| line |
true |
false |
branch |
|
186
|
0 |
8 |
unless @args |
|
221
|
21 |
1151 |
if not $self->in_element('hsp') and /^\s+$/ |
|
223
|
8 |
1143 |
if (/(\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+/)) { } |
|
|
8 |
1135 |
elsif (/(\d+)\s+residues\s+in\s+(\d+)\s+(?:library\s+)?sequences/) { } |
|
|
8 |
1127 |
elsif (/Lambda=\s*(\S+)/) { } |
|
|
0 |
1127 |
elsif (/K=\s*(\S+)/) { } |
|
|
0 |
1127 |
elsif (/^\s*(Smith-Waterman)/) { } |
|
|
8 |
1119 |
elsif (/The best( related| unrelated)? scores are:/) { } |
|
|
5 |
1114 |
elsif (/^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix[^\]]+?(xS)?\]\s*ktup:\s*(\d+)/) { } |
|
|
3 |
1111 |
elsif (/^Algorithm:\s+(\S+)\s+.*\s*\(([^)]+)\)\s+(\S+)/) { } |
|
|
3 |
1108 |
elsif (/^Parameters:/) { } |
|
|
0 |
1108 |
elsif (/^\s+ktup:\s*(\d+),/) { } |
|
|
180 |
928 |
elsif (/^(>--)$/ or /^>>(?!>)(.+?)\s+(?:\((\d+)\s*(aa|nt)\))?$/) { } |
|
|
8 |
920 |
elsif (/\d+\s*residues\s*in\s*\d+\s*query\s*sequences/) { } |
|
|
0 |
920 |
elsif (/^\s*\d+\s*>>>/) { } |
|
|
682 |
238 |
elsif ($self->in_element('hsp')) { } |
|
239
|
0 |
8 |
if ($seentop) |
|
257
|
1 |
7 |
if (/version/) { } |
|
265
|
0 |
8 |
unless defined $version |
|
277
|
6 |
36 |
if (/^ (
(?:\s+>) | # fa33 lead-in
(?:\s*\d+\s*>>>) # fa34 mlib lead-in
)
(.*)
/x) { } |
|
|
2 |
34 |
elsif (/^\s*vs\s+\S+/o) { } |
|
287
|
4 |
2 |
if ($leadin =~ />>>/) { } |
|
288
|
4 |
0 |
if ($querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o) |
|
297
|
2 |
0 |
if ($last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/) |
|
305
|
2 |
0 |
if ($last =~ /(\S+)[,:]\s+(\d+)\s+(aa|nt)/o) |
|
312
|
7 |
1 |
if ($self->{'_reporttype'} and $self->{'_reporttype'} eq 'FASTA') |
|
315
|
4 |
3 |
if ($querytype eq 'nt') { } |
|
|
3 |
0 |
elsif ($querytype eq 'aa') { } |
|
335
|
8 |
0 |
if ($querylen) { } |
|
346
|
8 |
0 |
if ($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+)/) { } |
|
|
0 |
0 |
elsif (/^\s+opt(?:\s+E\(\))?$/o) { } |
|
370
|
0 |
0 |
if /^>\d+/ |
|
428
|
0 |
0 |
defined $2 ? : |
|
434
|
0 |
0 |
if (m[\s*gap\-penalty:\s*(\-?\d+)/(\-?\d+)]) { } |
|
|
0 |
0 |
elsif (m[\s*open/ext:\s*(\-?\d+)/(\-?\d+)]) { } |
|
476
|
8 |
31 |
if ($_ =~ /^E\((\d+)\)$/o) { } |
|
|
0 |
8 |
$rel ? : |
|
484
|
1 |
30 |
if ($_ eq 'gapl') { } |
|
|
1 |
29 |
elsif ($_ eq 'gapq') { } |
|
|
0 |
29 |
elsif ($_ eq 'E2()') { } |
|
501
|
0 |
180 |
if ($line[-1] =~ /\=/o and $labels[-1] ne 'aln_code') |
|
506
|
0 |
180 |
if ($line[0] eq '+-') { } |
|
|
0 |
180 |
elsif ($line[0] eq '>>><<<') { } |
|
526
|
150 |
30 |
if ($line[-1] =~ /\[([1-6rf])\]/o) { } |
|
529
|
0 |
0 |
$fr <= 3 ? : |
|
|
85 |
65 |
$fr eq 'f' ? : |
|
|
0 |
150 |
$fr =~ /\d/o ? : |
|
539
|
180 |
0 |
if ($line[-1] =~ /^\(?(\d+)\)$/) { } |
|
542
|
81 |
99 |
if ($line[-1] =~ /^\($/) |
|
575
|
0 |
5 |
defined $3 ? : |
|
588
|
1 |
4 |
unless $self->{'_reporttype'} =~ /FAST[PN]/i |
|
597
|
5 |
0 |
if (m[(?:gap\-pen|open/ext):\s+([\-\+]?\d+)\s*/\s*([\-\+]?\d+)]) |
|
622
|
0 |
3 |
unless $self->{'_reporttype'} =~ /FAST[PN]/i |
|
632
|
0 |
3 |
defined $2 ? : |
|
638
|
3 |
0 |
if (/ktup:\s(\d+)/) |
|
645
|
3 |
0 |
if (/ktup:\s\d+$/) |
|
650
|
3 |
0 |
if (m[(?:gap\-pen|open/ext):\s+([\-\+]?\d+)\s*/\s*([\-\+]?\d+)]) |
|
683
|
172 |
8 |
if ($self->in_element('hsp')) |
|
688
|
180 |
0 |
if ($1 ne '>--') { } |
|
692
|
0 |
180 |
unless ($len and $alphabet) |
|
695
|
0 |
0 |
if (/(.*?)\s+\((\d+)\s*(aa|nt)\)/) |
|
697
|
0 |
0 |
$1 ? : |
|
700
|
0 |
0 |
if (/^>>(?!>)/) |
|
705
|
172 |
8 |
if ($self->in_element('hit')) |
|
707
|
172 |
0 |
if @hit_signifs |
|
753
|
0 |
180 |
unless defined $bits |
|
757
|
180 |
0 |
if ($firstHSP and not $m9HSP) { } |
|
759
|
180 |
0 |
if @hit_signifs and @{$hit_signifs[0]{'HSPs'};} |
|
766
|
180 |
0 |
if (defined $v) |
|
770
|
180 |
0 |
if ($firstHSP) |
|
774
|
180 |
0 |
$v ? : |
|
780
|
180 |
0 |
$v ? : |
|
790
|
180 |
0 |
$v ? : |
|
796
|
180 |
0 |
$v ? : |
|
804
|
180 |
0 |
$v && exists $v->{'evalue2'} ? : |
|
|
180 |
0 |
if $v and exists $v->{'evalue2'} or defined $e2 |
|
809
|
180 |
0 |
$v ? : |
|
814
|
0 |
180 |
if (s[global/.* score:\s*(\d+)\;?][]) |
|
822
|
91 |
89 |
if (s/Smith-Waterman score:\s*(\d+)\;?//) |
|
830
|
180 |
0 |
if (/ (\d*\.?\d+)\% \s* identity
(?:\s* \(\s*(\S+)\% \s* (?:ungapped|similar) \) )?
\s* in \s* (\d+) \s+ (?:aa|nt) \s+ overlap \s*
\( (\d+) \- (\d+) : (\d+) \- (\d+) \)
/x) |
|
890
|
180 |
0 |
if ($v) { } |
|
893
|
1 |
179 |
if exists $v->{'qgaps'} |
|
896
|
1 |
179 |
if exists $v->{'lgaps'} |
|
898
|
150 |
30 |
if ($self->{'_reporttype'} =~ /^FAST[NXY]$/o) { } |
|
899
|
1 |
149 |
if (8 == scalar grep({exists $v->{$_};} 'an0', 'ax0', 'pn0', 'px0', 'an1', 'ax1', 'pn1', 'px1')) { } |
|
902
|
0 |
1 |
if ($v->{'ax0'} < $v->{'an0'}) { } |
|
920
|
0 |
1 |
if ($v->{'ax1'} < $v->{'an1'}) { } |
|
963
|
8 |
0 |
if ($self->in_element('hsp')) |
|
966
|
8 |
0 |
if ($self->in_element('hit')) |
|
968
|
8 |
0 |
if @hit_signifs |
|
978
|
8 |
40 |
if /^Function used was/ |
|
979
|
0 |
40 |
if (/(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+)?
sequence/iox or /(\S+)\s+compares\s+a/io) |
|
988
|
0 |
8 |
if @hit_signifs |
|
994
|
0 |
0 |
if ($self->within_element('FastaOutput')) { } |
|
995
|
0 |
0 |
if ($self->in_element('hsp')) |
|
998
|
0 |
0 |
if ($self->in_element('hit')) |
|
1000
|
0 |
0 |
if @hit_signifs |
|
1004
|
0 |
0 |
if @hit_signifs |
|
1029
|
0 |
0 |
if (/^\s*\d+\s*>>>(.*)/) |
|
1031
|
0 |
0 |
if ($querydef =~ /^(.*?)\s+(?:\-\s+)?(\d+)\s+(aa|nt).*$/o) |
|
1037
|
0 |
0 |
if ($self->{'_reporttype'} and $self->{'_reporttype'} eq 'FASTA') |
|
1040
|
0 |
0 |
if ($querytype eq 'nt') { } |
|
|
0 |
0 |
elsif ($querytype eq 'aa') { } |
|
1061
|
0 |
0 |
if ($querylen) { } |
|
1072
|
0 |
0 |
if (defined($_ = $self->_readline) and /^\s*vs\s+(\S+)/ || /^Library:\s+(\S+)/) |
|
1093
|
8 |
4228 |
if (/residues in \d+\s+query\s+sequences/o) { } |
|
|
0 |
4228 |
elsif (m[^>>>(\*\*\*|///|<<<)]o) { } |
|
|
7 |
4221 |
elsif (/^>>/o) { } |
|
|
0 |
4221 |
elsif (/^\s*\d+\s*>>>/o) { } |
|
1109
|
872 |
3349 |
if ($count == 0) { } |
|
|
1341 |
2008 |
elsif ($count == 1 or $count == 3) { } |
|
|
674 |
1334 |
elsif ($count == 2) { } |
|
1110
|
0 |
872 |
if (/^(\S+)\s+/) { } |
|
|
674 |
198 |
elsif (/^\s+\d+/ or /^\s+$/) { } |
|
|
198 |
0 |
elsif (length $_ == 0) { } |
|
1127
|
1341 |
0 |
if (/^(\S+)\s+/) { } |
|
|
0 |
0 |
elsif (/^\s+(\d+)/) { } |
|
|
0 |
0 |
elsif (/^\s+$/ or length $_ == 0) { } |
|
|
0 |
0 |
elsif (/\s+\S+fasta3\d\s+/) { } |
|
1128
|
0 |
1341 |
if $len < length $1 |
|
1153
|
0 |
674 |
if (/^\s+\d+\s+/) { } |
|
1154
|
0 |
0 |
if $self->verbose > 0 |
|
1165
|
667 |
7 |
if (length $_ >= $len) |
|
1170
|
667 |
3554 |
if $count++ >= 5 |
|
1173
|
674 |
8 |
if (@{$data[0];} or @{$data[2];}) |
|
1195
|
1 |
237 |
unless ($seentop) |
|
1202
|
0 |
3 |
if ($self->in_element('result')) |
|
1203
|
0 |
0 |
if ($self->in_element('hsp')) |
|
1206
|
0 |
0 |
if ($self->in_element('hit')) |
|
1208
|
0 |
0 |
if @hit_signifs |
|
1231
|
368 |
4197 |
if (my $type = $Bio::SearchIO::fasta::MODEMAP{$nm}) |
|
1233
|
368 |
0 |
if (my $handler = $self->_will_handle($type)) |
|
1239
|
8 |
4557 |
if ($nm eq 'FastaOutput') |
|
1265
|
180 |
4385 |
if ($nm eq 'Hsp') |
|
1277
|
368 |
4197 |
if (my $type = $Bio::SearchIO::fasta::MODEMAP{$nm}) { } |
|
|
4197 |
0 |
elsif ($Bio::SearchIO::fasta::MAPPING{$nm}) { } |
|
1278
|
368 |
0 |
if (my $handler = $self->_will_handle($type)) |
|
1286
|
72 |
4125 |
if (ref($Bio::SearchIO::fasta::MAPPING{$nm}) =~ /hash/i) { } |
|
1300
|
8 |
4557 |
if $nm eq 'FastaOutput' |
|
1337
|
182 |
6037 |
unless defined $data->{'Data'} |
|
1338
|
64 |
5973 |
if ($data->{'Data'} =~ /^\s+$/) |
|
1339
|
0 |
64 |
unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/ |
|
1342
|
2562 |
3475 |
if ($self->in_element('hsp') and $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/) |
|
1366
|
368 |
0 |
if (defined $value) |
|
1389
|
0 |
0 |
if not defined $name || defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
1391
|
0 |
0 |
if ($_ eq $name or $_ eq $Bio::SearchIO::fasta::MODEMAP{$name}) |
|
1413
|
14 |
8494 |
unless defined $self->{'_elements'}[0] |
|
1472
|
8 |
682 |
if (defined $value) |
|
1549
|
712 |
24 |
defined $self->{'_will_handle_cache'}{$type} ? : |
|
1552
|
736 |
0 |
$will_handle ? : |
|
1583
|
0 |
0 |
if exists $hit->{'hit_len'} |
|
1589
|
0 |
0 |
if exists $hit->{'id'} |
|
1595
|
0 |
0 |
if exists $hit->{'acc'} |
|
1601
|
0 |
0 |
if exists $hit->{'desc'} |
|
1607
|
0 |
0 |
if exists $hit->{'evalue'} |
|
1613
|
0 |
0 |
if exists $hit->{'bits'} |
|
1619
|
0 |
0 |
if exists $hsp->{'z-sc'} |
|
1621
|
0 |
0 |
if exists $hsp->{'evalue'} |
|
1623
|
0 |
0 |
if exists $hsp->{'evalue2'} |
|
1626
|
0 |
0 |
if exists $hsp->{'bits'} |
|
1628
|
0 |
0 |
if exists $hsp->{'n-w'} |
|
1630
|
0 |
0 |
if exists $hsp->{'sw'} |
|
1632
|
0 |
0 |
if exists $hsp->{'%_gid'} |
|
1637
|
0 |
0 |
if exists $hsp->{'%_id'} and exists $hsp->{'alen'} |
|
1639
|
0 |
0 |
if (exists $hsp->{'%_gid'}) { } |
|
1646
|
0 |
0 |
if exists $hsp->{'%_gid'} and exists $hsp->{'alen'} |
|
1654
|
0 |
0 |
if exists $hsp->{'%_id'} and exists $hsp->{'alen'} |
|
1660
|
0 |
0 |
if exists $hsp->{'alen'} |
|
1664
|
0 |
0 |
if exists $hsp->{'an0'} |
|
1668
|
0 |
0 |
if exists $hsp->{'ax0'} |
|
1672
|
0 |
0 |
if exists $hsp->{'an1'} |
|
1676
|
0 |
0 |
if exists $hsp->{'ax1'} |
|
1681
|
0 |
0 |
if exists $hsp->{'qgaps'} |
|
1685
|
0 |
0 |
if exists $hsp->{'lgaps'} |
|
1687
|
0 |
0 |
if ($self->{'_reporttype'} =~ /^FAST[NXY]$/o) { } |
|
1688
|
0 |
0 |
if (8 == scalar grep({exists $hsp->{$_};} 'an0', 'ax0', 'pn0', 'px0', 'an1', 'ax1', 'pn1', 'px1')) { } |
|
1690
|
0 |
0 |
if ($hsp->{'ax0'} < $hsp->{'an0'}) { } |
|
1707
|
0 |
0 |
if ($hsp->{'ax1'} < $hsp->{'an1'}) { } |