| line |
true |
false |
branch |
|
139
|
3528 |
5 |
unless $nse |
|
141
|
5 |
3528 |
if defined $fs |
|
142
|
2295 |
1238 |
if defined $start |
|
143
|
2158 |
1375 |
if defined $end |
|
144
|
561 |
2971 |
if defined $strand |
|
163
|
2578 |
8281 |
if (@_) |
|
167
|
10142 |
717 |
if defined $self->{'start'} |
|
168
|
632 |
85 |
if $self->seq |
|
191
|
3029 |
4335 |
if (@_) |
|
196
|
2272 |
757 |
if ($self->seq and $st != 0) |
|
200
|
2 |
2270 |
if ($calend != $value) |
|
210
|
6887 |
475 |
if (defined $self->{'end'}) { } |
|
|
432 |
43 |
elsif (my $len = $self->_ungapped_len) { } |
|
224
|
43 |
2704 |
unless my $string = $self->seq |
|
227
|
4 |
2700 |
if (my(%data) = $self->frameshifts) |
|
254
|
674 |
4036 |
if (@_) |
|
277
|
3543 |
2718 |
if (@_) |
|
278
|
3543 |
0 |
ref $_[0] eq 'ARRAY' ? : |
|
279
|
0 |
3543 |
if @mapping != 2 |
|
281
|
18 |
7068 |
if $_ != 1 |
|
|
2 |
3541 |
if (grep {$_ != 3 if $_ != 1;} @mapping or $mapping[0] == 3 and $mapping[1] == 3) |
|
286
|
0 |
6259 |
unless exists $self->{'_mapping'} |
|
304
|
5 |
2704 |
if (@_) |
|
305
|
5 |
0 |
if (ref $_[0] eq 'HASH') { } |
|
313
|
11 |
2698 |
defined $self->{'_frameshifts'} && ref $self->{'_frameshifts'} eq 'HASH' ? : |
|
337
|
6 |
3091 |
if ($self->force_nse) |
|
343
|
1 |
3096 |
unless defined $id |
|
344
|
0 |
3096 |
unless defined $st |
|
345
|
0 |
3096 |
unless defined $end |
|
347
|
69 |
3027 |
if ($strand and $strand == -1) |
|
352
|
149 |
2947 |
$self->version ? : |
|
372
|
49 |
6582 |
if (defined $flag) |
|
373
|
6 |
43 |
$flag ? : |
|
404
|
0 |
41 |
unless $char =~ /[$Bio::LocatableSeq::GAP_SYMBOLS]/ |
|
408
|
0 |
41 |
unless $seq |
|
448
|
0 |
39 |
unless $resnumber =~ /^\d+$/ and $resnumber > 0 |
|
451
|
38 |
1 |
if ($resnumber >= $self->start and $resnumber <= $self->end) |
|
459
|
8 |
30 |
if ($strand == -1) { } |
|
474
|
34 |
64 |
if ($chunk =~ /^[$Bio::LocatableSeq::GAP_SYMBOLS]/o) { } |
|
478
|
26 |
38 |
if ($current_residue + length($chunk) < $resnumber) { } |
|
483
|
8 |
30 |
if ($strand == -1) { } |
|
541
|
0 |
78 |
unless $column =~ /^\d+$/ and $column > 0 |
|
543
|
0 |
78 |
unless $column <= $self->length |
|
555
|
15 |
63 |
$strand == -1 ? : |
|
558
|
66 |
12 |
if ($self->subseq($column, $column) =~ /[a-zA-Z\*]/) { } |
|
|
3 |
9 |
elsif ($pos == 0 and $self->start == 1) { } |
|
567
|
6 |
3 |
if ($strand == -1) |
|
599
|
0 |
14 |
if (grep {$_ != 1;} $self->mapping) |
|
604
|
7 |
7 |
if $self->strand |
|
605
|
14 |
0 |
if $self->start |
|
606
|
14 |
0 |
if $self->end |
|
628
|
8 |
56 |
if $self->strand and $self->strand == -1 |
|
631
|
63 |
1 |
$start ? : |
|
632
|
64 |
0 |
if $start |
|
657
|
0 |
4123 |
unless defined $seqstr |
|
658
|
8 |
4115 |
unless defined $throw |
|
659
|
1 |
4122 |
if (length $seqstr > 0 and not $seqstr =~ /^([$Bio::LocatableSeq::MATCHPATTERN]+)$/) |
|
661
|
1 |
0 |
if ($throw) |