| line |
!l |
l&&!r |
l&&r |
condition |
|
221
|
862 |
289 |
21 |
not $self->in_element('hsp') and /^\s+$/ |
|
223
|
1143 |
0 |
2 |
/^\#\s+/ and $_ = $self->_readline |
|
|
1143 |
0 |
2 |
/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox |
|
312
|
0 |
1 |
7 |
$self->{'_reporttype'} and $self->{'_reporttype'} eq 'FASTA' |
|
346
|
0 |
8 |
0 |
defined $_ and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ |
|
|
0 |
6 |
0 |
defined($_ = $self->_readline) and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ |
|
496
|
0 |
8 |
180 |
defined($_ = $self->_readline) and not /^\s+$/ |
|
501
|
180 |
0 |
0 |
$line[-1] =~ /\=/o and $labels[-1] ne 'aln_code' |
|
692
|
0 |
180 |
0 |
$len and $alphabet |
|
757
|
0 |
0 |
180 |
$firstHSP and not $m9HSP |
|
759
|
0 |
0 |
180 |
@hit_signifs and @{$hit_signifs[0]{'HSPs'};} |
|
804
|
0 |
180 |
0 |
$v && exists $v->{'evalue2'} |
|
|
0 |
180 |
0 |
$v and exists $v->{'evalue2'} |
|
1037
|
0 |
0 |
0 |
$self->{'_reporttype'} and $self->{'_reporttype'} eq 'FASTA' |
|
1072
|
0 |
0 |
0 |
defined($_ = $self->_readline) and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ |
|
1342
|
1222 |
2253 |
2562 |
$self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ |
|
1637
|
0 |
0 |
0 |
exists $hsp->{'%_id'} and exists $hsp->{'alen'} |
|
1646
|
0 |
0 |
0 |
exists $hsp->{'%_gid'} and exists $hsp->{'alen'} |
|
1654
|
0 |
0 |
0 |
exists $hsp->{'%_id'} and exists $hsp->{'alen'} |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
188
|
0 |
0 |
8 |
$idlength || $Bio::SearchIO::fasta::IDLENGTH |
|
223
|
5 |
1 |
1145 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ |
|
|
6 |
0 |
1145 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ |
|
|
1 |
0 |
1145 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ |
|
|
0 |
0 |
1145 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ or /(\S+)\s+finds\s+/ |
|
|
2 |
0 |
1143 |
/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ |
|
|
2 |
0 |
1143 |
/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ |
|
|
0 |
0 |
1143 |
/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ |
|
|
0 |
0 |
1143 |
/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ or /(\S+)\s+finds\s+/ |
|
|
0 |
0 |
1145 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ or /(\S+)\s+finds\s+/ or (/^\#\s+/ and $_ = $self->_readline and /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?sequence/iox or /(\S+)\s+compares\s+a/ or /(\S+)\s+performs\s+a/ or /(\S+)\s+produces\s/ or /(\S+)\s+finds\s+/) |
|
|
0 |
180 |
928 |
/^(>--)$/ or /^>>(?!>)(.+?)\s+(?:\((\d+)\s*(aa|nt)\))?$/ |
|
299
|
2 |
0 |
0 |
$querydef ||= $1 |
|
346
|
0 |
0 |
8 |
$last =~ /^\s*vs\s+(\S+)/ or $last =~ /^searching\s+(\S+)\s+library/ |
|
|
0 |
0 |
8 |
$last =~ /^\s*vs\s+(\S+)/ or $last =~ /^searching\s+(\S+)\s+library/ or $last =~ /^Library:\s+(\S+)\s+/ |
|
|
2 |
0 |
6 |
/^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ |
|
|
0 |
0 |
8 |
$last =~ /^\s*vs\s+(\S+)/ or $last =~ /^searching\s+(\S+)\s+library/ or $last =~ /^Library:\s+(\S+)\s+/ or defined $_ and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ |
|
|
3 |
3 |
0 |
/^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ |
|
|
2 |
0 |
6 |
$last =~ /^\s*vs\s+(\S+)/ or $last =~ /^searching\s+(\S+)\s+library/ or $last =~ /^Library:\s+(\S+)\s+/ or defined $_ and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)\s+/ or defined($_ = $self->_readline) and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ |
|
804
|
180 |
0 |
0 |
$v and exists $v->{'evalue2'} or defined $e2 |
|
979
|
0 |
0 |
40 |
/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?
sequence/iox or /(\S+)\s+compares\s+a/io |
|
1072
|
0 |
0 |
0 |
/^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/ |
|
1109
|
674 |
667 |
2008 |
$count == 1 or $count == 3 |
|
1110
|
670 |
4 |
198 |
/^\s+\d+/ or /^\s+$/ |
|
1127
|
0 |
0 |
0 |
/^\s+$/ or length $_ == 0 |
|
1173
|
674 |
0 |
8 |
@{$data[0];} or @{$data[2];} |
|
1389
|
0 |
0 |
0 |
defined $name || defined $self->{'_elements'} |
|
|
0 |
0 |
0 |
not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
1391
|
0 |
0 |
0 |
$_ eq $name or $_ eq $Bio::SearchIO::fasta::MODEMAP{$name} |
|
1417
|
6719 |
0 |
1775 |
$self->{'_elements'}[0] eq $name || exists $Bio::SearchIO::fasta::MODEMAP{$name} && $self->{'_elements'}[0] eq $Bio::SearchIO::fasta::MODEMAP{$name} |
|
1475
|
690 |
0 |
0 |
$self->{'_idlength'} || $Bio::SearchIO::fasta::IDLENGTH |