| line |
true |
false |
branch |
|
259
|
0 |
42 |
unless $format |
|
262
|
42 |
0 |
if $builder |
|
287
|
42 |
33 |
unless ($self->{'handlers'}) |
|
289
|
0 |
42 |
unless exists $HANDLERS{$self->format} |
|
316
|
16 |
0 |
exists $self->{'handlers'}{'_DEFAULT_'} ? : |
|
|
1630 |
16 |
exists $self->{'handlers'}{$nm} ? : |
|
318
|
0 |
1646 |
unless ($method) |
|
357
|
42 |
1259 |
if @_ |
|
378
|
818 |
0 |
if (!index($id, '-') == 0) |
|
381
|
814 |
4 |
if exists $self->{'_params'}{$id} |
|
416
|
42 |
62 |
if @_ |
|
436
|
58 |
4 |
if (defined $self->{'_params'}) |
|
441
|
58 |
4 |
if $seq |
|
459
|
0 |
42 |
if ($factory) { } |
|
|
42 |
0 |
elsif (not defined $self->{'_locfactory'}) { } |
|
460
|
0 |
0 |
unless ref $factory and $factory->isa('Bio::Factory::LocationFactoryI') |
|
484
|
0 |
746 |
if ($coll) { } |
|
|
57 |
689 |
elsif (not exists $self->{'_params'}{'-annotation'}) { } |
|
485
|
0 |
0 |
unless ref $coll and $coll->isa('Bio::AnnotationCollectionI') |
|
512
|
0 |
31 |
if (exists $VALID_ALPHABET{$seqlength}) { } |
|
525
|
31 |
0 |
exists $VALID_ALPHABET{$alphabet} ? : |
|
527
|
31 |
0 |
if ($self->{'_params'}{'-alphabet'} eq 'dna' or @tokens > 2) { } |
|
530
|
2 |
29 |
if ($circ eq 'circular') { } |
|
535
|
14 |
15 |
length $circ == 3 ? : |
|
539
|
0 |
0 |
if $self->{'_params'}{'-alphabet'} eq 'aa' |
|
544
|
30 |
1 |
if ($date and $date =~ s/\s*((\d{1,2})-(\w{3})-(\d{2,4})).*/$1/) |
|
546
|
0 |
30 |
if (length $date < 11) { } |
|
550
|
0 |
0 |
if (length $d == 1) |
|
554
|
0 |
0 |
if (length $y == 2) |
|
555
|
0 |
0 |
if ($y > 60) { } |
|
577
|
1 |
9 |
if ($idtype == 6) { } |
|
|
8 |
1 |
elsif ($idtype) { } |
|
584
|
1 |
0 |
if ($line =~ /^(\w+);\s+SV (\d+); (\w+); ([^;]+); (\w{3}); (\w{3}); (\d+) \w{2}\./) { } |
|
589
|
1 |
0 |
if (defined $sv) |
|
594
|
0 |
1 |
if ($topology eq 'circular') |
|
598
|
1 |
0 |
if (defined $mol) |
|
599
|
0 |
1 |
if ($mol =~ /DNA/) { } |
|
|
1 |
0 |
elsif ($mol =~ /RNA/) { } |
|
|
0 |
0 |
elsif ($mol =~ /AA/) { } |
|
611
|
8 |
0 |
if ($line =~ /^(\S+)[^;]*;\s+(\S+)[^;]*;\s+(\S+)[^;]*;/) |
|
616
|
8 |
0 |
if ($mol) |
|
617
|
0 |
8 |
if ($mol =~ /circular/) |
|
621
|
8 |
0 |
if (defined $mol) |
|
622
|
7 |
1 |
if ($mol =~ /DNA/) { } |
|
|
1 |
0 |
elsif ($mol =~ /RNA/) { } |
|
|
0 |
0 |
elsif ($mol =~ /AA/) { } |
|
636
|
0 |
10 |
unless (defined $name and length $name) |
|
641
|
9 |
1 |
if $div |
|
642
|
9 |
1 |
if $mol |
|
649
|
17 |
0 |
if ($data->{'DATA'} =~ /^
(\S+) \s+ # $1 entryname
([^\s;]+); \s+ # $2 DataClass
(?:PRT;)? \s+ # Molecule Type (optional)
[0-9]+[ ]AA \. # Sequencelength (capture?)
$
/ox) { } |
|
657
|
4 |
0 |
$seq_div eq 'Unreviewed' || $seq_div eq 'PRELIMINARY' ? : |
|
|
13 |
4 |
$seq_div eq 'Reviewed' || $seq_div eq 'STANDARD' ? : |
|
679
|
17 |
0 |
if ($genename) |
|
681
|
10 |
7 |
if ($genename =~ /\w=\w/) { } |
|
717
|
27 |
1 |
if ($acc =~ /^\w+\.(\d+)/mosx) |
|
721
|
24 |
4 |
if ($gi and index($gi, 'GI:') == 0) |
|
732
|
0 |
10 |
if ($version =~ /\(Rel\.\s(\d+),\sCreated\)/mosx) { } |
|
|
0 |
10 |
elsif ($version =~ /\(Rel\.\s(\d+),\sLast\supdated,\sVersion\s(\d+)\)/mosx) { } |
|
762
|
17 |
34 |
if ($version =~ /\(Rel\. (\d+), Last sequence update\)/ or $version =~ /sequence version (\d+)\./) { } |
|
|
17 |
17 |
elsif ($version =~ /\(Rel\. (\d+), Last annotation update\)/ or $version =~ /entry version (\d+)\./) { } |
|
803
|
9 |
47 |
if @accs |
|
817
|
30 |
26 |
if ($seqformat eq 'genbank' and $data->{'ORGANISM'} =~ /(.+?)\s(\S+;[^\n\.]+)/ox) |
|
828
|
17 |
39 |
if ($seqformat eq 'swiss') |
|
829
|
17 |
0 |
if ($data->{'DATA'} =~ /^([^,]+)/ox) |
|
832
|
16 |
1 |
if ($data->{'CROSSREF'} and $data->{'CROSSREF'} =~ /NCBI_TaxID=(\d+)/) |
|
843
|
56 |
0 |
if ($sl =~ /^(mitochondrion|chloroplast|plastid)? # GenBank format
\s*(.*?)
\s*(?: \( (.*?) \) )?\.?$
/mosx) { } |
|
852
|
26 |
30 |
if $seqformat ne 'genbank' |
|
855
|
0 |
56 |
unless $sci_name |
|
860
|
56 |
0 |
if @class > 0 |
|
861
|
16 |
40 |
if $common |
|
862
|
56 |
0 |
if $abbr_name |
|
863
|
2 |
54 |
if $organelle |
|
864
|
16 |
40 |
if $taxid |
|
877
|
0 |
1 |
if ($dbsource =~ s/(UniProt(?:KB)|swissprot):\s+locus\s+(\S+)\,.+\n//) { } |
|
884
|
0 |
0 |
if ($dbsource =~ s/\s*created:\s+([^\.]+)\.\n//) |
|
899
|
0 |
0 |
if ($dbsource =~ s/\s*xrefs:\s+((?:\S+,\s+)+\S+)\s+xrefs/xrefs/) { } |
|
|
0 |
0 |
elsif ($dbsource =~ s/\s*xrefs:\s+(.+)\s+xrefs/xrefs/i) { } |
|
904
|
0 |
0 |
if ($dbsrc =~ /(\S+)\.(\d+)/ or $dbsrc =~ /(\S+)/) |
|
906
|
0 |
0 |
unless defined $version |
|
908
|
0 |
0 |
if ($id =~ /^\d\S{3}/) { } |
|
911
|
0 |
0 |
$i++ % 2 ? : |
|
927
|
0 |
0 |
if ($id =~ /gi:\s+(\d+)/) { } |
|
|
0 |
0 |
elsif ($id =~ /pdb\s+accession\s+(\S+)/) { } |
|
929
|
0 |
0 |
$i++ % 2 ? : |
|
947
|
0 |
0 |
if ($dbsource =~ s/xrefs\s+\(non\-sequence\s+databases\):\s+
((?:\S+,\s+)+\S+)//x) |
|
957
|
0 |
0 |
unless (exists $DBSOURCE{$db}) |
|
969
|
1 |
0 |
if ($dbsource =~ /^(\S*?):?\s*accession\s+(\S+)\.(\d+)/) { } |
|
|
0 |
0 |
elsif ($dbsource =~ /(\S+)([\.:])(\d+)/) { } |
|
980
|
0 |
0 |
if ($2 eq ':') { } |
|
1008
|
351 |
0 |
if ($dblink =~ /([^\s;]+);\s*([^\s;]+);?\s*([^\s;]+)?/) { } |
|
1030
|
128 |
173 |
if ($data->{'CROSSREF'}) |
|
1038
|
109 |
192 |
if ($seqformat eq 'swiss') |
|
1044
|
127 |
174 |
if ($data->{'POSITION'}) |
|
1045
|
18 |
109 |
if ($seqformat eq 'embl') { } |
|
|
23 |
86 |
elsif ($data->{'POSITION'} =~ /.+? OF (\d+)-(\d+).*/) { } |
|
1051
|
59 |
242 |
if ($data->{'DATA'} =~ /^\d+\s+\([a-z]+\s+(\d+)\s+to\s+(\d+)\)/mosx) |
|
1067
|
59 |
242 |
if ($data->{'DATA'} =~ /^\d+\s+\((.*)\)/mosx) |
|
1087
|
30 |
818 |
if $data->{'FEATURE_KEY'} eq 'FEATURES' |
|
1091
|
36 |
5 |
if ($primary_tag eq 'source' and exists $data->{'db_xref'}) |
|
1092
|
35 |
1 |
if ($self->{'_params'}{'-species'} and $data->{'db_xref'} =~ /taxon:(\d+)/mosx) |
|
1105
|
0 |
818 |
unless ($loc) |
|
1113
|
0 |
818 |
if ($seqid and not $loc->is_remote) |