| line |
true |
false |
branch |
|
208
|
3 |
17 |
if ($trees) |
|
209
|
0 |
3 |
if (not ref($trees) =~ /ARRAY/i) { } |
|
219
|
10 |
10 |
if ($mlmat) |
|
220
|
0 |
10 |
if (not ref($mlmat) =~ /ARRAY/i) { } |
|
226
|
15 |
5 |
if ($seqs) |
|
227
|
0 |
15 |
if (not ref($seqs) =~ /ARRAY/i) { } |
|
235
|
16 |
4 |
if ($ngmatrix) |
|
236
|
0 |
16 |
if (not ref($ngmatrix) =~ /ARRAY/i) { } |
|
242
|
8 |
12 |
if ($codonfreq) |
|
243
|
8 |
0 |
if (ref($codonfreq) =~ /ARRAY/i) { } |
|
250
|
14 |
6 |
if ($codonpos) |
|
251
|
0 |
14 |
if (not ref($codonpos) =~ /ARRAY/i) { } |
|
258
|
18 |
2 |
if defined $version |
|
259
|
20 |
0 |
if defined $seqfile |
|
260
|
18 |
2 |
if defined $model |
|
261
|
18 |
2 |
if (defined $patterns) |
|
262
|
18 |
0 |
if (ref($patterns) =~ /HASH/i) { } |
|
270
|
2 |
18 |
if ($aafreq) |
|
271
|
2 |
0 |
if (ref($aafreq) =~ /HASH/i) { } |
|
277
|
4 |
16 |
if ($stats) |
|
278
|
4 |
0 |
if (ref($stats) =~ /HASH/i) { } |
|
286
|
2 |
18 |
if defined $aadistmat |
|
287
|
1 |
19 |
if defined $aamldistmat |
|
289
|
5 |
15 |
if (defined $NSSitesresults) |
|
290
|
0 |
5 |
if (not ref($NSSitesresults) =~ /ARRAY/i) { } |
|
300
|
2 |
18 |
if ($ntfreqs) |
|
301
|
2 |
0 |
if (ref($ntfreqs) =~ /HASH/i) { } |
|
308
|
2 |
18 |
if ($kappa_mat) |
|
311
|
2 |
18 |
if ($alpha_mat) |
|
315
|
8 |
12 |
if ($input_params) |
|
316
|
0 |
8 |
if (not ref($input_params) =~ /HASH/i) { } |
|
326
|
1 |
19 |
if ($rst) |
|
327
|
1 |
0 |
if (ref($rst) =~ /ARRAY/i) { } |
|
335
|
1 |
19 |
if (defined $rst_persite) |
|
339
|
1 |
19 |
if ($rst_trees) |
|
340
|
1 |
0 |
if (ref($rst_trees) =~ /ARRAY/i) { } |
|
380
|
0 |
2 |
unless $self->{'_trees'} |
|
410
|
3 |
0 |
if ($tree and ref $tree and $tree->isa('Bio::Tree::TreeI')) |
|
431
|
0 |
10 |
unless defined $mat |
|
432
|
0 |
10 |
unless (ref($mat) =~ /ARRAY/i) |
|
469
|
0 |
16 |
unless defined $mat |
|
470
|
0 |
16 |
unless (ref($mat) =~ /ARRAY/i) |
|
507
|
80 |
0 |
if ($seq) |
|
508
|
0 |
80 |
unless ($seq->isa('Bio::PrimarySeqI')) |
|
563
|
0 |
14 |
if (scalar @codonpos != 3) |
|
568
|
0 |
42 |
unless (ref($pos) =~ /HASH/i and exists $pos->{'A'}) |
|
608
|
18 |
6 |
if @_ |
|
625
|
20 |
0 |
if @_ |
|
643
|
18 |
9 |
if @_ |
|
665
|
18 |
2 |
if @_ |
|
684
|
2 |
0 |
if ($aafreqs and ref($aafreqs) =~ /HASH/i) |
|
709
|
5 |
1 |
if ($seqname) { } |
|
731
|
2 |
0 |
if ($freqs and ref($freqs) =~ /HASH/i) |
|
756
|
0 |
1 |
if ($seqname) { } |
|
777
|
0 |
11 |
unless defined $stat and defined $value |
|
811
|
0 |
1 |
unless $self->{'_stats'} |
|
843
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
881
|
0 |
1 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
903
|
9 |
0 |
if (defined $model) |
|
922
|
0 |
5 |
unless $self->{'_nssiteresult'} |
|
939
|
8 |
0 |
if @_ |
|
956
|
0 |
0 |
unless $self->{'_codonfreqs'} |
|
993
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
1032
|
0 |
2 |
unless ($d and ref $d and $d->isa('Bio::Matrix::PhylipDist')) |
|
1054
|
0 |
10 |
unless defined $p |
|
1071
|
0 |
0 |
unless $self->{'_input_parameters'} |
|
1105
|
20 |
0 |
if ($seq) |
|
1106
|
0 |
20 |
unless ($seq->isa('Bio::PrimarySeqI')) |
|
1144
|
0 |
1 |
unless $self->{'_rstseqs'} |
|
1161
|
1 |
0 |
if ($tree) |
|
1162
|
0 |
1 |
unless ($tree->isa('Bio::Tree::TreeI')) |
|
1199
|
0 |
1 |
unless $self->{'_rsttrees'} |
|
1216
|
1 |
0 |
if @_ |