| line |
true |
false |
branch |
|
101
|
69 |
14 |
if ($filename) |
|
134
|
0 |
69 |
unless (-e $filename) |
|
167
|
18 |
69 |
if (lc $$args{'format'} eq 'string') { } |
|
198
|
10 |
91674 |
if $text_char eq '"' |
|
200
|
212 |
91472 |
if ($text_char eq q['] and $quote_level == 0 and $comment_level == 0 and $found_nexus_token) { } |
|
|
4856 |
86616 |
elsif ($quote_level > 0) { } |
|
|
5434 |
81182 |
elsif ($text_char eq '[' || $comment_level > 0 and $in_tree_string == 0) { } |
|
|
526 |
80656 |
elsif (not $found_nexus_token) { } |
|
|
2392 |
78264 |
elsif ($command eq '') { } |
|
|
78264 |
0 |
elsif (not $command =~ /;$/) { } |
|
214
|
212 |
4644 |
if ($text_char eq q[']) |
|
215
|
0 |
212 |
$prev_text_char eq $text_char ? : |
|
229
|
161 |
5273 |
if $text_char eq '[' |
|
232
|
161 |
5273 |
if ($text_char eq ']') |
|
237
|
34 |
127 |
if ($comment_level == 0 and @command_level_strings == 0) |
|
250
|
86 |
440 |
if ($command =~ /^\s*#NEXUS/i) { } |
|
|
1 |
439 |
elsif (not $command =~ /^\s*(?:#(?:N(?:E(?:X(?:U(?:S)?)?)?)?)?)?$/i) { } |
|
264
|
25 |
2367 |
if ($comment) |
|
268
|
1050 |
1342 |
if ($text_char ne "\n") |
|
276
|
88 |
78176 |
if ($in_tree_string == 0 and $block_type eq 'trees' || $block_type eq 'history' and $text_char eq '=') { } |
|
280
|
76 |
12 |
if $command =~ /tree\s.+=/i |
|
282
|
1050 |
77126 |
if $text_char eq ';' |
|
289
|
1050 |
90633 |
if (not $comment_level || $quote_level and $text_char eq ';') |
|
292
|
231 |
819 |
if ($command =~ /begin\s+(.+)\s*;/i) { } |
|
|
231 |
588 |
elsif ($command =~ /^\s*end(?:block)?\s*;/i) { } |
|
|
588 |
0 |
elsif ($command =~ s/\s*;\s*$//) { } |
|
297
|
0 |
231 |
if ($comment) |
|
309
|
1 |
230 |
if ($comment) |
|
331
|
10 |
578 |
if ($comment) |
|
342
|
6 |
71 |
unless ($self->get_block('taxa')) |
|
385
|
224 |
8 |
if (defined $class) |
|
388
|
139 |
92 |
if (defined $self->get_block('taxa')) |
|
391
|
223 |
8 |
if ($class) { } |
|
399
|
6 |
216 |
if ($block_type =~ /taxa/i and my $title = $block->get_title) |
|
426
|
90 |
132 |
unless $taxablock |
|
432
|
112 |
20 |
if (lc $block_type eq 'characters' or lc $block_type eq 'trees') { } |
|
|
1 |
19 |
elsif (lc $block_type eq 'sets') { } |
|
438
|
372 |
0 |
if grep {$label eq $_;} @taxlabels |
|
451
|
8 |
0 |
if grep {$element eq $_;} @taxlabels |
|
543
|
0 |
0 |
if (_is_comment($block_or_comment)) |
|
612
|
0 |
5 |
if _is_comment($item) |
|
613
|
2 |
3 |
if ($item->get_type =~ /$blocktype/i) |
|
616
|
2 |
0 |
if (not $title or $item->get_title =~ /$title/i) |
|
635
|
0 |
2 |
if (not $found_block) |
|
637
|
0 |
0 |
if ($title) |
|
658
|
602 |
0 |
if ($block->get_type =~ /$blocktype/i) |
|
659
|
597 |
5 |
if (not $blockname) { } |
|
|
5 |
0 |
elsif ($block->get_title =~ /$blockname/i) { } |
|
688
|
1768 |
356 |
unless (_is_comment($item)) |
|
689
|
1037 |
731 |
if (not $blocktype or $item->get_type =~ /$blocktype/i) |
|
728
|
0 |
0 |
if (lc $block->get_link('characters') eq lc $characters) |
|
764
|
5 |
0 |
if (my $taxablock = $self->get_block('taxa')) |
|
767
|
0 |
0 |
if (my $charblock = $self->get_block('characters')) |
|
770
|
0 |
0 |
if (my $treesblock = $self->get_block('trees')) |
|
793
|
6 |
0 |
if ($block->can('rename_otus')) |
|
815
|
0 |
9 |
unless (defined $original_otu_name and defined $copy_otu_name) |
|
819
|
1 |
8 |
if ($original_otu_name eq $copy_otu_name) |
|
823
|
1 |
7 |
if (grep {$_ eq $copy_otu_name;} @{$self->get_taxlabels;}) |
|
834
|
7 |
17 |
if ($otu eq $original_otu_name) |
|
840
|
7 |
0 |
if ($contains_otu eq 'true') { } |
|
909
|
2 |
0 |
if ($block->can('select_otus')) |
|
932
|
1 |
3 |
if $otu eq $name and $exclude = 1 |
|
934
|
3 |
1 |
unless $exclude |
|
968
|
0 |
0 |
unless (defined $nodename) |
|
981
|
0 |
0 |
if ($block->can('select_otus')) |
|
1001
|
0 |
0 |
unless (defined $nodename) |
|
1013
|
0 |
0 |
if ($block->can('select_otus')) |
|
1051
|
0 |
0 |
if (not $block->get_charlabels or @{$block->get_charlabels;} == 0) |
|
1055
|
0 |
0 |
if ($block) |
|
1103
|
0 |
0 |
if (defined $treename) { } |
|
1126
|
0 |
1 |
if (@blocks1 != @blocks2) |
|
1139
|
0 |
0 |
unless ($blocks1[$i] or $blocks2[$i]) |
|
1140
|
0 |
3 |
unless ($blocks1[$i]->equals($blocks2[$i])) |
|
1164
|
1 |
1 |
if (ref $filename eq 'GLOB') { } |
|
|
0 |
1 |
elsif ($filename eq '-' or $filename eq \*STDOUT) { } |
|
1171
|
0 |
1 |
unless open $fh, ">$filename" |
|
1180
|
2 |
2 |
if (_is_comment($blocks_and_comments[$i])) { } |
|
1198
|
0 |
6 |
if (_is_comment($block_or_comment)) |
|
1203
|
2 |
4 |
if (lc $type eq 'taxa') |
|
1209
|
2 |
0 |
unless $fh == \*STDOUT |
|
1224
|
7 |
2 |
if (not defined $self->get_block('taxa')) |
|
1227
|
7 |
0 |
if ($block_type eq 'characters' or $block_type eq 'trees') |
|
1229
|
1 |
6 |
unless (defined $taxlabels and @$taxlabels) |
|
1230
|
1 |
0 |
if ($block_type eq 'trees') { } |
|
1250
|
0 |
0 |
if $Bio::NEXUS::AUTOLOAD =~ /DESTROY$/ |
|
1259
|
0 |
0 |
if (defined $synonym_for{$Bio::NEXUS::AUTOLOAD}) { } |