| line |
true |
false |
branch |
|
239
|
23 |
0 |
if (not defined $self->sequence_factory) |
|
266
|
5 |
31 |
unless defined $_ and /^ID\s/ |
|
274
|
0 |
31 |
unless (/^
ID \s+ #
(\S+) \s+ # $1 entryname
([^\s;]+); \s+ # $2 DataClass
(?:PRT;)? \s+ # Molecule Type (optional)
[0-9]+[ ]AA \. # Sequencelength (capture?)
$
/ox) |
|
288
|
4 |
1 |
$seq_div eq 'Unreviewed' || $seq_div eq 'PRELIMINARY' ? : |
|
|
26 |
5 |
$seq_div eq 'Reviewed' || $seq_div eq 'STANDARD' ? : |
|
304
|
31 |
950 |
if /^(FT|SQ)/ |
|
307
|
54 |
896 |
if (/^DE\s+(\S.*\S)/) { } |
|
|
36 |
860 |
elsif (/^GN\s+(.*)/) { } |
|
|
31 |
829 |
elsif (/^AC\s+(.+)/) { } |
|
|
90 |
739 |
elsif (/^DT\s+(.*)/) { } |
|
|
1 |
738 |
elsif (/^PE\s+(.*)/) { } |
|
|
30 |
708 |
elsif (/^O[SCG]/) { } |
|
|
30 |
678 |
elsif (/^R/) { } |
|
|
30 |
648 |
elsif (/^CC\s{3}(.*)/) { } |
|
|
599 |
49 |
elsif (/^DR\s+(\S+)\;\s+(\S+)\;\s+([^;]+)[\;\.](.*)$/) { } |
|
|
49 |
0 |
elsif (/^KW\s+(.*)$/) { } |
|
308
|
23 |
31 |
$desc ? : |
|
312
|
6 |
30 |
if $genename |
|
319
|
31 |
0 |
unless defined $params{'-accession_number'} |
|
327
|
30 |
60 |
if ($version =~ /\(Rel\. (\d+), Last sequence update\)/ or /sequence version (\d+)/) { } |
|
|
30 |
30 |
elsif ($version =~ /\(Rel\. (\d+), Last annotation update\)/ or /entry version (\d+)/) { } |
|
405
|
49 |
0 |
if defined $kw[-1] |
|
413
|
30 |
1 |
if ($genename) |
|
415
|
12 |
18 |
if ($genename =~ /\w=\w/) { } |
|
452
|
443 |
0 |
if ($ftunit) { } |
|
467
|
31 |
211 |
if m[^//] |
|
501
|
0 |
4 |
unless defined $seq |
|
503
|
0 |
4 |
unless (ref $seq and $seq->isa('Bio::SeqI')) |
|
514
|
1 |
3 |
unless ($seq->can('division') and defined($div = $seq->division)) |
|
519
|
3 |
1 |
if (defined $ns and $ns ne '') { } |
|
520
|
0 |
0 |
$ns eq 'TrEMBL' ? : |
|
|
3 |
0 |
$ns eq 'Swiss-Prot' ? : |
|
528
|
0 |
4 |
if $seq->display_id =~ /\s/ |
|
532
|
0 |
4 |
if ($self->_id_generation_func) { } |
|
554
|
0 |
4 |
if ($self->_ac_generation_func) { } |
|
|
4 |
0 |
elsif ($seq->can('accession_number')) { } |
|
560
|
3 |
1 |
if ($seq->can('get_secondary_accessions')) |
|
575
|
3 |
1 |
if ($seq->can('get_dates')) |
|
581
|
3 |
6 |
if $ct == 1 |
|
584
|
3 |
6 |
if $ct == 2 |
|
587
|
3 |
6 |
if $ct == 3 |
|
600
|
2 |
1 |
if ($gene->isa('Bio::Annotation::TagTree')) { } |
|
607
|
2 |
6 |
if (exists $genedata{$tag}) |
|
609
|
0 |
2 |
ref $genedata{$tag} eq 'ARRAY' ? : |
|
617
|
0 |
0 |
ref $genedata{$tag} eq 'ARRAY' ? : |
|
633
|
3 |
1 |
if ($seq->can('species') and my $spec = $seq->species) |
|
639
|
0 |
3 |
if ($class[-1] =~ /viruses/i) |
|
641
|
0 |
0 |
if $spec->sub_species |
|
644
|
0 |
3 |
if $_ |
|
649
|
0 |
3 |
if ($spec->organelle) |
|
652
|
3 |
0 |
if ($spec->ncbi_taxid) |
|
664
|
3 |
0 |
if ($ref->rp) |
|
668
|
2 |
1 |
if ($ref->comment) |
|
672
|
0 |
3 |
if ($ref->medline or $ref->pubmed or $ref->doi) |
|
677
|
0 |
0 |
if $ref->medline |
|
678
|
0 |
0 |
if $ref->pubmed |
|
679
|
0 |
0 |
if $ref->doi |
|
687
|
3 |
0 |
if $ref->authors |
|
688
|
0 |
3 |
if $ref->title |
|
689
|
0 |
3 |
if $ref->rg |
|
692
|
0 |
3 |
if $rg |
|
693
|
3 |
0 |
if $author |
|
694
|
0 |
3 |
if $title |
|
716
|
12 |
15 |
if (defined $dblink->comment and $dblink->comment) { } |
|
|
15 |
0 |
elsif ($dblink->optional_id) { } |
|
738
|
0 |
4 |
if (my $func = $self->_kw_generation_func) { } |
|
|
3 |
1 |
elsif ($seq->can('keywords')) { } |
|
742
|
0 |
3 |
if (ref($kw) =~ /ARRAY/i) |
|
745
|
3 |
0 |
if $kw and not $kw =~ /\.$/ |
|
748
|
3 |
1 |
if $kw |
|
754
|
4 |
0 |
$seq->can('top_SeqFeatures') ? : |
|
755
|
3 |
1 |
if ($feats[0]) |
|
756
|
0 |
3 |
if (defined $self->_post_sort) { } |
|
778
|
0 |
9 |
unless ($fth->isa('Bio::SeqIO::FTHelper')) |
|
786
|
0 |
3 |
if ($self->_show_dna == 0) |
|
804
|
24 |
140 |
if (($i + 10) % 60 == 0 and $i + 10 < length $str) |
|
810
|
4 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
839
|
0 |
0 |
if ($crc & 1) { } |
|
865
|
0 |
0 |
unless ref $str eq 'SCALAR' |
|
868
|
0 |
0 |
unless exists $self->{'_crcTable'} |
|
905
|
4 |
0 |
unless ($initialized) |
|
913
|
0 |
8192 |
if $parth & 1 |
|
915
|
4096 |
4096 |
if $rflag |
|
951
|
0 |
9 |
unless (ref $fth and $fth->isa('Bio::SeqIO::FTHelper')) |
|
958
|
9 |
0 |
if (exists $fth->field->{$tag}) |
|
966
|
0 |
9 |
if (exists $fth->field->{'FTId'}) |
|
972
|
6 |
3 |
if ($loc =~ /(\?|\d+|\>\d+|<\d+)?\.\.(\?|\d+|<\d+|>\d+)?/) { } |
|
|
0 |
3 |
elsif ($loc =~ /join\((\d+)((?:,\d+)+)?\)/) { } |
|
973
|
6 |
0 |
if defined $1 |
|
974
|
6 |
0 |
if defined $2 |
|
980
|
0 |
0 |
if (defined(my $m = $2)) |
|
996
|
9 |
0 |
if ($desc) { } |
|
1011
|
0 |
9 |
if ($ftid) |
|
1039
|
257 |
1556 |
if (/^[^R]/ or /^RN/) { } |
|
|
35 |
1521 |
elsif (/^RP\s{3}(.+? OF (\d+)-(\d+).*)/) { } |
|
|
198 |
1323 |
elsif (/^RP\s{3}(.*)/) { } |
|
|
177 |
1146 |
elsif (/^RX\s{3}(.*)/) { } |
|
|
382 |
764 |
elsif (/^RA\s{3}(.*)/) { } |
|
|
16 |
748 |
elsif (/^RG\s{3}(.*)/) { } |
|
|
381 |
367 |
elsif (/^RT\s{3}(.*)/) { } |
|
|
227 |
140 |
elsif (/^RL\s{3}(.*)/) { } |
|
|
140 |
0 |
elsif (/^RC\s{3}(.*)/) { } |
|
1040
|
227 |
30 |
if ($rp) |
|
1041
|
16 |
211 |
if defined $rg |
|
1042
|
223 |
4 |
if (defined $au) { } |
|
1047
|
204 |
23 |
if defined $title |
|
1065
|
30 |
227 |
if (index($_, 'R') != 0) |
|
1077
|
6 |
192 |
if ($rp) { } |
|
1084
|
157 |
20 |
if $line =~ /MEDLINE=(\d+);/ |
|
1085
|
167 |
10 |
if $line =~ /PubMed=(\d+);/ |
|
1086
|
13 |
164 |
if $line =~ /DOI=(.+);/ |
|
1088
|
159 |
223 |
$au ? : |
|
1090
|
0 |
16 |
$rg ? : |
|
1092
|
177 |
204 |
if ($title) { } |
|
1094
|
163 |
14 |
$title =~ /[\w;,:\?!]$/ ? : |
|
1099
|
0 |
227 |
$loc ? : |
|
1101
|
0 |
140 |
$com ? : |
|
1132
|
30 |
153 |
unless /^O[SCGX]/ |
|
1135
|
30 |
123 |
if (/^OS\s+(\S.+)/ and not defined $sci_name) { } |
|
|
62 |
61 |
elsif (s/^OC\s+(\S.+)$//) { } |
|
|
0 |
61 |
elsif (/^OG\s+(.*)/) { } |
|
|
29 |
62 |
elsif (/^OX\s+(.*)/ and not defined $ncbi_taxid) { } |
|
1136
|
0 |
30 |
if $osline |
|
1138
|
30 |
0 |
if ($osline =~ s/(,|, and|\.)$//) |
|
1145
|
0 |
30 |
if ($osline =~ /[^\(\)]+\(.+\)[^\(\)]+$/) { } |
|
1161
|
0 |
13 |
if (not defined $variant and $item =~ /(^|[^\(\w])([Ss]train|isolate|serogroup|serotype|subtype|clone)\b/ || $item =~ /^(biovar|pv\.|type\s+)/) { } |
|
|
0 |
13 |
elsif ($item =~ s/^subsp\.\s+//) { } |
|
|
13 |
0 |
elsif (not defined $common) { } |
|
1166
|
0 |
0 |
if (not $sub_species) { } |
|
|
0 |
0 |
elsif (not $variant) { } |
|
1174
|
0 |
13 |
if (index($common, '(') >= 0 and index($common, ')') < 0) |
|
1188
|
29 |
0 |
if ($taxstring =~ /NCBI_TaxID=([\w\d]+)/) { } |
|
1198
|
0 |
30 |
unless $sci_name |
|
1201
|
0 |
30 |
if grep {$_ eq $sci_name;} @Bio::SeqIO::swiss::Unknown_names |
|
1210
|
0 |
30 |
if ($class[0] =~ /viruses/i) { } |
|
|
30 |
0 |
elsif ($do_genus_check) { } |
|
1213
|
0 |
0 |
@virusnames > 1 ? : |
|
1219
|
30 |
0 |
if $class[-2] |
|
1220
|
30 |
0 |
if ($sci_name =~ /^($possible_genus)/) { } |
|
1228
|
0 |
30 |
if ($species and $species =~ /subsp\.|var\./) |
|
1234
|
30 |
0 |
unless ($class[-1] eq $sci_name) |
|
1242
|
13 |
17 |
if $common |
|
1243
|
0 |
30 |
if $sub_species |
|
1244
|
0 |
30 |
if $org |
|
1245
|
29 |
1 |
if $ncbi_taxid |
|
1246
|
0 |
30 |
if $variant |
|
1291
|
443 |
0 |
if (/^FT\s{3}(\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/ox) |
|
1296
|
384 |
59 |
if ($4 and length $4 > 0) { } |
|
1306
|
272 |
40 |
if ($continuation_line =~ /.FTId=(.*)\./) { } |
|
|
40 |
0 |
elsif ($desc) { } |
|
1317
|
0 |
443 |
unless ($key) |
|
1329
|
384 |
59 |
if ($desc and length $desc) |
|
1334
|
272 |
171 |
if ($ftid) |
|
1356
|
0 |
0 |
unless $length |
|
1393
|
0 |
44 |
unless $length |
|
1395
|
0 |
44 |
if (length $pre1 != length $pre2) |
|
1405
|
9 |
45 |
if $pre1 eq 'RA ' or $pre1 eq 'KW ' |
|
1408
|
10 |
44 |
if substr($s, -1, 1) eq ' ' |
|
1409
|
44 |
10 |
if ($first_line) { } |
|
1432
|
0 |
3 |
if (@_) |
|
1453
|
23 |
3 |
if (@_) |
|
1474
|
0 |
4 |
if (@_) |
|
1495
|
0 |
4 |
if (@_) |
|
1516
|
0 |
0 |
if (@_) |
|
1537
|
0 |
4 |
if (@_) |