| line |
true |
false |
branch |
|
159
|
1 |
2 |
if /^\s+$/ |
|
160
|
2 |
0 |
if (/^(\d+)\s+ # alignment number - we'll throw this away anyways
(\S+)\s+ # Query name
(\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based)
(\S+)\s+ # Hit name
(\d+)\s+(\d+)\s+ # Hit start Hit end (0 based)
([\-\+])\s+ # Hit strand
([\d\.\-]+)\s+ # Score
/ox) |
|
175
|
0 |
2 |
if (defined $curquery and $curquery ne $qname) |
|
182
|
0 |
2 |
if (defined $curhit and $curhit ne $hname) { } |
|
|
1 |
1 |
elsif (not defined $curquery) { } |
|
209
|
2 |
0 |
if ($hstrand eq '-') |
|
244
|
1 |
0 |
if (defined $curquery) |
|
276
|
4 |
26 |
if (my $type = $Bio::SearchIO::axt::MODEMAP{$nm}) |
|
278
|
4 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
284
|
1 |
29 |
if ($nm eq 'AXTOutput') |
|
310
|
4 |
26 |
if (my $type = $Bio::SearchIO::axt::MODEMAP{$nm}) { } |
|
|
26 |
0 |
elsif ($Bio::SearchIO::axt::MAPPING{$nm}) { } |
|
311
|
4 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
319
|
0 |
26 |
if (ref($Bio::SearchIO::axt::MAPPING{$nm}) =~ /hash/i) { } |
|
330
|
1 |
29 |
if $nm eq 'AXTOutput' |
|
368
|
0 |
26 |
unless defined $data->{'Data'} |
|
369
|
0 |
26 |
if ($data->{'Data'} =~ /^\s+$/) |
|
370
|
0 |
0 |
unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/ |
|
373
|
4 |
22 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/) |
|
396
|
4 |
0 |
if (defined $value) |
|
419
|
0 |
0 |
if not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
421
|
0 |
0 |
if ($_ eq $name) |
|
443
|
0 |
26 |
unless defined $self->{'_elements'}[0] |