| line |
true |
false |
branch |
|
76
|
0 |
87 |
if (defined $l[0] and not ref $l[0])
|
|
79
|
3 |
84 |
unless defined $$self{'_loci'}
|
|
82
|
0 |
87 |
unless UNIVERSAL::can($locus, 'isa') and $locus->isa('Bio::Polloc::LocusI')
|
|
84
|
0 |
87 |
if defined $space
|
|
97
|
0 |
9 |
unless defined $$self{'_loci'}
|
|
121
|
0 |
0 |
unless defined $self->genomes
|
|
124
|
0 |
0 |
unless defined $locus->genome
|
|
127
|
0 |
0 |
unless defined $$struct[$space]
|
|
128
|
0 |
0 |
if ($genome->name eq $locus->genome->name)
|
|
149
|
0 |
0 |
if $locus->id eq $id
|
|
168
|
0 |
3 |
if defined $value
|
|
184
|
1 |
2 |
if defined $value
|
|
185
|
2 |
1 |
unless defined $$self{'_genomes'}
|
|
186
|
0 |
1 |
unless ref $$self{'_genomes'} and ref($$self{'_genomes'}) =~ /ARRAY/i
|
|
201
|
0 |
3 |
if defined $value
|
|
229
|
0 |
0 |
if ($#{$self->loci;} >= 1) { }
|
|
|
0 |
0 |
elsif ($#{$self->loci;} == 0) { }
|
|
233
|
0 |
0 |
unless wantarray
|
|
240
|
0 |
0 |
wantarray ? :
|
|
271
|
0 |
0 |
if $from == $to and $ref != 0
|
|
279
|
0 |
0 |
unless defined $seq
|
|
280
|
0 |
0 |
if defined $locus->id
|
|
283
|
0 |
0 |
unless $#seqs > -1
|
|
285
|
0 |
0 |
unless $#seqs > 0
|
|
314
|
0 |
0 |
if not $force and defined $$self{'_fixed_strands'} and $$self{'_fixed_strands'} == $#{$self->loci;}
|
|
318
|
0 |
0 |
unless $#{$self->loci;} > 0
|
|
337
|
0 |
0 |
if (defined $$ref[0] and defined $$ref[1]) { }
|
|
|
0 |
0 |
elsif (defined $$ref[0] or defined $$ref[1]) { }
|
|
339
|
0 |
0 |
if defined $$ref_test[0] and defined $$ref_test[1] and $$ref_test[0]->length >= $$ref[0]->length and $$ref_test[1]->length >= $$ref[1]->length
|
|
345
|
0 |
0 |
if defined $$ref_test[0] and defined $$ref_test[1]
|
|
348
|
0 |
0 |
if defined $$ref_test[0] or defined $$ref_test[1]
|
|
351
|
0 |
0 |
unless (defined $$ref[0] or defined $$ref[1])
|
|
355
|
0 |
0 |
defined $$ref[1] ? :
|
|
|
0 |
0 |
defined $$ref[0] ? :
|
|
370
|
0 |
0 |
unless $tgt
|
|
373
|
0 |
0 |
if defined $self->loci->[$k]->id
|
|
376
|
0 |
0 |
if ($factory->align([$ref, $tgt])->$eval_fun < $factory->align([$ref, $tgtrc])->$eval_fun) { }
|