| line |
true |
false |
branch |
|
110
|
50 |
0 |
unless defined $v |
|
156
|
0 |
22 |
unless $entry |
|
157
|
0 |
22 |
unless $entry and $entry =~ /^#NEXUS/i |
|
164
|
3 |
61 |
if /\[TITLE. *([^\]]+)]\s+/i |
|
165
|
22 |
42 |
if /^begin +data/i or /^begin +taxa/i |
|
167
|
3 |
19 |
if $aln_name |
|
173
|
182 |
220 |
if s/\[[^\]]+\]//g |
|
174
|
6 |
214 |
if (s/\[[^\]]+$//) { } |
|
|
39 |
175 |
elsif ($incomment) { } |
|
|
13 |
162 |
elsif (/taxlabels/i) { } |
|
177
|
6 |
0 |
if /^\s*$/ |
|
179
|
6 |
33 |
if (s/^[^\]]*\]//) { } |
|
189
|
22 |
140 |
if /ntax\s*=\s*(\d+)/i |
|
190
|
22 |
140 |
if /nchar\s*=\s*(\d+)/i |
|
191
|
2 |
160 |
if /matchchar\s*=\s*(.)/i |
|
192
|
22 |
140 |
if /gap\s*=\s*(.)/i |
|
193
|
21 |
141 |
if /missing\s*=\s*(.)/i |
|
194
|
0 |
162 |
if /equate\s*=\s*\"([^\"]+)/i |
|
195
|
22 |
140 |
if /datatype\s*=\s*(\w+)/i |
|
196
|
7 |
155 |
if /interleave/i |
|
197
|
22 |
140 |
if /matrix/io |
|
200
|
0 |
22 |
unless $alphabet |
|
203
|
0 |
22 |
unless $Bio::AlignIO::nexus::valid_type{$alphabet} |
|
204
|
0 |
22 |
if $gap and $gap =~ m"[\(\)\[\]\{\}/\\\,\;\:\=\*\'\`\<\>\^]" |
|
206
|
0 |
22 |
if $missing and $missing =~ m"[\(\)\[\]\{\}/\\\,\;\:\=\*\'\`\<\>\^]" |
|
217
|
22 |
3 |
unless ($entry =~ /^\s+$/) |
|
227
|
22 |
0 |
if (@names == 0) |
|
230
|
205 |
262 |
if (s/\[[^\]]+\]//g) |
|
231
|
8 |
197 |
if /^\s*$/ |
|
234
|
78 |
381 |
if ($interleave and defined $count and $count <= $seqcount) { } |
|
235
|
7 |
71 |
if /^\s+$/ |
|
237
|
4 |
377 |
if /^\s+$/ |
|
239
|
6 |
442 |
if /^\s*;/ |
|
241
|
442 |
0 |
if (/^\s*([\"\'](.+?)[\"\']|(\S+))\s+(.*)\s*$/) |
|
246
|
432 |
10 |
if ($4) { } |
|
258
|
10 |
1850 |
if length $str == $residuecount |
|
268
|
0 |
442 |
if $count > $seqcount |
|
269
|
9 |
433 |
if /;/ |
|
275
|
7 |
15 |
if ($interleave) |
|
278
|
826 |
177 |
if (s/\[[^\]]+\]//g) |
|
279
|
58 |
768 |
if /^\s*$/ |
|
281
|
6 |
939 |
if /^\s*;/ |
|
282
|
67 |
872 |
if $entry =~ /^\s*$/ |
|
283
|
872 |
0 |
if (/^\s*(\'([^\']*?)\'|([^\']\S*))\s+(.*)$/) |
|
289
|
0 |
872 |
if $count > $seqcount |
|
291
|
1 |
871 |
if /;/ |
|
295
|
0 |
22 |
if @names < 1 |
|
301
|
0 |
442 |
if ($name =~ m[(\S+)/(\d+)-(\d+)]) { } |
|
311
|
0 |
442 |
unless length $hash{$count} == $residuecount |
|
323
|
2 |
20 |
if $match |
|
326
|
0 |
22 |
if ($equate) |
|
335
|
22 |
0 |
if $aln->num_sequences |
|
343
|
0 |
0 |
if $entry =~ /^\s*(END)?;/i |
|
344
|
0 |
0 |
if ($entry =~ /\s*(\S+)\s+/) |
|
376
|
0 |
2 |
unless ($aln and $aln->isa('Bio::Align::AlignI')) |
|
380
|
0 |
2 |
unless $aln->is_flush($self->verbose) |
|
387
|
0 |
2 |
if $aln->match_char |
|
388
|
1 |
1 |
if $aln->missing_char |
|
389
|
2 |
0 |
if $aln->gap_char |
|
391
|
2 |
0 |
if $self->flag('symbols') and $aln->symbol_chars |
|
404
|
1 |
9 |
if ($nmid =~ /[^\w\d\.]/) { } |
|
431
|
10 |
48 |
if ($index < 5) |
|
442
|
2 |
0 |
if ($self->flag('endblock')) { } |
|
448
|
2 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
465
|
50 |
4 |
if defined $val |