| line |
true |
false |
branch |
|
184
|
186 |
186 |
if ($class =~ /Bio::SearchIO::(\S+)/) { } |
|
197
|
1 |
185 |
if (defined $output_format) |
|
198
|
0 |
1 |
if (defined $param{'-writer'}) |
|
203
|
0 |
1 |
if ($output_format =~ /^blast$/i) |
|
216
|
0 |
186 |
unless $class->_load_format_module($format) |
|
241
|
5 |
196 |
if $writer |
|
242
|
0 |
201 |
if defined $it |
|
243
|
0 |
201 |
if defined $min_qlen |
|
244
|
0 |
201 |
if defined $best |
|
245
|
0 |
201 |
if defined $check_all |
|
265
|
0 |
0 |
unless my $self = $class->new(@_) |
|
319
|
0 |
293 |
unless $handler |
|
320
|
0 |
293 |
unless ($handler->isa('Bio::SearchIO::EventHandlerI')) |
|
391
|
0 |
5 |
unless (ref $self->{'_result_writer'}) |
|
394
|
1 |
4 |
unless @args |
|
398
|
5 |
0 |
if defined $str |
|
400
|
5 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
424
|
0 |
0 |
unless (ref $self->{'_result_writer'}) |
|
427
|
0 |
0 |
unless @args |
|
431
|
0 |
0 |
if defined $str |
|
433
|
0 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
451
|
5 |
587 |
if (ref $writer and $writer->isa('Bio::SearchIO::SearchWriterI')) { } |
|
|
0 |
587 |
elsif (defined $writer) { } |
|
549
|
0 |
0 |
if (@_) |
|
551
|
0 |
0 |
if ($min_qlen =~ /\D/ or $min_qlen <= 0) |
|
579
|
0 |
0 |
if (@_) |
|
598
|
0 |
0 |
if (@_) |
|
621
|
0 |
215 |
if ($@) |
|
648
|
5 |
2642 |
unless defined $id |
|
650
|
238 |
2404 |
if ($id =~ /^gi\|(\d+)\|/) |
|
653
|
1019 |
1623 |
if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|(.*)/) { } |
|
|
19 |
1604 |
elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { } |
|
694
|
0 |
42 |
unless $_ = shift() |
|
695
|
10 |
32 |
if /\.(blast|t?bl\w)$/i |
|
696
|
18 |
14 |
if /\.
(?: t? fas (?:ta)? |
m\d+ |
(?: t? (?: fa | fx | fy | ff | fs ) ) |
(?: (?:ss | os | ps) (?:earch)? ))
$/xi |
|
702
|
4 |
10 |
if /\.(blast)?xml$/i |
|
703
|
4 |
6 |
if /\.exon(erate)?/i |
|
709
|
5 |
567 |
if ($self->writer) |
|
718
|
185 |
1 |
if defined $self->_fh |
|
729
|
0 |
0 |
unless wantarray |