| line |
true |
false |
branch |
|
160
|
2 |
46 |
unless $self->{'_parsed_features'} |
|
161
|
47 |
1 |
if (not defined $f and $self->_parse_pair) |
|
162
|
0 |
47 |
unless $self->{'_parsed_features'} |
|
172
|
12 |
915 |
if /^\#\-\-/o |
|
173
|
2 |
913 |
if (/^\#\s+(qrna)\s+(\S+)\s+\(([^\)]+)\)/o) { } |
|
|
2 |
911 |
elsif (/^\#\s+(PAM model)\s+\=\s+(.+)\s+$/o) { } |
|
|
2 |
909 |
elsif (/^\#\s+(RNA model)\s+\=\s+(\S+)/o) { } |
|
|
2 |
907 |
elsif (/^\#\s+(seq file)\s+\=\s+(.+)\s+$/o) { } |
|
|
94 |
813 |
elsif (/^\#\s+(\d+)\s+\[([\-+])\s+strand\]/o) { } |
|
|
4 |
809 |
elsif (/^\#/) { } |
|
|
96 |
713 |
elsif (/>(\S+)\s+\((\d+)\)/) { } |
|
|
51 |
662 |
elsif (/^length alignment:\s+(\d+)\s+\(id\=(\d+(\.\d+)?)\)/o) { } |
|
|
102 |
560 |
elsif (/^pos([XY]):\s+(\d+)\-(\d+)\s+\[(\d+)\-(\d+)\]\((\d+)\)\s+
\-\-\s+\((\S+\s+\S+\s+\S+\s+\S+)\)/ox) { } |
|
|
51 |
509 |
elsif (/^winner\s+\=\s+(\S{3})/) { } |
|
|
153 |
356 |
elsif (/^(\S{3})\s+ends\s+\=\s+(\-?\d+)\s+(\-?\d+)/) { } |
|
|
102 |
254 |
elsif (/^\s+(logoddspost)?OTH\s+\=\s+/ox) { } |
|
184
|
46 |
48 |
if ($seenstart) |
|
185
|
46 |
0 |
if ($data{'alignment_len'}) |
|
195
|
48 |
48 |
unless $data{'seqs'} |
|
|
0 |
96 |
if (@{[] unless $data{'seqs'};} == 2) { } |
|
203
|
3 |
48 |
if ($data{'alignment_len'}) |
|
209
|
0 |
51 |
if (/\(((sre_)?shuffled)\)/) |
|
227
|
153 |
153 |
if ($model =~ s/^logoddspost//) { } |
|
236
|
47 |
1 |
if (@features) |
|
257
|
2 |
1 |
if @_ |
|
276
|
2 |
1 |
if @_ |
|
295
|
2 |
1 |
if @_ |
|
315
|
2 |
50 |
if @_ |
|
334
|
2 |
1 |
if @_ |
|
352
|
2 |
1 |
if @_ |
|
366
|
3 |
46 |
if ($qid =~ m[(\S+)/(\d+)\-(\d+)]) |
|
369
|
3 |
46 |
if ($hid =~ m[(\S+)/(\d+)\-(\d+)]) |
|
379
|
23 |
26 |
$s < $e ? : |
|
403
|
0 |
147 |
if (not $data->{'model_location'}{$model}) { } |
|
404
|
0 |
0 |
if ($self->verbose > 0) |
|
418
|
0 |
49 |
if $self->verbose > 0 |
|
419
|
0 |
49 |
if ($data->{'shuffled'}) |