| line |
true |
false |
branch |
|
46
|
3 |
17 |
if ($trees) |
|
47
|
0 |
3 |
if (not ref($trees) =~ /ARRAY/i) { } |
|
57
|
10 |
10 |
if ($mlmat) |
|
58
|
0 |
10 |
if (not ref($mlmat) =~ /ARRAY/i) { } |
|
64
|
15 |
5 |
if ($seqs) |
|
65
|
0 |
15 |
if (not ref($seqs) =~ /ARRAY/i) { } |
|
73
|
16 |
4 |
if ($ngmatrix) |
|
74
|
0 |
16 |
if (not ref($ngmatrix) =~ /ARRAY/i) { } |
|
80
|
8 |
12 |
if ($codonfreq) |
|
81
|
8 |
0 |
if (ref($codonfreq) =~ /ARRAY/i) { } |
|
88
|
14 |
6 |
if ($codonpos) |
|
89
|
0 |
14 |
if (not ref($codonpos) =~ /ARRAY/i) { } |
|
96
|
18 |
2 |
if defined $version |
|
97
|
20 |
0 |
if defined $seqfile |
|
98
|
18 |
2 |
if defined $model |
|
99
|
18 |
2 |
if (defined $patterns) |
|
100
|
18 |
0 |
if (ref($patterns) =~ /HASH/i) { } |
|
108
|
2 |
18 |
if ($aafreq) |
|
109
|
2 |
0 |
if (ref($aafreq) =~ /HASH/i) { } |
|
115
|
4 |
16 |
if ($stats) |
|
116
|
4 |
0 |
if (ref($stats) =~ /HASH/i) { } |
|
124
|
2 |
18 |
if defined $aadistmat |
|
125
|
1 |
19 |
if defined $aamldistmat |
|
127
|
5 |
15 |
if (defined $NSSitesresults) |
|
128
|
0 |
5 |
if (not ref($NSSitesresults) =~ /ARRAY/i) { } |
|
138
|
2 |
18 |
if ($ntfreqs) |
|
139
|
2 |
0 |
if (ref($ntfreqs) =~ /HASH/i) { } |
|
146
|
2 |
18 |
if ($kappa_mat) |
|
149
|
2 |
18 |
if ($alpha_mat) |
|
153
|
8 |
12 |
if ($input_params) |
|
154
|
0 |
8 |
if (not ref($input_params) =~ /HASH/i) { } |
|
164
|
1 |
19 |
if ($rst) |
|
165
|
1 |
0 |
if (ref($rst) =~ /ARRAY/i) { } |
|
173
|
1 |
19 |
if (defined $rst_persite) |
|
177
|
1 |
19 |
if ($rst_trees) |
|
178
|
1 |
0 |
if (ref($rst_trees) =~ /ARRAY/i) { } |
|
199
|
0 |
2 |
unless $self->{'_trees'} |
|
210
|
3 |
0 |
if ($tree and ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
220
|
0 |
10 |
unless defined $mat |
|
221
|
0 |
10 |
unless (ref($mat) =~ /ARRAY/i) |
|
237
|
0 |
16 |
unless defined $mat |
|
238
|
0 |
16 |
unless (ref($mat) =~ /ARRAY/i) |
|
255
|
80 |
0 |
if ($seq) |
|
256
|
0 |
80 |
unless ($seq->isa('Bio::PrimarySeqI')) |
|
280
|
0 |
14 |
if (scalar @codonpos != 3) |
|
285
|
0 |
42 |
unless (ref($pos) =~ /HASH/i and exists $pos->{'A'}) |
|
302
|
18 |
6 |
if @_ |
|
309
|
20 |
0 |
if @_ |
|
317
|
18 |
9 |
if @_ |
|
325
|
18 |
2 |
if @_ |
|
333
|
2 |
0 |
if ($aafreqs and ref($aafreqs) =~ /HASH/i) |
|
343
|
5 |
1 |
if ($seqname) { } |
|
354
|
2 |
0 |
if ($freqs and ref($freqs) =~ /HASH/i) |
|
364
|
0 |
1 |
if ($seqname) { } |
|
374
|
0 |
11 |
unless defined $stat and defined $value |
|
388
|
0 |
1 |
unless $self->{'_stats'} |
|
400
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
418
|
0 |
1 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
430
|
9 |
0 |
if (defined $model) |
|
439
|
0 |
5 |
unless $self->{'_nssiteresult'} |
|
446
|
8 |
0 |
if @_ |
|
453
|
0 |
0 |
unless $self->{'_codonfreqs'} |
|
466
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
485
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
497
|
0 |
10 |
unless defined $p |
|
504
|
0 |
0 |
unless $self->{'_input_parameters'} |
|
516
|
20 |
0 |
if ($seq) |
|
517
|
0 |
20 |
unless ($seq->isa('Bio::PrimarySeqI')) |
|
535
|
0 |
1 |
unless $self->{'_rstseqs'} |
|
542
|
1 |
0 |
if ($tree) |
|
543
|
0 |
1 |
unless ($tree->isa('Bio::Tree::TreeI')) |
|
560
|
0 |
1 |
unless $self->{'_rsttrees'} |
|
567
|
1 |
0 |
if @_ |