| line |
true |
false |
branch |
|
85
|
0 |
3 |
unless (eval 'require Bio::Phylo; 1') |
|
146
|
0 |
0 |
unless ($mol_type eq 'dna' or $mol_type eq 'rna' or $mol_type eq 'protein') |
|
161
|
0 |
0 |
$caller->{'_ID'} ? : |
|
166
|
0 |
0 |
if ($taxa) |
|
168
|
0 |
0 |
if $taxa->get_name |
|
192
|
0 |
0 |
unless (defined($rowlabel = $row->get_name)) |
|
202
|
0 |
0 |
if ($taxa) |
|
204
|
0 |
0 |
if (my $taxon = $taxa->get_by_name($row->get_taxon->get_name)) |
|
259
|
0 |
0 |
if defined $taxa_label |
|
260
|
0 |
0 |
if defined $taxa_id |
|
264
|
0 |
0 |
if $caller->{'_ID'} |
|
268
|
0 |
0 |
if defined $taxon->get_name |
|
282
|
0 |
0 |
if (exists $created_nodes{$new_node_id}) { } |
|
296
|
0 |
0 |
if ($taxa) |
|
298
|
0 |
0 |
if $taxon and $taxon->get_name |
|
302
|
0 |
0 |
if ($terminal->is_root) |
|
312
|
0 |
0 |
if (exists $created_nodes{$parentID}) { } |
|
329
|
0 |
0 |
if ($parent->is_terminal) |
|
331
|
0 |
0 |
if $terminal->get_parent |
|
362
|
0 |
0 |
unless ($mol_type eq 'dna' or $mol_type eq 'rna' or $mol_type eq 'protein') |
|
377
|
0 |
0 |
if defined $matrix->get_name |
|
380
|
0 |
0 |
if defined $taxa_id |
|
381
|
0 |
0 |
if defined $taxa_label |
|
388
|
0 |
0 |
if (not defined($rowlabel = $row->get_name)) { } |
|
403
|
0 |
0 |
$caller->{'_ID'} ? : |
|
404
|
0 |
0 |
$caller->{'_ID'} ? : |
|
407
|
0 |
0 |
if ($taxa) |
|
410
|
0 |
0 |
if defined $taxon->get_name |
|
411
|
0 |
0 |
if ($taxon eq $row->get_taxon) |
|
414
|
0 |
0 |
if defined $taxon_name |
|
446
|
0 |
0 |
if (ref $bptree and $bptree->isa('Bio::Tree::TreeI')) { } |
|
452
|
0 |
0 |
if defined $name |
|
456
|
0 |
0 |
if defined $score |
|
469
|
0 |
0 |
if ($parent) |
|
472
|
0 |
0 |
if (my $bptaxon_name = $bpnode->get_tag_values('taxon')) |
|
500
|
0 |
0 |
if defined $name |
|
504
|
0 |
0 |
if defined $branch_length |
|
508
|
0 |
0 |
if defined $desc |
|
512
|
0 |
0 |
if defined $bootstrap and $bootstrap->looks_like_number |
|
538
|
0 |
0 |
if ($aln->isa('Bio::Align::AlignI')) { } |
|
543
|
0 |
0 |
if ($seqs[0]) { } |
|
599
|
0 |
0 |
if ($seqstring and $seqstring =~ /\S/) |
|
601
|
0 |
0 |
if ($@ and UNIVERSAL::isa($@, 'Bio::Phylo::Util::Exceptions::InvalidData')) |
|
612
|
0 |
0 |
if defined $desc |
|
616
|
0 |
0 |
if $seq->can($field) |
|
636
|
0 |
0 |
if (UNIVERSAL::isa($obj, 'Bio::Align::AlignI') or UNIVERSAL::isa($obj, 'Bio::Seq')) { } |
|
|
0 |
0 |
elsif (UNIVERSAL::isa($obj, 'Bio::Tree::TreeI')) { } |
|
651
|
0 |
0 |
unless ($tree->has_tag('taxa_id')) |
|
675
|
0 |
0 |
if (my $taxa_id = ($feat->get_tag_values('taxa_id'))[0]) |
|
678
|
0 |
0 |
if defined $taxa_label |
|
679
|
0 |
0 |
if defined $taxa_label |
|
710
|
0 |
0 |
if (@args % 2) |
|
712
|
0 |
0 |
unless (ref $feats eq 'ARRAY') |
|
720
|
0 |
0 |
if ($seqstring and $seqstring =~ /\S/) |
|
722
|
0 |
0 |
if ($@ and UNIVERSAL::isa($@, 'Bio::Phylo::Util::Exceptions::InvalidData')) |
|
729
|
0 |
0 |
if defined $name |
|
731
|
0 |
0 |
defined $feats ? : |
|
736
|
0 |
0 |
if $feat->has_tag('id') |
|
737
|
0 |
0 |
if ($taxa_id and $name eq $taxa_id) |
|
740
|
0 |
0 |
if ($feat->has_tag('my_taxon')) { } |
|
752
|
0 |
0 |
if defined $desc |
|
756
|
0 |
0 |
if $seq->can($field) |
|
779
|
0 |
0 |
unless (grep /^type/, ('seq', 'aln', 'tree')) |