| line |
true |
false |
branch |
|
42
|
0 |
7 |
unless $format |
|
43
|
0 |
7 |
if $verbose |
|
53
|
7 |
0 |
unless ($self->{'handlers'}) |
|
55
|
0 |
7 |
unless exists $HANDLERS{$self->format} |
|
67
|
85 |
0 |
exists $self->{'handlers'}{'_DEFAULT_'} ? : |
|
|
477 |
85 |
exists $self->{'handlers'}{$nm} ? : |
|
69
|
0 |
562 |
unless ($method) |
|
85
|
7 |
23 |
if (@_) |
|
87
|
0 |
7 |
unless exists $HANDLERS{$format} |
|
96
|
183 |
9 |
if (scalar @ids) { } |
|
98
|
0 |
201 |
if (!index($id, '-') == 0) |
|
101
|
192 |
9 |
if exists $self->{'_params'}{$id} |
|
119
|
9 |
0 |
if (defined $$param{-'seqs'}) |
|
127
|
0 |
134 |
if ($coll) { } |
|
|
9 |
125 |
elsif (not exists $self->{'_params'}{'-annotation'}) { } |
|
128
|
0 |
0 |
unless ref $coll and $coll->isa('Bio::AnnotationCollectionI') |
|
140
|
0 |
0 |
if ($coll) { } |
|
|
0 |
0 |
elsif (not exists $self->{'_params'}{'-seq_annotation'}) { } |
|
141
|
0 |
0 |
unless ref $coll and $coll->isa('Bio::AnnotationCollectionI') |
|
157
|
5 |
4 |
unless (exists $self->{'_loaded_modules'}{$class}) |
|
162
|
8 |
1 |
if ($$data{-'consensus_meta'} and not UNIVERSAL::isa($$data{-'consensus_meta'}, 'Bio::Seq::Meta')) |
|
164
|
0 |
8 |
unless (exists $self->{'_loaded_modules'}{'Bio::Seq::Meta'}) |
|
176
|
0 |
168 |
if UNIVERSAL::isa($seq, 'Bio::LocatableI') |
|
178
|
168 |
0 |
if $seq->{'NSE'} |
|
179
|
168 |
0 |
if (UNIVERSAL::isa($seq, 'HASH')) |
|
182
|
1503 |
0 |
if exists $seq->{$p} |
|
187
|
1 |
167 |
if (defined $seq->{'NSE'} and exists $self->{'_features'} and exists $self->{'_features'}{$seq->{'NSE'}}) |
|
205
|
0 |
319 |
unless $data |
|
206
|
0 |
319 |
unless exists $data->{'BLOCK_LINE'} |
|
207
|
0 |
319 |
if $data->{'BLOCK_LINE'} < 1 |
|
210
|
151 |
168 |
if (my $nse = $self->{'_params'}{'-seqs'}[$index]{'NSE'}) { } |
|
211
|
0 |
151 |
unless $nse eq $data->{'NSE'} |
|
215
|
317 |
2 |
if ($data->{'NAME'} eq 'SEQUENCE') { } |
|
|
2 |
0 |
elsif ($data->{'NAME'} eq 'NAMED_META') { } |
|
224
|
0 |
18 |
unless $data |
|
225
|
18 |
0 |
if ($data->{'NAME'} eq 'CONSENSUS_META') |
|
233
|
0 |
0 |
unless $data |
|
234
|
0 |
0 |
unless exists $data->{'BLOCK_LINE'} |
|
235
|
0 |
0 |
if $data->{'BLOCK_LINE'} < 1 |
|
237
|
0 |
0 |
if (my $nse = $self->{'_params'}{'-seqs'}[$index]{'NSE'}) { } |
|
238
|
0 |
0 |
if $nse ne $data->{'NSE'} |
|
242
|
0 |
0 |
if ($data->{'NAME'} eq 'SEQUENCE') |
|
253
|
0 |
85 |
unless $data |
|
254
|
32 |
53 |
if ($data->{'ALIGNMENT'}) { } |
|
304
|
21 |
6 |
if ($data->{'ALIGNMENT'}) { } |
|
314
|
6 |
0 |
if $data->{'NSE'} |
|
316
|
0 |
0 |
unless $data->{'ACCESSION_NUMBER'} or $data->{'DISPLAY_ID'} |
|
336
|
0 |
174 |
unless my $nse = $data->{'NSE'} |
|
341
|
59 |
115 |
if (exists $self->{'_params'}{'-seq_accession'}) |
|
344
|
172 |
2 |
if ($nse =~ m[(\S+?)(?:\.(\d+))?/(\d+)-(\d+)]mosx) { } |
|
345
|
113 |
59 |
$data->{'ALPHABET'} eq 'dna' || $data->{'ALPHABET'} eq 'rna' ? : |
|
347
|
44 |
128 |
if ($start > $end) |
|
365
|
0 |
27 |
unless my $raw = $data->{'DATA'} |
|
368
|
12 |
15 |
if ($rawdata[0] eq 'PDB') { } |
|
|
3 |
12 |
elsif ($rawdata[0] eq 'SCOP') { } |
|
370
|
0 |
12 |
if (scalar @rawdata == 3 and $rawdata[2] =~ /-/) |
|
373
|
0 |
12 |
if scalar @rawdata != 4 |
|
383
|
0 |
3 |
if scalar @rawdata != 3 |
|
390
|
0 |
12 |
if scalar @rawdata > 2 |
|
397
|
93 |
0 |
if $v |