| line |
true |
false |
branch |
|
148
|
0 |
1 |
$interleave ? : |
|
|
1 |
13 |
if defined $interleave |
|
150
|
0 |
14 |
if $idlinebreak |
|
151
|
0 |
14 |
if defined $linelen and $linelen > 0 |
|
152
|
0 |
14 |
if $flag_SI |
|
153
|
14 |
0 |
if $tag_length or $Bio::AlignIO::phylip::DEFAULTTAGLEN |
|
154
|
0 |
14 |
$ws ? : |
|
155
|
2 |
12 |
$longid ? : |
|
183
|
0 |
10 |
if ($entry =~ /^\s?$/) { } |
|
|
10 |
0 |
elsif ($entry =~ /\s*(\d+)\s+(\d+)/) { } |
|
193
|
0 |
10 |
unless $seqcount and $residuecount |
|
200
|
4 |
70 |
if ($entry =~ /^\s?$/) |
|
208
|
12 |
58 |
if ($self->longid) { } |
|
209
|
1 |
11 |
if ($entry =~ /^'(.+)'\s+(.+)$/) { } |
|
230
|
4 |
66 |
if ($self->interleaved == 0) |
|
235
|
0 |
20 |
if ($entry =~ /^\s*$/) |
|
245
|
10 |
60 |
if ($count == $seqcount) |
|
251
|
9 |
1 |
if ($self->interleaved) |
|
255
|
106 |
321 |
if ($entry =~ /^\s*$/) { } |
|
256
|
0 |
106 |
if ($count != 0) |
|
266
|
106 |
215 |
if ($count >= $seqcount) |
|
272
|
0 |
10 |
if (scalar @names != $seqcount) |
|
279
|
0 |
70 |
if (length $str != $residuecount) |
|
309
|
0 |
4 |
unless ($aln and $aln->isa('Bio::Align::AlignI')) |
|
313
|
0 |
4 |
unless $aln->is_flush(1) |
|
319
|
0 |
4 |
if ($flag_SI) { } |
|
320
|
0 |
0 |
if ($self->interleaved) { } |
|
334
|
0 |
16 |
if ($self->longid) { } |
|
335
|
0 |
0 |
if length $name > 50 |
|
339
|
1 |
15 |
if length $name > $idlength |
|
341
|
16 |
0 |
if ($self->interleaved) { } |
|
|
0 |
0 |
elsif ($self->id_linebreak) { } |
|
354
|
4 |
0 |
if ($self->interleaved) { } |
|
356
|
4 |
0 |
if ($tag_length <= $line_length) { } |
|
367
|
42 |
16 |
if $wrapped |
|
371
|
16 |
42 |
if $count % 100000 == 0 |
|
381
|
16 |
42 |
if ($index < $numtags) |
|
397
|
0 |
0 |
if ($self->wrap_sequential) |
|
404
|
4 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
421
|
1 |
100 |
if (defined $value) |
|
422
|
0 |
1 |
if ($value) { } |
|
425
|
95 |
6 |
unless defined $self->{'_interleaved'} |
|
445
|
0 |
4 |
if (defined $value) |
|
464
|
14 |
14 |
if (defined $value) |
|
483
|
0 |
8 |
if (defined $value) |
|
504
|
0 |
18 |
if (defined $value) |
|
524
|
0 |
0 |
if (defined $value) |
|
544
|
14 |
0 |
if (defined $value) |
|
563
|
14 |
86 |
if (defined $value) |