| line |
true |
false |
branch |
|
245
|
2 |
0 |
if not $INC{'AnyDBM_File.pm'} |
|
391
|
1 |
19 |
if ($ref eq 'ARRAY') { } |
|
397
|
9 |
10 |
if (-d $path) { } |
|
|
10 |
0 |
elsif (-f _) { } |
|
400
|
0 |
9 |
if $^O =~ /^MSWin/i and eval 'use Win32; 1' |
|
432
|
0 |
1 |
unless tie $$fh, 'Bio::DB::Indexed::Stream', $self |
|
450
|
38 |
0 |
unless my $args = $self->{'dbmargs'} |
|
451
|
0 |
0 |
ref $args eq 'ARRAY' ? : |
|
485
|
0 |
9 |
if scalar @files == 0 |
|
531
|
9 |
9 |
if -d $path |
|
621
|
0 |
22 |
unless defined $id |
|
622
|
4 |
18 |
unless exists $self->{'offsets'}{$id} |
|
657
|
12 |
8 |
if ($force_reindex) |
|
659
|
0 |
12 |
if -e $index |
|
661
|
2 |
10 |
if -e "$index.dir" |
|
662
|
2 |
10 |
if -e "$index.pag" |
|
676
|
20 |
43 |
if ($m > $modtime) |
|
679
|
63 |
0 |
if ($m > $indextime) |
|
689
|
0 |
20 |
unless $self->{'offsets'} = $self->_open_index($index, $reindex) |
|
690
|
20 |
0 |
if ($reindex) |
|
710
|
20 |
18 |
$write ? : |
|
712
|
0 |
38 |
unless tie %offsets, 'AnyDBM_File', $index_file, $flags, 420, @dbmargs |
|
741
|
20 |
25 |
if (not defined $start || defined $stop || defined $strand and $id =~ /$compound_id/x) |
|
751
|
7 |
2 |
$stop > 0 ? : |
|
758
|
8 |
37 |
if ($start > $stop) |
|
774
|
44 |
0 |
$alphabet eq 'protein' ? : |
|
|
11 |
44 |
$alphabet eq 'rna' ? : |
|
|
2942 |
55 |
$alphabet eq 'dna' ? : |
|
784
|
14 |
3039 |
ref $self->{'makeid'} eq 'CODE' ? : |
|
791
|
9 |
96 |
unless defined $linelength |
|
792
|
0 |
96 |
if $linelength > 65535 |
|
803
|
0 |
20 |
unless my $fh = 'IO::File'->new($file) |
|
815
|
0 |
20 |
$curr_line =~ /\r\n$/ ? : |
|
827
|
2 |
86 |
if $n < 0 |
|
828
|
2 |
86 |
if $n >= $seqlen |
|
836
|
0 |
49 |
unless defined $id |
|
837
|
1 |
48 |
unless my $file = $self->file($id) |
|
838
|
0 |
0 |
unless return $self->_fhcache('File::Spec'->catfile($self->{'dirname'}, $file)) |
|
845
|
9 |
39 |
unless ($self->{'fhcache'}{$path}) |
|
846
|
0 |
9 |
if ($self->{'curopen'} >= $self->{'maxopen'}) |
|
882
|
0 |
1 |
unless defined $id |
|
883
|
0 |
1 |
unless my $offset = $self->{'offsets'}{$id} |
|
900
|
0 |
16 |
unless defined $id |
|
901
|
0 |
16 |
unless my $offset = $self->{'offsets'}{$id} |
|
918
|
0 |
30 |
unless defined $id |
|
919
|
1 |
29 |
unless my $offset = $self->{'offsets'}{$id} |
|
936
|
0 |
0 |
unless defined $id |
|
937
|
0 |
0 |
unless my $offset = $self->{'offsets'}{$id} |
|
954
|
0 |
0 |
unless defined $id |
|
955
|
0 |
0 |
unless my $offset = $self->{'offsets'}{$id} |
|
973
|
0 |
0 |
unless defined $id |
|
974
|
0 |
0 |
unless $self->{'offsets'}{$id} |
|
991
|
0 |
13 |
unless defined $id |
|
992
|
0 |
13 |
unless my $offset = $self->{'offsets'}{$id} |
|
994
|
2 |
1 |
$alphabet == 3 ? : |
|
|
2 |
3 |
$alphabet == 2 ? : |
|
|
8 |
5 |
$alphabet == 1 ? : |
|
1014
|
0 |
59 |
unless defined $id |
|
1015
|
1 |
58 |
unless my $offset = $self->{'offsets'}{$id} |
|
1028
|
63 |
62 |
unless (exists $self->{'filepath2no'}{$path}) |
|
1064
|
0 |
20 |
if ($maxsize > $fourGB) { } |
|
1125
|
10 |
0 |
if (defined $fh) |
|
1131
|
6 |
21 |
if ($self->{'clean'} or $self->{'indexing'}) |
|
1136
|
0 |
6 |
if -e $index |
|
1138
|
5 |
1 |
if -e "$index.dir" |
|
1139
|
5 |
1 |
if -e "$index.pag" |
|
1165
|
1 |
9 |
unless defined $key |