branch |
|
183
|
18 |
54 |
if /^\s+$/ |
|
186
|
6 |
48 |
unless ($seentop) |
|
187
|
0 |
6 |
if (/^\#:lav/) { } |
|
|
0 |
6 |
elsif (/^<|>/) { } |
|
189
|
0 |
6 |
if $format |
|
193
|
7 |
47 |
if (/^seq1\s*=\s*(\S+),\s+(\d+)/) { } |
|
|
7 |
40 |
elsif (/^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/) { } |
|
|
2 |
38 |
elsif (/^>(\S+)\s*(.*)?/) { } |
|
|
2 |
36 |
elsif (/^\(complement\)/) { } |
|
|
28 |
8 |
elsif (/^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/) { } |
|
|
8 |
0 |
elsif (/^\s+(\d+)\s/) { } |
|
196
|
6 |
1 |
if (not $seentop) { } |
|
|
0 |
1 |
elsif ($nm ne $lastquery) { } |
|
208
|
0 |
7 |
if $self->in_element('hsp') |
|
210
|
1 |
6 |
if ($self->in_element('hit')) |
|
219
|
1 |
0 |
if @hsps |
|
237
|
1 |
1 |
if ($qfull) { } |
|
238
|
1 |
0 |
unless $format |
|
253
|
14 |
14 |
$hit_direction >= 0 ? : |
|
|
14 |
14 |
$hit_direction >= 0 ? : |
|
271
|
24 |
8 |
$i != 2 ? : |
|
277
|
2 |
6 |
if ($alignment{'Ruler'}{'start'} == 0) |
|
278
|
1 |
0 |
@hsps ? : |
|
|
1 |
1 |
unless $format |
|
280
|
0 |
2 |
if $self->in_element('hsp') |
|
287
|
2 |
0 |
@hsps ? : |
|
290
|
4 |
4 |
if ($alignment{'Mid'}{'string'} =~ /<|>/g) { } |
|
293
|
2 |
2 |
if ($self->in_element('hsp')) { } |
|
304
|
0 |
2 |
if ($alignment{'Mid'}{'string'} =~ /\|/g) |
|
308
|
0 |
0 |
@hsps ? : |
|
324
|
2 |
0 |
@hsps ? : |
|
337
|
0 |
4 |
unless ($self->in_element('hsp')) |
|
343
|
0 |
0 |
@hsps ? : |
|
364
|
6 |
0 |
if ($seentop) |
|
366
|
2 |
4 |
if $self->in_element('hsp') |
|
368
|
6 |
0 |
if ($self->in_element('hit')) |
|
379
|
3 |
3 |
defined $format ? : |
|
404
|
41 |
337 |
if ($type) |
|
405
|
41 |
0 |
if ($self->_will_handle($type)) |
|
411
|
6 |
35 |
if ($type eq 'result') |
|
436
|
28 |
350 |
if ($nm eq 'Hsp') |
|
453
|
41 |
337 |
if ($type = $Bio::SearchIO::sim4::MODEMAP{$nm}) { } |
|
|
337 |
0 |
elsif ($Bio::SearchIO::sim4::MAPPING{$nm}) { } |
|
454
|
41 |
0 |
if ($self->_will_handle($type)) |
|
463
|
0 |
337 |
if (ref($Bio::SearchIO::sim4::MAPPING{$nm}) =~ /hash/i) { } |
|
474
|
6 |
372 |
if defined $type and $type eq 'result' |
|
509
|
0 |
337 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/ |
|
511
|
36 |
301 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/) |
|
536
|
0 |
0 |
if not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
538
|
0 |
0 |
if ($_ eq $name) |
|
561
|
0 |
373 |
unless defined $self->{'_elements'}[0] |
|
606
|
0 |
0 |
unless (defined $self->writer) |
|
652
|
64 |
18 |
defined $self->{'_will_handle_cache'}{$type} ? : |
|
655
|
82 |
0 |
$will_handle ? : |