| line |
true |
false |
branch |
|
453
|
0 |
13 |
unless (defined $aln and ref $aln and $aln->isa('Bio::Align::AlignI')) |
|
458
|
13 |
45 |
if (defined $m and $method =~ /$m/i) |
|
505
|
0 |
2 |
unless $self->_check_arg($aln) |
|
506
|
2 |
0 |
unless defined $gappenalty |
|
560
|
0 |
2 |
unless $self->_check_arg($aln) |
|
561
|
2 |
0 |
unless defined $gappenalty |
|
615
|
3 |
0 |
unless defined $gappenalty |
|
616
|
0 |
3 |
unless $self->_check_arg($aln) |
|
642
|
2 |
11 |
unless $denom |
|
645
|
11 |
1 |
$denom ? : |
|
649
|
11 |
1 |
$denom ? : |
|
679
|
0 |
2 |
unless $self->_check_arg($aln) |
|
698
|
0 |
2 |
unless ($L) |
|
705
|
0 |
2 |
if ($denom == 0) |
|
711
|
0 |
2 |
if ($a < 0 or $b < 0) { } |
|
748
|
0 |
0 |
unless $self->_check_arg($aln) |
|
767
|
0 |
0 |
unless ($L) |
|
775
|
0 |
0 |
if ($a_denom > 0 and $b_denom > 0) { } |
|
829
|
0 |
2 |
unless $self->_check_arg($aln) |
|
850
|
120 |
1412 |
if ($c1 =~ /^$Bio::Align::DNAStatistics::GapChars$/ or $c2 =~ /^$Bio::Align::DNAStatistics::GapChars$/) { } |
|
|
960 |
452 |
elsif ($c2 =~ /^$Bio::Align::DNAStatistics::GCChhars$/i) { } |
|
877
|
2 |
0 |
if ($P) |
|
911
|
0 |
0 |
unless $self->_check_arg($aln) |
|
919
|
0 |
0 |
if (not length $id or $id =~ /^\s+$/) |
|
963
|
0 |
2 |
unless $self->_check_arg($aln) |
|
992
|
8 |
0 |
$fi && $fj ? : |
|
1000
|
10 |
2 |
if ($fij) |
|
1009
|
10 |
0 |
if ($fij) |
|
1025
|
0 |
2 |
if ($h == 0) { } |
|
1031
|
0 |
2 |
if ($c < 0) { } |
|
1110
|
0 |
12 |
unless $self->_check_arg($aln) |
|
1111
|
0 |
12 |
unless ($aln->is_flush) |
|
1119
|
480 |
1818 |
if ($c1 ne $c2) |
|
1121
|
120 |
357 |
if ($nt eq $c2) |
|
1128
|
120 |
1905 |
if ($_) |
|
1151
|
151 |
1823 |
if ($ti =~ /^$Bio::Align::DNAStatistics::GapChars$/) |
|
1152
|
318 |
1505 |
if ($tj =~ /^$Bio::Align::DNAStatistics::GapChars$/) |
|
1157
|
0 |
1505 |
unless (defined $ti_index) |
|
1164
|
159 |
1346 |
if ($ti ne $tj) |
|
1178
|
0 |
0 |
if (grep {$amb eq $_;} @amb2) |
|
1183
|
0 |
0 |
if ($pmatch) { } |
|
1193
|
0 |
25 |
if (not defined $aln && $aln->isa('Bio::Align::AlignI')) { } |
|
|
0 |
25 |
elsif ($aln->get_seq_by_pos(1)->alphabet ne 'dna') { } |
|
1220
|
2 |
16 |
if (defined $value) |
|
1243
|
0 |
1 |
if @_ != 4 |
|
1245
|
0 |
1 |
unless $aln->isa('Bio::Align::AlignI') |
|
1252
|
0 |
1 |
if (length $seqs[0]{'seq'} != length $seqs[1]{'seq'}) |
|
1279
|
0 |
1 |
unless $aln->isa('Bio::Align::AlignI') |
|
1307
|
0 |
1 |
unless $aln->isa('Bio::Align::AlignI') |
|
1379
|
2 |
101 |
if @_ |
|
1388
|
0 |
307 |
if (length $seqarray[$i]{'seq'} != length $seqarray[$j]{'seq'}) |
|
1411
|
0 |
307 |
unless $d_nc >= 0 and $d_syn >= 0 |
|
1418
|
4 |
303 |
if ($caller[3] =~ /calc_KaKs_pair/ or $caller[3] =~ /calc_all_KaKs_pairs/) |
|
1425
|
4 |
0 |
$d_syn_var + $d_nc_var ? : |
|
1438
|
0 |
4 |
if $syn_count < 10 || $non_syn_count < 10 and $self->verbose > -1 |
|
1449
|
2 |
101 |
if $caller[3] =~ /calc_all_KaKs/ or $caller[3] =~ /calc_KaKs_pair/ |
|
1457
|
0 |
614 |
if ($p > 0.75) |
|
1501
|
0 |
17499 |
if ($input{'cod1'} =~ /\-/ or $input{'cod2'} =~ /\-/) |
|
1509
|
12587 |
4912 |
if $diff_cnt == 0 |
|
1510
|
3921 |
991 |
if ($diff_cnt == 1) { } |
|
|
991 |
0 |
elsif ($diff_cnt == 2) { } |
|
|
0 |
0 |
elsif ($diff_cnt == 3) { } |
|
1526
|
0 |
3964 |
if ($t[$Bio::Align::DNAStatistics::CODONS->{$altered}] eq '*') { } |
|
1539
|
991 |
0 |
if ($tot_muts != 0) |
|
1555
|
0 |
0 |
if ($t[$Bio::Align::DNAStatistics::CODONS->{$altered}] eq '*') { } |
|
1572
|
0 |
0 |
if ($tot_muts != 0) |
|
1592
|
5903 |
46594 |
if (substr($ref->{'cod1'}, $_, 1) ne substr($ref->{'cod2'}, $_, 1)) { } |
|
1631
|
18432 |
5760 |
if substr($cod1, $pos, 1) ne substr($codons[$j], $pos, 1) |
|
1633
|
6912 |
1152 |
if $diff_cnt != 1 |
|
1636
|
276 |
876 |
if ($t[$Bio::Align::DNAStatistics::CODONS->{$cod1}] eq $t[$$Bio::Align::DNAStatistics::CODONS{$codons[$j]}]) { } |
|
|
92 |
784 |
elsif ($t[$Bio::Align::DNAStatistics::CODONS->{$cod1}] eq '*' or $t[$$Bio::Align::DNAStatistics::CODONS{$codons[$j]}] eq '*') { } |
|
1674
|
1 |
614 |
if length($seq) % 3 != 0 |
|
1678
|
0 |
34998 |
if $cod =~ /\-/ |
|
1702
|
768 |
2304 |
if substr($cod, $i, 1) eq $nuc |
|
1705
|
552 |
1752 |
if ($t[$Bio::Align::DNAStatistics::CODONS->{$test}] eq $aa) |
|
1708
|
108 |
2196 |
if ($t[$Bio::Align::DNAStatistics::CODONS->{$test}] eq '*') |