| line |
true |
false |
branch |
|
56
|
0 |
219 |
unless $_[0] |
|
72
|
104 |
867 |
if (not are_disjoint($tgt, $try)) { } |
|
81
|
432 |
67 |
unless ($tgt_not_disjoint) |
|
116
|
0 |
432 |
unless $_[0] |
|
138
|
1 |
431 |
if ($flat[1] - $flat[0] == 1) |
|
142
|
17 |
377 |
if ($a - $flat[-2] == 2) |
|
147
|
0 |
432 |
if ($flat[-1] - $flat[-2] == 1 and @flat % 2) |
|
161
|
846 |
470 |
unless (are_disjoint($decomp[$i], $ints[$j])) |
|
162
|
208 |
638 |
if (defined $coverage[$i]) { } |
|
186
|
1337 |
950 |
if $int1->[1] < $int2->[0] or $int2->[1] < $int1->[0] |
|
221
|
0 |
219 |
if (ref($type) =~ /HSP/) { } |
|
|
0 |
219 |
elsif (not grep(/^$type$/, ('hit', 'subject', 'query'))) { } |
|
228
|
0 |
219 |
if $type eq 'subject' |
|
298
|
0 |
0 |
unless (grep /^$type$/, ('h', 'q', 's')) |
|
302
|
0 |
0 |
if $type eq 's' |
|
306
|
0 |
0 |
if $alg =~ /^RPS/ |
|
309
|
0 |
0 |
if (/MEGABLAST/i) |
|
312
|
0 |
0 |
if (/(.?)BLAST(.?)/i) |
|
315
|
0 |
0 |
if (/(.?)FAST(.?)/) |
|
344
|
0 |
519 |
if $alg =~ /^RPS/ |
|
347
|
4 |
515 |
if (/MEGABLAST/i) |
|
357
|
515 |
0 |
if (/(.?)BLAST(.?)/i) |
|
368
|
0 |
0 |
if (/(.?)FAST(.?)/) |
|
399
|
0 |
6568 |
unless (ref $obj and $obj->can('algorithm')) |
|
404
|
0 |
6568 |
unless (grep /^$type$/, ('query', 'hit', 'subject')) |
|
408
|
0 |
6568 |
if $type eq 'subject' |
|
412
|
0 |
6568 |
if $alg =~ /^RPS/ |
|
415
|
520 |
6048 |
if (/MEGABLAST/i) |
|
418
|
6048 |
0 |
if (/(.?)BLAST(.?)/i) |
|
421
|
0 |
0 |
if (/(.?)FAST(.?)/) |
|
445
|
0 |
0 |
length $_ > $max ? : |
|
448
|
0 |
0 |
unless substr $_, $j, 1 |
|
480
|
13 |
83 |
if $start <= $beg and $end <= $stop |
|
501
|
0 |
1 |
unless @intervals |
|
506
|
6 |
5 |
if ($intvl->[0] - $grp->[-1][1] == 1) { } |
|
548
|
0 |
2664 |
unless defined $type |
|
549
|
0 |
2664 |
unless grep /^$type$/, ('query', 'hit', 'subject') |
|
550
|
0 |
2664 |
if $type eq 'subject' |
|
553
|
0 |
2664 |
unless defined $action |
|
554
|
0 |
2664 |
unless grep /^$action$/, @actions |
|
558
|
0 |
2664 |
if (defined $beg and not defined $end or not defined $beg and defined $end) { } |
|
|
1688 |
976 |
elsif (not +(defined $beg || defined $end) && $self->seq_str('match')) { } |
|
564
|
156 |
1532 |
unless $self->seq_str('match') |
|
567
|
450 |
1238 |
if ($_ eq 'identities') |
|
570
|
450 |
788 |
if ($_ eq 'conserved') |
|
573
|
788 |
0 |
if ($_ eq 'searchutils') |
|
584
|
0 |
976 |
if ($beg < $start or $stop < $end) |
|
590
|
764 |
212 |
if ($self->gaps) |
|
611
|
0 |
976 |
unless (CORE::length $seq) |
|
620
|
0 |
976 |
if ($_ eq 'identities') |
|
623
|
0 |
976 |
if ($_ eq 'conserved') |
|
626
|
976 |
0 |
if ($_ eq 'searchutils') |
|
674
|
0 |
12 |
unless (defined $self->{'_as_feat'}) |
|
677
|
0 |
12 |
if ($tag) { } |
|
678
|
0 |
0 |
$_->primary_tag eq $tag ? : |
|
698
|
0 |
0 |
if (defined $self->{'_as_feat'}) { } |
|
722
|
12 |
0 |
unless $self->{'_as_feat'} |
|
724
|
0 |
24 |
unless ($feat->isa('Bio::SeqFeatureI')) |
|
751
|
0 |
0 |
unless $self->{'_as_feat'} |