| line |
true |
false |
branch |
|
147
|
0 |
2 |
if defined $est_is_first |
|
165
|
0 |
20 |
if ($method and not $method =~ /sim4/i) |
|
225
|
4 |
28 |
if (/^seq1/) |
|
226
|
1 |
3 |
if ($started) |
|
233
|
0 |
3 |
unless /^seq1\s+=\s+(\S+)\,\s+(\d+)/ |
|
239
|
3 |
25 |
if (/^seq2/) |
|
242
|
0 |
3 |
unless /^seq2\s+=\s+(\S+)\s+\(>?(\S+)\s*\)\,\s+(\d+)/ |
|
249
|
0 |
25 |
if (/^>(\S+)\s*(.*)$/) |
|
254
|
0 |
0 |
if $2 |
|
257
|
0 |
0 |
if (defined($_ = $self->_readline) and /^>(\S+)\s*(.*)$/) |
|
259
|
0 |
0 |
if $2 |
|
263
|
1 |
24 |
if (/^\(complement\)/) |
|
269
|
18 |
6 |
if (/(\d+)-(\d+)\s+\((\d+)-(\d+)\)\s+(\d+)%/) |
|
276
|
3 |
15 |
unless (defined $estseq) |
|
279
|
2 |
1 |
unless (exists $self->{'_est_is_first'}) |
|
284
|
2 |
0 |
if ($seq1props{'length'} > $seq2props{'length'}) { } |
|
290
|
0 |
3 |
if ($self->{'_est_is_first'}) { } |
|
295
|
0 |
0 |
$output_fmt == 4 ? : |
|
304
|
10 |
8 |
if ($hit_direction == -1) |
|
316
|
0 |
18 |
if (exists $genomseq->{'seqname'}) { } |
|
327
|
18 |
0 |
if ($exon->feature1->can('seqlength')) { } |
|
339
|
18 |
0 |
if (exists $estseq->{'seqname'}) { } |
|
394
|
0 |
3 |
unless (@exons) |
|
395
|
0 |
0 |
if eof $self->_fh |