| line |
true |
false |
branch |
|
141
|
1 |
1 |
if defined $seqname |
|
175
|
0 |
47 |
if ($method and not $method =~ /Genemark\.hmm/i) |
|
229
|
2 |
14 |
unless $self->_predictions_parsed |
|
266
|
45 |
32 |
if (/^\s*(\d+)\s+(\d+)/ or /^\s*(\d+)\s+[\+\-]/) |
|
274
|
43 |
2 |
if ($2) |
|
287
|
2 |
43 |
if ($self->analysis_method =~ /PROKARYOTIC/i) { } |
|
289
|
2 |
0 |
$flds[1] eq '+' ? : |
|
295
|
14 |
29 |
$flds[2] eq '+' ? : |
|
314
|
0 |
45 |
if $signalnr |
|
318
|
45 |
0 |
if defined $seqname and $seqname ne 'unknown' |
|
325
|
15 |
30 |
if ($prednr != $current_gene_no) |
|
327
|
13 |
2 |
if (defined $gene) |
|
338
|
15 |
0 |
if defined $seqname and $seqname ne 'unknown' |
|
343
|
2 |
43 |
$exontag eq '_na_' ? : |
|
347
|
2 |
75 |
if (/^(Genemark\.hmm\s*[PROKARYOTIC]*)\s+\(Version (.*)\)$/i) |
|
357
|
1 |
74 |
if (/^Matrices file:\s+(\S+)?/i) |
|
362
|
1 |
0 |
if (defined(my $_date = $self->_readline)) |
|
369
|
1 |
74 |
if (/^Model file name:\s+(\S+)/) |
|
375
|
1 |
0 |
if (defined($_date = $self->_readline)) |
|
381
|
1 |
74 |
if (/^Sequence[ file]? name:\s+(.+)\s*$/i) |
|
388
|
1 |
73 |
if (/^>/) |
|
396
|
1 |
13 |
unless $aa_id |
|
402
|
13 |
78 |
if ($aa_id =~ /\|gene.$geneno\|/) |
|
421
|
0 |
2 |
if (defined $self->analysis_query) |
|
453
|
1 |
15 |
unless exists $self->{'_preds'} and @{$self->{'_preds'};} |
|
470
|
0 |
15 |
unless (exists $self->{'_preds'}) |
|
489
|
2 |
16 |
if $val |
|
490
|
0 |
18 |
unless (exists $self->{'_preds_parsed'}) |
|
509
|
0 |
0 |
if $val |
|
510
|
0 |
0 |
unless (exists $self->{'_has_cds'}) |
|
533
|
1 |
13 |
unless my $entry = $self->_readline |
|
538
|
1 |
1 |
unless $_ = $self->_readline |
|
546
|
13 |
0 |
if ($entry =~ s/^(.+)\n//) { } |
|
572
|
1 |
2 |
if $val |
|
573
|
1 |
2 |
unless (exists $self->{'_seqname'}) |