| line |
true |
false |
branch |
|
102
|
1 |
3 |
unless $seq
|
|
131
|
57 |
7 |
if $self->count_seqs == &uniq(@ids)
|
|
138
|
72 |
5 |
if &List::AllUtils::any(sub {
|
|
145
|
3 |
307 |
unless $self->guessing
|
|
146
|
191 |
116 |
if &List::AllUtils::any(sub {
|
|
153
|
85 |
104 |
if $self->is_aligned
|
|
180
|
0 |
2 |
unless $n
|
|
281
|
78 |
55 |
$abbr ? :
|
|
283
|
133 |
0 |
if $new_id
|
|
299
|
245 |
5 |
unless $list->is_listed($self->get_seq($i)->full_id)
|
|
312
|
0 |
40 |
unless $self->is_aligned
|
|
319
|
0 |
40 |
unless &List::AllUtils::any(sub {
|
|
325
|
1 |
39 |
unless $a_width == $m_width
|
|
356
|
69 |
4 |
(shift())->is_protein ? :
|
|
371
|
83 |
47 |
unless $state =~ /$Bio::MUST::Core::Ali::GAP/msx
|
|
405
|
147 |
3944 |
if $line =~ /$Bio::MUST::Core::Ali::EMPTY_LINE/msx or $ali->is_comment($line)
|
|
410
|
1662 |
2282 |
if ($defline)
|
|
413
|
1593 |
69 |
if ($seq)
|
|
428
|
69 |
0 |
if ($seq)
|
|
519
|
5 |
4 |
wantarray ? :
|
|
541
|
33 |
8524 |
if $line =~ /$Bio::MUST::Core::Ali::EMPTY_LINE/msx
|
|
544
|
105 |
8419 |
if ($line =~ /$Bio::MUST::Core::Ali::DIM_LINE/msx)
|
|
553
|
0 |
8419 |
unless $seq
|
|
560
|
8089 |
330 |
if ($ali->count_seqs < $seq_n) { }
|
|
563
|
0 |
8089 |
unless $seq_id
|
|
576
|
110 |
220 |
if ($seq_id and $seq_id ne $curr_seq->full_id)
|
|
585
|
138 |
8281 |
if ++$n == $seq_n
|
|
589
|
0 |
105 |
if $width != $site_n
|
|
719
|
17 |
27 |
if $ali->is_comment($line, $Bio::MUST::Core::Ali::STK_COMMENT)
|
|
722
|
16 |
11 |
if $line =~ /$Bio::MUST::Core::Ali::EMPTY_LINE/msx or $line =~ /$Bio::MUST::Core::Ali::COMMENT_LINE/msx
|
|
724
|
2 |
9 |
if $line =~ /$Bio::MUST::Core::Ali::END_LINE/msx
|
|
752
|
0 |
1 |
unless $infile
|
|
756
|
0 |
1 |
unless $coderef
|
|
770
|
2 |
90 |
if $line =~ /$Bio::MUST::Core::Ali::EMPTY_LINE/msx or $line =~ /$Bio::MUST::Core::Ali::COMMENT_LINE/msx
|
|
775
|
3 |
87 |
if ($defline)
|
|
778
|
2 |
1 |
if ($seq)
|
|
793
|
1 |
0 |
if ($seq)
|
|
809
|
250 |
252 |
if /^>/msx
|