| line |
true |
false |
branch |
|
151
|
11 |
27 |
unless ($LOADED_WRAPPERS)
|
|
152
|
0 |
0 |
if $_[0]->get_nse eq $name
|
|
|
0 |
0 |
if (defined $acc)
|
|
|
0 |
0 |
if (defined $anno)
|
|
|
0 |
0 |
unless ($self->is_flush)
|
|
|
0 |
0 |
unless $countHashes[$index]
|
|
|
0 |
0 |
if (exists $countHashes[$column]{$char})
|
|
|
0 |
0 |
$divisor > 0 ? :
|
|
|
0 |
0 |
if $char[$i] ne $gap
|
|
|
0 |
0 |
if ($col + 1 == $resnumber)
|
|
|
0 |
0 |
if (my $seq = $self->get_by_name($seqname))
|
|
|
0 |
0 |
if (defined $meta)
|
|
|
0 |
0 |
if (defined $desc)
|
|
|
0 |
0 |
unless $seq
|
|
|
0 |
0 |
if ($disname and $name) { }
|
|
|
0 |
0 |
elsif (defined $disnames->{$name}) { }
|
|
|
0 |
0 |
if (defined $gap)
|
|
|
0 |
0 |
if (defined $name)
|
|
|
0 |
0 |
if (defined $match) { }
|
|
|
0 |
0 |
if ($char[$j] eq $firstseq[$j])
|
|
|
0 |
0 |
if (defined $match)
|
|
|
0 |
0 |
unless defined $alphabet
|
|
|
0 |
0 |
if $pos == $self->length
|
|
|
0 |
0 |
unless (defined $refchar)
|
|
|
0 |
0 |
if $pos >= scalar @$seq
|
|
|
0 |
0 |
if $seq->[$pos] eq '-' or $seq->[$pos] eq '.' or $seq->[$pos] eq ' '
|
|
|
0 |
0 |
if defined $seq->[$pos]
|
|
|
0 |
0 |
if scalar @$cols != scalar @colresidues
|
|
|
0 |
0 |
if $cols->[$_] ne $colresidues[$_]
|
|
|
0 |
0 |
if ($dash) { }
|
|
|
0 |
0 |
elsif (@colresidues == 1) { }
|
|
|
0 |
0 |
elsif ($alphabet eq 'protein') { }
|
|
|
0 |
0 |
unless $seq->isa('Bio::Seq::MetaI')
|
|
|
0 |
0 |
if ($len > $maxname)
|
|
|
0 |
0 |
unless $meta
|
|
|
0 |
0 |
if ($len > $maxname)
|
|
|
0 |
0 |
if ($len > $maxname)
|
|
|
0 |
0 |
if (defined $missing)
|
|
|
0 |
0 |
if $length_measure and not $enum{$length_measure}
|
|
|
0 |
0 |
unless ($self->is_flush)
|
|
|
0 |
0 |
unless $countHashes[$index]
|
|
|
0 |
0 |
if (exists $countHashes[$column]{$char})
|
|
|
0 |
0 |
if $_ == 0
|
|
|
0 |
0 |
if $_ == scalar @seqs
|
|
|
0 |
0 |
if $count < $len
|
|
|
0 |
0 |
if ($len) { }
|
|
|
0 |
0 |
if $count > $len
|
|
|
0 |
0 |
if ($len) { }
|
|
|
0 |
0 |
if ($length_measure eq 'short') { }
|
|
|
0 |
0 |
elsif ($length_measure eq 'long') { }
|
|
|
0 |
0 |
if (defined $score)
|
|
|
0 |
0 |
if ($i < $start - 1 or $i > $end - 1)
|
|
|
0 |
0 |
unless (exists $keep{$i})
|
|
|
0 |
0 |
unless (grep {not $_ =~ /^\Q$gap\E$/;} @slice)
|
|
|
0 |
0 |
unless ($include_gapped)
|
|
|
0 |
0 |
if (defined $source)
|
|
|
0 |
0 |
if $includeextra
|
|
|
0 |
0 |
if (defined $match) { }
|
|
|
0 |
0 |
if ($char[$j] eq $match)
|
|
153
|
0 |
11 |
if $@
|
|
185
|
0 |
0 |
if (&looks_like_instance($aln, 'Bio::Align::AlignI')) { }
|
|
190
|
0 |
0 |
if ($seqs[0]) { }
|
|
259
|
0 |
0 |
if (@_ == 1 and ref $_[0] eq 'HASH' and (%args) = %{$_[0];} or (%args) = &looks_like_hash(@_))
|
|
262
|
0 |
0 |
unless (defined $args{'-missing'} and defined $args{'-gap'} and defined $args{'-matchchar'})
|
|
272
|
0 |
0 |
if (scalar @values < 3)
|
|
289
|
0 |
0 |
if (not $old_special_symbols{$sym}) { }
|
|
|
0 |
0 |
elsif ($old_special_symbols{$sym} eq $new_special_symbols{$sym}) { }
|
|
301
|
0 |
0 |
unless ($new_special_symbols{$dummy} or $old_special_symbols{$dummy} or $dummies{$dummy})
|
|
337
|
4 |
0 |
if (&looks_like_instance($charlabels, 'ARRAY')) { }
|
|
|
0 |
0 |
elsif (defined $charlabels and not &looks_like_instance($charlabels, 'ARRAY')) { }
|
|
339
|
0 |
15 |
if (ref $label)
|
|
385
|
12 |
0 |
if (defined $raw)
|
|
386
|
12 |
0 |
if (&looks_like_instance($raw, 'ARRAY')) { }
|
|
389
|
46 |
0 |
if (defined $row)
|
|
390
|
46 |
0 |
if (&looks_like_instance($row, 'ARRAY')) { }
|
|
483
|
199 |
440 |
if $rowlength > $nchar
|
|
554
|
19 |
10 |
unless $seen{$gap}
|
|
586
|
29 |
29 |
unless $args{'-gap'}
|
|
587
|
58 |
0 |
unless $args{'-missing'}
|
|
588
|
35 |
23 |
if @states and @states == 1
|
|
632
|
0 |
0 |
if ($row->[$i] eq $gap) { }
|
|
633
|
0 |
0 |
if ($previous) { }
|
|
636
|
0 |
0 |
if ($previous eq $gap) { }
|
|
653
|
0 |
0 |
if ($previous and $previous eq $gap)
|
|
665
|
0 |
0 |
if ($args{'-trim'})
|
|
674
|
0 |
0 |
if (@starting_here)
|
|
677
|
0 |
0 |
if (@ending_here)
|
|
682
|
0 |
0 |
if (scalar @ending_here > $ntax / 2) { }
|
|
683
|
0 |
0 |
if $args{'-insertions'}
|
|
687
|
0 |
0 |
unless $args{'-insertions'}
|
|
724
|
2 |
0 |
unless (exists $args{"-$sym"})
|
|
737
|
2 |
2 |
if scalar @symbols_in_column <= 1
|
|
798
|
2 |
0 |
if ($total > 0)
|
|
857
|
2 |
21 |
unless $index{$col_pattern}
|
|
863
|
0 |
2 |
if ($indices) { }
|
|
898
|
0 |
1 |
unless ($type =~ /^(?:d|r)na/i)
|
|
904
|
2 |
4 |
if exists $freq->{$_}
|
|
937
|
0 |
0 |
if ($type =~ /continuous/i) { }
|
|
961
|
0 |
0 |
if (@top == 1) { }
|
|
965
|
0 |
0 |
if ($args{'-ambig'}) { }
|
|
973
|
0 |
0 |
unless ($args{'-gaps'})
|
|
976
|
0 |
0 |
unless ($args{'-missing'})
|
|
979
|
0 |
0 |
wantarray ? :
|
|
1012
|
0 |
16 |
if (@anno)
|
|
1043
|
6 |
7 |
unless exists $indices{$i}
|
|
1073
|
11 |
14 |
if $state eq $missing
|
|
1077
|
2 |
3 |
if scalar @states <= 1
|
|
1112
|
1 |
4 |
if scalar @states <= 1
|
|
1113
|
4 |
1 |
if (scalar @states > 1)
|
|
1118
|
4 |
6 |
if ($seen{$state} == 1) { }
|
|
1126
|
4 |
2 |
if $seen{$state} < $non_missing
|
|
1128
|
2 |
2 |
unless $seen_informative
|
|
1162
|
0 |
0 |
if ($state ne $m and $state ne $g)
|
|
1165
|
0 |
0 |
if not keys %col
|
|
1232
|
0 |
0 |
if (not &looks_like_number($prop) or $prop >= 1 or $prop < 0)
|
|
1272
|
0 |
0 |
unless (&looks_like_object($tree, 3))
|
|
1277
|
0 |
0 |
if ($type =~ /dna/i) { }
|
|
|
0 |
0 |
elsif ($type =~ /standard/i) { }
|
|
1305
|
0 |
0 |
if (scalar @{$self->get_entities;} < 3)
|
|
1311
|
0 |
0 |
if (&looks_like_class('Statistics::R'))
|
|
1315
|
0 |
0 |
if $seed
|
|
1321
|
0 |
0 |
if ($R->get('phylosim') eq 'FALSE')
|
|
1337
|
0 |
0 |
unless ($model)
|
|
1353
|
0 |
0 |
if ($random_rootseq) { }
|
|
1369
|
0 |
0 |
if ($m =~ /([^\:\:]+$)/)
|
|
1378
|
0 |
0 |
if ($type =~ /(?:F81|GTR|K80|HKY)/)
|
|
1382
|
0 |
0 |
if ($type =~ /GTR/)
|
|
1393
|
0 |
0 |
if ($type =~ /(?:K80|HKY)/)
|
|
1405
|
0 |
0 |
if (keys %deletions)
|
|
1417
|
0 |
0 |
if (keys %insertions)
|
|
1438
|
0 |
0 |
if (scalar @invariant)
|
|
1440
|
0 |
0 |
if ($pinvar == 1)
|
|
1477
|
0 |
0 |
if (&looks_like_class('Statistics::R'))
|
|
1485
|
0 |
0 |
if $seed
|
|
1502
|
0 |
0 |
if (keys %pat == 1) { }
|
|
1508
|
0 |
0 |
unless ($model)
|
|
1520
|
0 |
0 |
if $fw == 0
|
|
1521
|
0 |
0 |
if $rev == 0
|
|
1551
|
0 |
0 |
if ($node->is_terminal)
|
|
1583
|
1 |
119 |
if ($@ or $obj_container != $self->_type)
|
|
1587
|
0 |
119 |
unless ($self->get_type_object->is_same($obj->get_type_object))
|
|
1593
|
0 |
224 |
if ($obj->get_id == $ents->get_id)
|
|
1596
|
1 |
223 |
if ($taxon1)
|
|
1599
|
0 |
1 |
if ($taxon2 and $taxon1->get_id == $taxon2->get_id)
|
|
1653
|
0 |
0 |
unless (exists $seen{$state})
|
|
1680
|
44 |
4 |
if (my $taxa = $self->get_taxa) { }
|
|
1684
|
105 |
11 |
if (my $taxon = $row->get_taxon)
|
|
1685
|
105 |
0 |
if exists $taxa{$taxon->get_name}
|
|
1688
|
11 |
0 |
if (exists $taxa{$name}) { }
|
|
1724
|
0 |
1 |
if (my $taxa = $self->get_taxa) { }
|
|
1732
|
2 |
0 |
unless ($taxa{$name})
|
|
1736
|
1 |
0 |
if (keys %taxa)
|
|
1768
|
0 |
0 |
if (@_)
|
|
1774
|
0 |
0 |
$args{'-compact'} ? :
|
|
1827
|
0 |
0 |
if ($self->get_type =~ /^standard$/i) { }
|
|
1831
|
0 |
0 |
if (my(@letters) = (sort {$a cmp $b;} grep({/[a-z]/i;} @states))) { }
|
|
1896
|
0 |
1 |
$args{'-data_block'} ? :
|
|
1904
|
0 |
1 |
if ($args{'-links'})
|
|
1906
|
0 |
0 |
if $self->get_taxa
|
|
1912
|
0 |
1 |
if ($args{'-data_block'}) { }
|
|
1923
|
0 |
0 |
$self->get_respectcase ? :
|
|
|
0 |
1 |
if $args{'-respectcase'}
|
|
1924
|
0 |
1 |
if $self->get_matchchar
|
|
1926
|
1 |
0 |
if $self->get_gap
|
|
1930
|
0 |
1 |
if ($args{'-gapmode'} or $args{'-polymorphism'})
|
|
1934
|
0 |
0 |
$self->get_gapmode ? :
|
|
|
0 |
0 |
if $args{'-gapmode'}
|
|
1938
|
0 |
0 |
$self->get_polymorphism ? :
|
|
|
0 |
0 |
if $args{'-polymorphism'}
|
|
1943
|
0 |
1 |
if ($args{'-charlabels'})
|
|
1945
|
0 |
0 |
if (my(@labels) = @{$self->get_charlabels;})
|
|
1948
|
0 |
0 |
$label =~ /\s/ ? :
|
|
1959
|
0 |
1 |
if ($args{'-statelabels'})
|
|
1961
|
0 |
0 |
if (my(@labels) = @{$self->get_statelabels;})
|
|
1966
|
0 |
0 |
$label =~ /\s/ ? :
|
|
1979
|
0 |
1 |
if ($args{'-charstatelabels'})
|
|
1982
|
0 |
0 |
if (@charlabels and @statelabels)
|
|
1987
|
0 |
0 |
if (my $label = $charlabels[$i]) { }
|
|
1988
|
0 |
0 |
$label =~ /\s/ ? :
|
|
1994
|
0 |
0 |
if (my $labelset = $statelabels[$i]) { }
|
|
1996
|
0 |
0 |
$label =~ /\s/ ? :
|
|
2003
|
0 |
0 |
if $i < $nlabels
|
|
2013
|
1 |
2 |
if CORE::length $datum->get_nexus_name > $length
|
|
2023
|
3 |
0 |
if (not $args{'-seqnames'}) { }
|
|
|
0 |
0 |
elsif ($args{'-seqnames'} =~ /^internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-seqnames'} =~ /^taxon/i and $datum->get_taxon) { }
|
|
2030
|
0 |
0 |
if ($args{'-seqnames'} =~ /^taxon_internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-seqnames'} =~ /^taxon$/i) { }
|
|
2040
|
0 |
3 |
unless $name
|
|
2071
|
0 |
0 |
if (&looks_like_instance($dom, 'SCALAR') and $dom->_type == 18) { }
|
|
2078
|
0 |
0 |
unless ($dom)
|
|
2084
|
0 |
0 |
if @args
|
|
2086
|
0 |
0 |
$args{'-compact'} ? :
|
|
2103
|
0 |
0 |
%{$ids_for_states;} ? :
|
|
2144
|
0 |
0 |
if $label
|
|
2145
|
0 |
0 |
if $states_id
|
|
2161
|
26 |
111 |
if (scalar @defined != $nchar)
|
|
2163
|
157 |
0 |
unless ($chars[$i])
|
|
2174
|
0 |
137 |
if (scalar @chars > $nchar)
|