| line |
true |
false |
branch |
|
176
|
0 |
1 |
$interleave ? : |
|
|
1 |
13 |
if defined $interleave |
|
178
|
0 |
14 |
if $idlinebreak |
|
179
|
0 |
14 |
if defined $linelen and $linelen > 0 |
|
180
|
0 |
14 |
if $flag_SI |
|
181
|
14 |
0 |
if $tag_length or $Bio::AlignIO::phylip::DEFAULTTAGLEN |
|
182
|
0 |
14 |
$ws ? : |
|
183
|
2 |
12 |
$longid ? : |
|
213
|
0 |
10 |
if ($entry =~ /^\s?$/) { } |
|
|
10 |
0 |
elsif ($entry =~ /\s*(\d+)\s+(\d+)/) { } |
|
225
|
0 |
10 |
unless $seqcount and $residuecount |
|
232
|
4 |
70 |
if ($entry =~ /^\s?$/) |
|
240
|
12 |
58 |
if ($self->longid) { } |
|
241
|
1 |
11 |
if ($entry =~ /^'(.+)'\s+(.+)$/) { } |
|
263
|
4 |
66 |
if ($self->interleaved == 0) |
|
268
|
0 |
20 |
if ($entry =~ /^\s*$/) |
|
282
|
10 |
60 |
if ($count == $seqcount) |
|
288
|
9 |
1 |
if ($self->interleaved) |
|
292
|
106 |
321 |
if ($entry =~ /^\s*$/) { } |
|
293
|
0 |
106 |
if ($count != 0) |
|
305
|
106 |
215 |
if ($count >= $seqcount) |
|
311
|
0 |
10 |
if (scalar @names != $seqcount) |
|
321
|
0 |
70 |
if (length $str != $residuecount) |
|
358
|
0 |
4 |
unless ($aln and $aln->isa('Bio::Align::AlignI')) |
|
364
|
0 |
4 |
unless $aln->is_flush(1) |
|
370
|
0 |
4 |
if ($flag_SI) { } |
|
371
|
0 |
0 |
if ($self->interleaved) { } |
|
394
|
0 |
16 |
if ($self->longid) { } |
|
395
|
0 |
0 |
if length $name > 50 |
|
400
|
1 |
15 |
if length $name > $idlength |
|
403
|
16 |
0 |
if ($self->interleaved) { } |
|
|
0 |
0 |
elsif ($self->id_linebreak) { } |
|
417
|
4 |
0 |
if ($self->interleaved) { } |
|
419
|
4 |
0 |
if ($tag_length <= $line_length) { } |
|
430
|
42 |
16 |
if $wrapped |
|
435
|
16 |
42 |
if $count % 100000 == 0 |
|
452
|
16 |
42 |
if ($index < $numtags) |
|
471
|
0 |
0 |
if ($self->wrap_sequential) |
|
478
|
4 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
495
|
1 |
100 |
if (defined $value) |
|
496
|
0 |
1 |
if ($value) { } |
|
502
|
95 |
6 |
unless defined $self->{'_interleaved'} |
|
522
|
0 |
4 |
if (defined $value) |
|
541
|
14 |
14 |
if (defined $value) |
|
560
|
0 |
8 |
if (defined $value) |
|
581
|
0 |
18 |
if (defined $value) |
|
600
|
0 |
0 |
if (defined $value) |
|
619
|
14 |
0 |
if (defined $value) |
|
638
|
14 |
86 |
if (defined $value) |