| line |
true |
false |
branch |
|
104
|
0 |
5 |
if defined $preferred_groups |
|
107
|
0 |
5 |
if $file |
|
108
|
0 |
5 |
if $fasta |
|
115
|
0 |
0 |
if (-f $fasta and -w dirname($fasta) or -d $fasta and -w $fasta) { } |
|
119
|
0 |
0 |
unless my $dna_db = eval {
do {
'Bio::DB::Fasta'->new($fasta)
}
} |
|
121
|
0 |
0 |
if $dna_db |
|
130
|
0 |
120 |
if @_ |
|
145
|
0 |
120 |
if (my $dna_db = $self->dna_db) |
|
148
|
0 |
120 |
unless $self->{'dna'} |
|
150
|
5 |
115 |
unless defined $start or defined $stop |
|
151
|
0 |
115 |
unless defined $start |
|
154
|
55 |
60 |
if ($start > $stop) |
|
159
|
55 |
60 |
if ($reversed) |
|
189
|
0 |
175 |
if $feature_hash->{'strand'} and $feature_hash->{'strand'} eq '.' |
|
190
|
0 |
175 |
if $feature_hash->{'phase'} and $feature_hash->{'phase'} eq '.' |
|
191
|
0 |
175 |
unless length $feature_hash->{'gclass'} > 0 |
|
203
|
0 |
193 |
if ($name =~ /[*?]/) |
|
220
|
6560 |
0 |
if (defined $feature->{'gname'}) { } |
|
230
|
6170 |
390 |
if ($no_match_class_name) |
|
233
|
6165 |
5 |
unless ($self->_matching_attributes($feature_attributes, $attributes)) |
|
242
|
8 |
185 |
unless (%refs) |
|
254
|
0 |
185 |
if defined $refseq and lc $ref ne lc $refseq |
|
259
|
0 |
395 |
if $strand and $strand eq '.' |
|
260
|
185 |
210 |
if not defined $start or $start > $_->{'start'} |
|
261
|
185 |
210 |
if not defined $stop or $stop < $_->{'stop'} |
|
282
|
0 |
0 |
unless defined $feature->{'gclass'} and defined $feature->{'gname'} |
|
283
|
0 |
0 |
unless $feature->{'attributes'} |
|
292
|
0 |
0 |
unless $matches |
|
301
|
0 |
0 |
if defined $limit and @results >= $limit |
|
324
|
0 |
75 |
unless $_ >= 0 and $_ < @{$self->{'data'};} |
|
339
|
10 |
11 |
if (@$ranges) { } |
|
|
5 |
6 |
elsif (@$types) { } |
|
340
|
5 |
5 |
@$types ? : |
|
348
|
3 |
3 |
unless $force |
|
378
|
20 |
30 |
if (defined $tag and lc $attr_name eq lc $tag) { } |
|
|
15 |
15 |
elsif (not defined $tag) { } |
|
389
|
0 |
5 |
unless $callback |
|
401
|
10 |
55 |
if (lc $_ eq lc $attr_name and lc $attributes->{$_} eq lc $attr_value) |
|
428
|
0 |
85 |
if $options->{'sort_by_group'} |
|
462
|
0 |
16 |
unless $callback |
|
466
|
0 |
16 |
if ($name =~ /[*?]/) |
|
474
|
486 |
74 |
unless $regexp and $feature->{'gname'} =~ /$name/i or lc $feature->{'gname'} eq lc $name |
|
475
|
0 |
74 |
if defined $feature->{'gclass'} and length $feature->{'gclass'} > 0 and $feature->{'gclass'} ne $class |
|
477
|
0 |
74 |
if ($location) |
|
478
|
0 |
0 |
if $location->[0] ne $feature->{'ref'} |
|
479
|
0 |
0 |
if $location->[1] and $location->[1] > $feature->{'stop'} |
|
480
|
0 |
0 |
if $location->[2] and $location->[2] < $feature->{'start'} |
|
494
|
0 |
5 |
unless $callback |
|
499
|
5 |
0 |
if ($type eq 'feature') |
|
502
|
5 |
0 |
if $callback |
|
512
|
25 |
0 |
unless ref $ids =~ /ARRAY/ |
|
518
|
0 |
25 |
wantarray ? : |
|
528
|
0 |
15 |
unless $callback |
|
562
|
525 |
350 |
if (defined $srcseq) |
|
563
|
270 |
255 |
unless lc $feature_ref eq lc $srcseq |
|
566
|
0 |
605 |
if (defined $class) |
|
567
|
0 |
0 |
unless defined $feature_class and $feature_class eq $class |
|
571
|
255 |
350 |
if (defined $start or defined $stop) |
|
572
|
0 |
255 |
unless defined $start |
|
573
|
0 |
255 |
unless defined $stop |
|
574
|
0 |
255 |
unless $feature_stop >= $start and $feature_start <= $stop |
|
577
|
0 |
605 |
if (defined $typelist and @$typelist) |
|
578
|
0 |
0 |
unless $self->_matching_typelist($feature_method, $feature_source, $typelist) |
|
587
|
15 |
10 |
$want_count ? : |
|
624
|
2905 |
365 |
if (defined $refseq) |
|
625
|
1940 |
965 |
unless lc $feature_ref eq lc $refseq |
|
628
|
455 |
875 |
if (defined $start or defined $stop) |
|
629
|
0 |
455 |
unless defined $start |
|
630
|
0 |
455 |
unless defined $stop |
|
632
|
385 |
70 |
if ($rangetype eq 'overlaps') { } |
|
|
70 |
0 |
elsif ($rangetype eq 'contains') { } |
|
|
0 |
0 |
elsif ($rangetype eq 'contained_in') { } |
|
633
|
100 |
285 |
unless $feature_stop >= $start and $feature_start <= $stop |
|
635
|
20 |
50 |
unless $feature_start >= $start and $feature_stop <= $stop |
|
637
|
0 |
0 |
unless $feature_start <= $start and $feature_stop >= $stop |
|
639
|
0 |
0 |
unless $feature_start == $start and $feature_stop == $stop |
|
647
|
375 |
835 |
if (defined $types and @$types) |
|
648
|
240 |
135 |
unless $self->_matching_typelist($feature_method, $feature_source, $types) |
|
652
|
255 |
715 |
if (defined $attributes) |
|
653
|
230 |
25 |
unless $self->_matching_attributes($feature_attributes, $attributes) |
|
673
|
559 |
270 |
wantarray ? : |
|
688
|
955 |
135 |
if lc $search_method ne lc $feature_method |
|
689
|
0 |
135 |
if defined $search_source and lc $search_source ne lc $feature_source |
|
698
|
6395 |
45 |
unless _match_all_attr_in_feature($_, $attributes->{$_}, $feature_attributes) |
|
707
|
2360 |
45 |
if $attr_name ne $feature_attr_name or $attr_value ne $feature_attr_value |