| line |
true |
false |
branch |
|
223
|
3 |
4 |
if defined $model |
|
224
|
3 |
4 |
if defined $database |
|
225
|
4 |
3 |
if defined $accession |
|
226
|
3 |
4 |
if defined $convert |
|
227
|
4 |
3 |
if defined $desc |
|
251
|
7 |
2 |
unless (exists $self->{'_handlerset'}) |
|
255
|
2 |
7 |
if $line =~ /^\s*$/ |
|
257
|
4 |
3 |
if ($line =~ /^\#\s+cmsearch\s/) { } |
|
|
1 |
2 |
elsif ($line =~ /^CM\s\d+:/) { } |
|
259
|
3 |
1 |
if ($secondline =~ /INFERNAL 1\.1/) { } |
|
285
|
1 |
2 |
$self->{'_handlerset'} eq 'pre-1.0' ? : |
|
|
1 |
3 |
$self->{'_handlerset'} eq 'latest' ? : |
|
|
5 |
4 |
$self->{'_handlerset'} eq '1.1' ? : |
|
299
|
1 |
4 |
if (not defined $buffer or $buffer =~ /^\[ok/) { } |
|
313
|
3 |
49 |
if ($buffer =~ /^\#\s(\S+)\s\:\:\s/) { } |
|
|
3 |
46 |
elsif ($buffer =~ /^\#\sINFERNAL\s+(\S+)\s+\((.+)\)/) { } |
|
|
3 |
43 |
elsif ($buffer =~ /^\#\squery (?:\w+ )?file\:\s+(\S+)/) { } |
|
|
3 |
40 |
elsif ($buffer =~ /^\#\starget\s\S+\sdatabase\:\s+(\S+)/) { } |
|
|
4 |
36 |
elsif ($buffer =~ /^Query:\s+(\S+)\s+\[CLEN=(\d+)\]$/) { } |
|
|
3 |
33 |
elsif ($buffer =~ s/^Accession:\s+// and not $accession) { } |
|
|
2 |
31 |
elsif ($buffer =~ s/^Description:\s+// and not $description) { } |
|
|
4 |
27 |
elsif ($buffer =~ /^Hit scores:/) { } |
|
|
4 |
23 |
elsif ($buffer =~ /^Hit alignments:/) { } |
|
|
4 |
19 |
elsif ($buffer =~ /Internal CM pipeline statistics summary:/) { } |
|
365
|
4 |
34 |
if ($buffer =~ /^Hit alignments:/) { } |
|
|
19 |
15 |
elsif ($buffer =~ /^\s+rank\s+E-value/ or $buffer =~ /\-\-\-/ or $buffer =~ /^$/ or $buffer =~ /No hits detected/) { } |
|
382
|
0 |
15 |
unless defined $desc |
|
394
|
4 |
34 |
if ($buffer =~ /^Internal CM pipeline statistics summary/) |
|
398
|
15 |
19 |
if ($buffer =~ /^\>\>\s(\S*)\s+(.*)/) { } |
|
|
15 |
4 |
elsif ($buffer =~ /NC$/) { } |
|
411
|
15 |
60 |
if ($buffer =~ /^Internal CM pipeline statistics/ or $buffer =~ /NC$/ or $buffer =~ /^\>\>/) { } |
|
|
45 |
15 |
elsif ($buffer =~ /^\s+rank\s+E-value/ or $buffer =~ /^\s----/ or $buffer =~ /^$/ or $buffer =~ /No hits detected/) { } |
|
435
|
10 |
5 |
$seq_cov =~ /\]$/ ? : |
|
438
|
0 |
15 |
unless (defined $tmphit) |
|
470
|
15 |
153 |
if ($buffer =~ /^>>\s/ or $buffer =~ /^Internal CM pipeline statistics/) { } |
|
|
27 |
231 |
elsif ($ct % 6 == 0 and $buffer =~ /^$/) { } |
|
480
|
21 |
105 |
if $iterator == 0 |
|
495
|
0 |
15 |
$self->convert_meta ? : |
|
510
|
4 |
64 |
if $buffer =~ m[^//] |
|
512
|
4 |
60 |
if ($buffer =~ /^Target sequences:\s+(\d+)\s+\((\d+) residues/) |
|
544
|
15 |
0 |
if (defined $hsp) |
|
550
|
10 |
5 |
if ($hitlength != 0) |
|
602
|
69 |
0 |
if ($type) |
|
603
|
69 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
609
|
7 |
62 |
if (defined $type and $type eq 'result') |
|
633
|
70 |
13 |
if ($type) { } |
|
|
13 |
0 |
elsif ($MAPPING{$nm}) { } |
|
634
|
70 |
0 |
if ($self->_eventHandler->will_handle($type)) |
|
644
|
23 |
47 |
if ($type eq 'hit') |
|
650
|
0 |
13 |
if (ref($MAPPING{$nm}) =~ /hash/i) { } |
|
664
|
8 |
75 |
if defined $type and $type eq 'result' |
|
700
|
0 |
124 |
unless $data and ref $data |
|
702
|
8 |
707 |
if $data->{$nm} and $data->{$nm} =~ /^\s*$/o |
|
703
|
707 |
0 |
if ($MAPPING{$nm}) |
|
704
|
0 |
707 |
if (ref($MAPPING{$nm}) =~ /hash/i) { } |
|
729
|
0 |
13 |
unless defined $data->{'Data'} and not $data->{'Data'} =~ /^\s+$/o |
|
750
|
3 |
40 |
if not defined $name && defined $self->{'_elements'} or scalar @{$self->{'_elements'};} == 0 |
|
752
|
28 |
24 |
if $_ eq $name |
|
771
|
0 |
86 |
unless defined $self->{'_elements'}[0] |
|
836
|
3 |
2 |
if @_ |
|
853
|
3 |
3 |
if @_ |
|
870
|
7 |
3 |
if @_ |
|
887
|
4 |
9 |
if @_ |
|
904
|
4 |
9 |
if @_ |
|
920
|
7 |
2 |
if @_ |
|
937
|
3 |
39 |
if @_ |
|
953
|
7 |
2 |
if @_ |
|
974
|
7 |
3 |
if ($delim) |
|
975
|
7 |
0 |
if (ref($delim) =~ /HASH/) { } |
|
978
|
35 |
0 |
if (exists $data{$d}) |
|
1005
|
0 |
3 |
unless $str |
|
1033
|
7 |
48 |
if $line =~ /^\s+$/ |
|
1035
|
1 |
47 |
if ($line =~ /^\#\s+cmsearch/msx) { } |
|
|
1 |
46 |
elsif ($line =~ /^\#\sINFERNAL\s+(\d+\.\d+)/msx) { } |
|
|
1 |
45 |
elsif ($line =~ /^\#\scommand:.*?\s(\S+)$/msx) { } |
|
|
1 |
44 |
elsif ($line =~ /^\#\s+dbsize\(Mb\):\s+(\d+\.\d+)/msx) { } |
|
|
1 |
43 |
elsif ($line =~ /^CM(?:\s(\d+))?:\s*(\S+)/msx) { } |
|
|
1 |
42 |
elsif ($line =~ /^>\s*(\S+)/) { } |
|
|
3 |
39 |
elsif ($line =~ m[
^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end
Target\s=\s(\d+)\s-\s(\d+) # Target start/end
]mosx) { } |
|
|
3 |
36 |
elsif ($line =~ /
^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now)
(?:E\s=\s([\d\.e-]+),\s # E-val optional
P\s=\s([\d\.e-]+),\s)? # P-val optional
GC\s= # GC not captured
/mosx) { } |
|
|
3 |
33 |
elsif ($line =~ /^(\s+)[<>\{\}\(\)\[\]:_,-\.]+/msx) { } |
|
|
1 |
32 |
elsif ($line =~ m[^//]msx) { } |
|
1070
|
0 |
1 |
if ($self->in_element('hit')) |
|
1096
|
3 |
0 |
if ($lasteval and $lastpval) |
|
1099
|
0 |
3 |
$mineval > $lasteval ? : |
|
1101
|
0 |
3 |
$minpval > $lastpval ? : |
|
1104
|
0 |
3 |
$maxscore < $lastscore ? : |
|
1106
|
1 |
2 |
unless ($self->within_element('hit')) |
|
1109
|
1 |
0 |
$acc ? : |
|
|
0 |
1 |
$ver ? : |
|
1116
|
3 |
0 |
unless ($self->in_element('hsp')) |
|
1136
|
8 |
23 |
unless $line |
|
1143
|
3 |
20 |
if ($line =~ /^\s{0,2}\S+/) |
|
1150
|
5 |
15 |
if $iterator == 0 |
|
1162
|
3 |
0 |
if ($self->in_element('hsp')) |
|
1178
|
0 |
3 |
$self->convert_meta ? : |
|
1193
|
3 |
0 |
if $lasteval and $lastpval |
|
1201
|
1 |
0 |
if ($self->within_element('result') and $seentop) |
|
1202
|
1 |
0 |
if ($self->in_element('hit')) |
|
1206
|
1 |
0 |
if $mineval |
|
1207
|
1 |
0 |
if $minpval |
|
1214
|
0 |
1 |
if $self->within_element('hit') |
|
1215
|
1 |
0 |
if $seentop |
|
1232
|
25 |
60 |
if $line =~ /^\s+$/ |
|
1234
|
1 |
59 |
if ($line =~ /CM\s\d+:\s*(\S+)/msx) { } |
|
|
3 |
56 |
elsif ($line =~ /^>\s*(\S+)/) { } |
|
|
15 |
41 |
elsif ($line =~ m[
^\sQuery\s=\s\d+\s-\s\d+,\s # Query start/end
Target\s=\s(\d+)\s-\s(\d+) # Target start/end
]mosx) { } |
|
|
15 |
26 |
elsif ($line =~ /
^\sScore\s=\s([\d\.]+),\s # Score = Bitscore (for now)
(?:E\s=\s([\d\.e-]+),\s # E-val optional
P\s=\s([\d\.e-]+),\s)? # P-val optional
GC\s= # GC not captured
/mosx) { } |
|
|
15 |
11 |
elsif ($line =~ /^(\s+)[<>\{\}\(\)\[\]:_,-\.]+/msx) { } |
|
|
1 |
10 |
elsif ($line =~ m[^//]msx) { } |
|
1236
|
1 |
0 |
unless ($self->within_element('result')) |
|
1249
|
2 |
1 |
if ($self->in_element('hit')) |
|
1275
|
15 |
0 |
if ($lasteval and $lastpval) |
|
1278
|
0 |
15 |
$mineval > $lasteval ? : |
|
1280
|
0 |
15 |
$minpval > $lastpval ? : |
|
1283
|
0 |
15 |
$maxscore < $lastscore ? : |
|
1285
|
3 |
12 |
unless ($self->within_element('hit')) |
|
1288
|
0 |
0 |
$acc ? : |
|
|
3 |
0 |
$ver ? : |
|
1295
|
15 |
0 |
unless ($self->in_element('hsp')) |
|
1315
|
45 |
135 |
unless $line |
|
1322
|
15 |
120 |
if ($line =~ /^\s{0,2}\S+/) |
|
1329
|
30 |
90 |
if $iterator == 0 |
|
1341
|
15 |
0 |
if ($self->in_element('hsp')) |
|
1346
|
0 |
15 |
$self->convert_meta ? : |
|
1361
|
15 |
0 |
if $lasteval and $lastpval |
|
1369
|
1 |
0 |
if ($self->within_element('result') and $seentop) |
|
1374
|
1 |
0 |
if ($self->in_element('hit')) |
|
1378
|
1 |
0 |
if $mineval |
|
1385
|
0 |
1 |
if $self->within_element('hit') |
|
1386
|
1 |
0 |
if $seentop |
|
1407
|
0 |
88 |
if $line =~ /^\s+$/ |
|
1409
|
0 |
88 |
if $line =~ /^HMM\shit/ |
|
1411
|
4 |
84 |
if ($line =~ /^sequence:\s+(\S+)/) { } |
|
|
52 |
32 |
elsif ($line =~ /^hit\s+\d+\s+:\s+(\d+)\s+(\d+)\s+(\d+\.\d+)\s+bits/msx) { } |
|
|
26 |
6 |
elsif ($line =~ /^(\s+)[<>\{\}\(\)\[\]:_,-\.]+/msx) { } |
|
|
2 |
4 |
elsif ($line =~ /^memory/msx or $line =~ /^CYK\smemory/msx) { } |
|
1412
|
2 |
2 |
unless ($self->within_element('result')) |
|
1423
|
2 |
2 |
if ($self->in_element('hit')) |
|
1432
|
4 |
48 |
unless $maxscore |
|
1433
|
12 |
40 |
if ($lastscore > $cutoff) |
|
1434
|
4 |
8 |
unless ($self->within_element('hit')) |
|
1437
|
0 |
0 |
$acc ? : |
|
|
4 |
0 |
$ver ? : |
|
1445
|
6 |
6 |
unless ($self->in_element('hsp')) |
|
1448
|
2 |
10 |
$maxscore < $lastscore ? : |
|
1464
|
54 |
234 |
if $line =~ /^\s*$/ |
|
1467
|
26 |
208 |
if (not defined $line or $line =~ /^\S+/) |
|
1474
|
52 |
156 |
if $iterator == 0 |
|
1484
|
6 |
20 |
if ($self->in_element('hsp')) |
|
1490
|
3 |
3 |
$self->convert_meta ? : |
|
1508
|
2 |
0 |
if ($self->within_element('result') and $seentop) |
|
1513
|
2 |
0 |
if ($self->in_element('hit')) |
|
1522
|
0 |
2 |
if $self->within_element('hit') |
|
1523
|
2 |
0 |
if $seentop |