| line |
true |
false |
branch |
|
296
|
0 |
1 |
if ($self->index_directory and $self->read_config_file) |
|
306
|
1 |
0 |
if ($self->write_flag and not $primary_namespace) |
|
352
|
0 |
0 |
unless (defined $self->format) |
|
356
|
0 |
0 |
unless $fh |
|
358
|
0 |
0 |
if (not defined $self->{'_seqio'}) { } |
|
409
|
0 |
0 |
unless ($self->record_size) |
|
410
|
0 |
0 |
if ($self->index_directory and $self->read_config_file) |
|
422
|
0 |
0 |
unless $self->record_size |
|
433
|
0 |
0 |
unless ($newid) |
|
439
|
0 |
0 |
unless open my $IN, '<', $file |
|
465
|
0 |
0 |
if ($self->primary_namespace eq 'ACC') { } |
|
490
|
0 |
0 |
if ($self->primary_namespace eq 'VERSION') { } |
|
516
|
0 |
0 |
if ($name eq $tmpname) |
|
521
|
0 |
0 |
if ($found == 0) |
|
574
|
0 |
0 |
if ($current_id eq $newid) |
|
586
|
0 |
0 |
unless (defined $newid) |
|
595
|
0 |
0 |
wantarray ? : |
|
701
|
0 |
0 |
$id le $entryid ? : |
|
704
|
0 |
0 |
if ($id eq $entryid) { } |
|
|
0 |
0 |
elsif ($first eq $id) { } |
|
|
0 |
0 |
elsif ($second eq $id) { } |
|
711
|
0 |
0 |
if ($end - $start <= 1) |
|
723
|
0 |
0 |
if ($end - $start <= 1) |
|
747
|
0 |
1 |
unless $self->write_flag |
|
752
|
0 |
1 |
unless (defined $rootdir) |
|
756
|
0 |
1 |
unless (-d $rootdir) |
|
763
|
0 |
1 |
unless (-d $dbpath) |
|
765
|
0 |
0 |
unless mkdir $dbpath, 511 |
|
768
|
0 |
1 |
unless (@files) |
|
773
|
1 |
0 |
unless 'File::Spec'->file_name_is_absolute($file) |
|
775
|
0 |
1 |
unless (-e $file) |
|
780
|
0 |
1 |
if (my $filehash = $self->{'_dbfile'}) |
|
818
|
0 |
1 |
unless open my $FILE, '<', $file |
|
856
|
7 |
51 |
if ($_ =~ /$start_pattern/) |
|
857
|
6 |
1 |
if ($done == 0) { } |
|
865
|
0 |
6 |
unless (defined $id) |
|
868
|
0 |
6 |
unless (defined $fileid) |
|
871
|
0 |
6 |
unless (defined $pos) |
|
874
|
0 |
6 |
unless (defined $length) |
|
882
|
0 |
6 |
if ($count > 0 and $count % 1000 == 0) |
|
883
|
0 |
0 |
if $v > 0 |
|
893
|
7 |
51 |
if ($_ =~ /$primary/) |
|
902
|
0 |
0 |
if ($_ =~ /$pattern/) |
|
918
|
0 |
1 |
unless (defined $id) |
|
921
|
0 |
1 |
unless (defined $fileid) |
|
924
|
0 |
1 |
unless (defined $pos) |
|
927
|
0 |
1 |
unless (defined $length) |
|
957
|
0 |
1 |
unless open my $INDEX, '>', $self->primary_index_file |
|
971
|
0 |
7 |
unless (defined $self->{'_id'}{$id}{'_fileid'}) |
|
974
|
0 |
7 |
unless (defined $self->{'_id'}{$id}{'_pos'}) |
|
977
|
0 |
7 |
unless (defined $self->{'_id'}{$id}{'_length'}) |
|
1024
|
0 |
0 |
if ($recordlen > $length) |
|
1044
|
0 |
0 |
if (length $record > $length) { } |
|
1078
|
0 |
0 |
unless open my $fh, '>', $secindex |
|
1097
|
0 |
0 |
unless (defined $self->{'_secondary_filehandle'}{$name}) |
|
1102
|
0 |
0 |
unless (-e $secindex) |
|
1106
|
0 |
0 |
unless open my $newfh, '<', $secindex |
|
1132
|
0 |
7 |
unless (defined $id) |
|
1135
|
0 |
7 |
unless (defined $pos) |
|
1138
|
0 |
7 |
unless (defined $fileid) |
|
1141
|
0 |
7 |
if (not defined $length or $length <= 0) |
|
1159
|
5 |
2 |
if not exists $self->{'_maxidlength'} or length $id >= $self->{'_maxidlength'} |
|
1163
|
7 |
0 |
if not exists $self->{'_maxfileidlength'} or length $fileid >= $self->{'_maxfileidlength'} |
|
1167
|
7 |
0 |
if not exists $self->{'_maxposlength'} or length $pos >= $self->{'_maxposlength'} |
|
1171
|
7 |
0 |
if not exists $self->{'_maxlengthlength'} or length $length >= $self->{'_maxlengthlength'} |
|
1192
|
0 |
2 |
unless open my $CON, '>', $configfile |
|
1224
|
0 |
2 |
if (@second) |
|
1235
|
0 |
2 |
if (not defined $self->format) { } |
|
1242
|
0 |
2 |
$alphabet ? : |
|
1262
|
1 |
0 |
unless -e $configfile |
|
1264
|
0 |
0 |
unless open my $CON, '<', $configfile |
|
1273
|
0 |
0 |
if ($line =~ m[index\tflat/(\d+)]) { } |
|
1289
|
0 |
0 |
if ($_ =~ /^fileid_(\d+)\t(.+)\t(\d+)/) |
|
1294
|
0 |
0 |
unless (-e $filename) |
|
1297
|
0 |
0 |
if (-s $filename != $filesize) |
|
1312
|
0 |
0 |
if (/(.*)_namespaces?\t(.+)/) |
|
1313
|
0 |
0 |
if ($1 eq 'primary') { } |
|
|
0 |
0 |
elsif ($1 eq 'secondary') { } |
|
1325
|
0 |
0 |
if ($_ =~ /format\t(\S+)/) |
|
1331
|
0 |
0 |
if ($format =~ m[^URN:LSID:open-bio\.org:(\w+)(?:/(\w+))?]) { } |
|
1347
|
0 |
0 |
unless (@fileid_keys) |
|
1353
|
0 |
0 |
unless (defined $self->primary_namespace) |
|
1357
|
0 |
0 |
unless (-e $self->primary_index_file) |
|
1380
|
0 |
1 |
unless (defined $self->{'_dbfile'}) |
|
1403
|
0 |
0 |
unless (defined $self->{'_file'}{$fileid}) |
|
1407
|
0 |
0 |
unless open my $fh, '<', $self->{'_file'}{$fileid} |
|
1445
|
0 |
0 |
unless (defined $self->{'_primary_index_handle'}) |
|
1447
|
0 |
0 |
unless open $self->{'_primary_index_handle'}, '<', $primary_file |
|
1467
|
1 |
69 |
if (defined $value) |
|
1476
|
0 |
2 |
if (defined $value) |
|
1496
|
1 |
2 |
if (defined $value) |
|
1517
|
1 |
5 |
if @_ |
|
1536
|
1 |
6 |
if (defined $arg) |
|
1537
|
1 |
0 |
unless ($arg =~ m[/$]) |
|
1573
|
0 |
0 |
if @_ |
|
1590
|
1 |
3 |
if @_ |
|
1608
|
0 |
0 |
if @_ |
|
1626
|
0 |
0 |
if @_ |
|
1644
|
1 |
1 |
if @_ |
|
1662
|
1 |
1 |
if @_ |
|
1680
|
0 |
61 |
if (defined $value) |
|
1708
|
0 |
1 |
if (@values) |
|
1711
|
1 |
0 |
unless $obj->{'secondary_namespaces'} |
|
1797
|
0 |
64 |
if $format eq 'swissprot' |
|
1799
|
0 |
64 |
if ($format eq 'genbank') |
|
1800
|
0 |
0 |
unless $line =~ /^LOCUS/ |
|
1801
|
0 |
0 |
if $line =~ /\s+\d+\s+bp/i |
|
1805
|
0 |
64 |
if ($format eq 'embl') |
|
1806
|
0 |
0 |
unless $line =~ /^ID/ |
|
1807
|
0 |
0 |
if $line =~ / DNA;/i |
|
1808
|
0 |
0 |
if $line =~ / RNA;/i |
|
1819
|
0 |
1 |
if ($format =~ /swiss(prot)?/i) |
|
1824
|
0 |
1 |
if ($format =~ /embl/i) |
|
1834
|
0 |
1 |
if ($format =~ /genbank/i) |
|
1846
|
1 |
0 |
if ($format =~ /fasta/i) |