| line |
true |
false |
branch |
|
208
|
0 |
519 |
unless $hit |
|
209
|
0 |
519 |
unless ref $hit and $hit->isa('Bio::Search::Hit::HitI') |
|
216
|
0 |
519 |
if (defined $filter) |
|
217
|
0 |
0 |
if (ref $filter eq 'CODE') { } |
|
218
|
0 |
0 |
&$filter($_) ? : |
|
239
|
415 |
104 |
unless @hsps |
|
323
|
0 |
1 |
if ($t and ref $t eq 'ARRAY') { } |
|
361
|
12 |
0 |
if (/query/) |
|
366
|
0 |
0 |
if (/subject|hit/) |
|
378
|
0 |
12 |
$qseq->strand && $qseq->strand < 0 ? : |
|
|
0 |
12 |
$qseq->strand && $qseq->strand < 0 ? : |
|
391
|
0 |
12 |
$hseq->strand && $hseq->strand < 0 ? : |
|
|
0 |
12 |
$hseq->strand && $hseq->strand < 0 ? : |
|
451
|
531 |
7 |
unless (defined $$self{"identities_${type}_${action}_$context"}) |
|
479
|
0 |
538 |
unless (defined $$self{"conserved_${type}_${action}_$context"}) |
|
508
|
1 |
1050 |
unless (defined $$self{"length_${type}_${action}_$context"}) |
|
544
|
0 |
1058 |
unless ($method and grep /^$method$/, ('identical', 'conserved')) |
|
548
|
0 |
1058 |
unless (grep /^$denom/, ('total', 'aligned')) |
|
554
|
529 |
529 |
if ($_ eq 'identical') |
|
558
|
529 |
0 |
if ($_ eq 'conserved') |
|
566
|
1046 |
12 |
unless (defined $self->{$key}) |
|
568
|
0 |
1046 |
if (/total/) |
|
573
|
1046 |
0 |
if (/aligned/) |
|
667
|
4 |
0 |
unless ($$self{"frac_aligned_${type}_${action}_$context"}) |
|
719
|
0 |
0 |
unless (defined $$self{"num_unaligned_${type}_${action}_$context"}) |
|
771
|
203 |
129 |
unless (defined $$self{"coverage_map_${type}_$context"}) |
|
777
|
0 |
332 |
unless (defined $$self{"coverage_map_${type}_$context"}) |
|
827
|
0 |
0 |
if ($legend_q) |
|
855
|
0 |
5229 |
if @_ |
|
872
|
519 |
1249 |
if @_ |
|
896
|
403 |
629 |
unless defined $context |
|
897
|
0 |
629 |
unless $$self{"_contexts_$type"}{$context} |
|
953
|
0 |
0 |
if @_ |
|
995
|
0 |
207 |
unless ($self->{'hsps'}) |
|
1113
|
204 |
328 |
if ($action eq 'fast') |
|
1133
|
328 |
204 |
if ($action ne 'fast') |
|
1137
|
393 |
991 |
$action eq 'max' ? : |
|
1141
|
788 |
976 |
if ($_ eq 'est') |
|
1151
|
483 |
493 |
if ($_ eq 'max') |
|
1158
|
40 |
443 |
$acc_i > $inc_i ? : |
|
1159
|
49 |
434 |
$acc_c > $inc_c ? : |
|
1162
|
493 |
0 |
if (not $_ or $_ eq 'exact') |
|
1230
|
2 |
269 |
if (my $rewind = shift()) |
|
1237
|
3 |
266 |
if $FINISHED |
|
1246
|
1086 |
3396 |
unless ($finished_incrementing) |
|
1247
|
823 |
263 |
if ($n == $#$hsps) { } |
|
1253
|
3 |
263 |
unless $finished_incrementing |
|
1289
|
2 |
268 |
unless (defined $$self{"_tiling_iterator_${type}_$context"}) |
|
1305
|
0 |
8297 |
unless grep /^$$typeref$/, ('hit', 'query', 'subject') |
|
1306
|
266 |
8031 |
if $$typeref eq 'subject' |
|
1313
|
17 |
3704 |
if (not $$actionref) { } |
|
1314
|
13 |
4 |
$self->_has_sequence_data ? : |
|
1317
|
0 |
3704 |
unless grep /^$$actionref$/, ('est', 'exact', 'fast', 'max') |
|
1318
|
12 |
3692 |
if ($$actionref ne 'est' and not $self->_has_sequence_data) |
|
1329
|
298 |
4315 |
if (not $$contextref) { } |
|
1330
|
0 |
298 |
unless $self->mapping($type) == 1 |
|
1335
|
0 |
4315 |
if ($$contextref =~ /^[mp]$/) |
|
1336
|
0 |
4315 |
unless $$contextref =~ /all|[mp][0-2_]/ |
|
1362
|
0 |
546 |
unless defined $strand or defined $frame |
|
1363
|
211 |
335 |
if (defined $strand and $self->_has_strand($type)) { } |
|
1364
|
94 |
117 |
if (defined $frame and $self->_has_frame($type)) { } |
|
1365
|
53 |
41 |
$strand >= 0 ? : |
|
1368
|
86 |
31 |
$strand >= 0 ? : |
|
1372
|
0 |
335 |
if (defined $frame and $self->_has_frame($type)) { } |
|
1411
|
0 |
2253 |
unless defined $self->hit |
|
1412
|
2237 |
16 |
($self->hit->hsps)[0]->seq_str('match') ? : |
|
1424
|
0 |
0 |
unless defined $self->mapping($type) |
|
1470
|
4 |
4 |
unless (defined $$self{"_contig_intersection_${type}_$context"}) |