| line |
true |
false |
branch |
|
142
|
0 |
1 |
if ref $class |
|
149
|
0 |
1 |
unless defined $flat_directory |
|
151
|
0 |
1 |
unless defined $dbname |
|
158
|
0 |
1 |
unless -e $flat_directory |
|
160
|
0 |
1 |
unless -d _ |
|
163
|
1 |
0 |
unless (-d $dbpath) |
|
165
|
0 |
1 |
unless mkdir $dbpath, 511 |
|
172
|
0 |
1 |
unless $self->indexing_scheme |
|
176
|
1 |
0 |
$self->indexing_scheme eq 'flat/1' ? : |
|
|
0 |
1 |
$self->indexing_scheme eq 'BerkeleyDB/1' ? : |
|
184
|
1 |
0 |
if ($index_type eq 'Binary') |
|
187
|
0 |
1 |
if $@ |
|
195
|
0 |
0 |
if $@ |
|
212
|
1 |
0 |
if defined $flat_write_flag |
|
214
|
1 |
0 |
if (defined $flat_indexing) |
|
216
|
0 |
1 |
if $flat_indexing =~ /bdb/ |
|
217
|
1 |
0 |
if $flat_indexing =~ /^(flat|binary)/ |
|
221
|
0 |
1 |
if defined $flat_verbose |
|
222
|
1 |
0 |
if defined $dbname |
|
223
|
0 |
1 |
if defined $flat_outfile |
|
224
|
1 |
0 |
if defined $flat_format |
|
231
|
0 |
0 |
unless defined $self->{'flat_primary_namespace'} |
|
234
|
0 |
0 |
unless defined $self->{'flat_secondary_namespaces'} |
|
237
|
0 |
0 |
unless defined $self->{'flat_format'} |
|
259
|
0 |
0 |
unless my $location = $config{'location'} |
|
261
|
0 |
0 |
unless my $dbname = $config{'dbname'} |
|
274
|
1 |
1 |
if @_ |
|
280
|
1 |
0 |
if @_ |
|
286
|
1 |
1 |
if @_ |
|
292
|
0 |
0 |
if @_ |
|
298
|
2 |
1 |
if @_ |
|
304
|
0 |
0 |
if @_ |
|
314
|
0 |
0 |
ref $_[0] eq 'ARRAY' ? : |
|
|
0 |
0 |
if @_ |
|
315
|
0 |
0 |
unless $d |
|
316
|
0 |
0 |
if $d and ref $d ne 'ARRAY' |
|
317
|
0 |
0 |
wantarray ? : |
|
324
|
1 |
1 |
if @_ |
|
332
|
0 |
0 |
if @_ |
|
342
|
0 |
0 |
unless my $seq = $parser->next_seq |
|
353
|
1 |
3 |
if @_ |
|
362
|
0 |
0 |
unless ('File::Spec'->file_name_is_absolute($file_path)) |
|
366
|
0 |
0 |
unless -r $file_path |
|
369
|
0 |
0 |
if (defined $file_length) { } |
|
370
|
0 |
0 |
unless $current_size == $file_length |
|
376
|
0 |
0 |
unless (defined $nf) |
|
377
|
0 |
0 |
unless exists $self->{'flat_file_index'} |
|
387
|
0 |
0 |
unless $self->write_flag |
|
390
|
0 |
0 |
unless open my $F, '>', $path |
|
397
|
0 |
0 |
$alphabet ? : |
|
400
|
0 |
0 |
unless my(@filenos) = $self->_filenos |
|
408
|
0 |
0 |
unless my $primary_ns = $self->primary_namespace |
|
417
|
0 |
0 |
unless CORE::close $F |
|
422
|
0 |
0 |
unless $self->{'flat_flat_file_no'} |
|
430
|
0 |
0 |
unless $self->write_flag |
|
432
|
0 |
0 |
unless my $file = $self->out_file |
|
433
|
0 |
0 |
unless my $seqio = ($self->{'flat_cached_parsers'}{$file} ||= 'Bio::SeqIO'->new('-Format', $self->file_format, '-file', ">$file")) |
|
438
|
0 |
0 |
unless my $fh = $seqio->_fh |
|
450
|
1 |
0 |
unless $self->{'flat_outfile_dirty'} |
|
459
|
0 |
0 |
unless $self->{'flat_flat_file_path'} |
|
467
|
1 |
0 |
unless -e $path |
|
469
|
0 |
0 |
unless open my $F, '<', $path |
|
476
|
0 |
0 |
unless CORE::close $F |
|
478
|
0 |
0 |
unless $config{'index'}[0] =~ m[(flat/1|BerkeleyDB/1)] |
|
483
|
0 |
0 |
if ($config{'format'}) |
|
485
|
0 |
0 |
if ($config{'format'}[0] =~ m[^URN:LSID:open-bio\.org:(\w+)(?:/(\w+))]) { } |
|
494
|
0 |
0 |
unless my $primary_namespace = $config{'primary_namespace'}[0] |
|
502
|
0 |
0 |
if /^fileid_(\S+)/ |
|
528
|
0 |
0 |
unless exists $self->{'flat_flat_file_no'}{$path} |
|
577
|
0 |
0 |
if @_ == 1 |