| line |
!l |
l&&!r |
l&&r |
condition |
|
206
|
0 |
0 |
1331 |
defined $self->{'QUERY_LENGTH'} and defined $self->{'HIT_LENGTH'} |
|
218
|
105 |
0 |
208 |
defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'} |
|
316
|
0 |
602 |
0 |
defined $type and $type =~ /subject|sbjct/ |
|
358
|
6 |
434 |
0 |
defined $type and $type =~ /subject|sbjct/ |
|
936
|
2 |
2 |
2 |
$self->{'_query_offset'} == 3 && $self->{'_sbjct_offset'} == 3 |
|
1045
|
306 |
279 |
2 |
$type =~ /^q/i and defined $self->{'QUERY_STRAND'} |
|
|
279 |
304 |
2 |
$type =~ /^(hit|subject|sbjct)/i and defined $self->{'HIT_STRAND'} |
|
1139
|
2 |
0 |
71 |
defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'} |
|
1249
|
0 |
1 |
67 |
$1 eq 'BLAST' and $2 eq 'X' |
|
1442
|
13 |
67 |
1837 |
$qchar ne $self->{'GAP_SYMBOL'} and $hchar ne $self->{'GAP_SYMBOL'} |
|
1525
|
0 |
0 |
1176 |
defined $qe and defined $qs |
|
1567
|
263 |
310 |
603 |
defined $strand and not defined $qframe |
|
|
573 |
0 |
603 |
defined $strand and not defined $qframe and $queryfactor |
|
1576
|
553 |
623 |
0 |
$qframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0 |
|
1603
|
0 |
0 |
562 |
defined $he and defined $hs |
|
1638
|
257 |
302 |
3 |
defined $strand and not defined $hframe |
|
|
559 |
0 |
3 |
defined $strand and not defined $hframe and $hitfactor |
|
1647
|
430 |
132 |
0 |
$hframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0 |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
244
|
0 |
0 |
7397 |
defined $value or not defined $previous |
|
318
|
0 |
85 |
517 |
not defined $type or $type eq 'hsp' |
|
|
85 |
0 |
517 |
not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
321
|
313 |
0 |
289 |
defined $value or not defined $previous |
|
323
|
104 |
104 |
105 |
$type eq 'hit' or $type eq 'query' |
|
359
|
6 |
4 |
430 |
not defined $type or $type eq 'hsp' |
|
|
10 |
0 |
430 |
not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
362
|
313 |
0 |
127 |
defined $value or not defined $previous |
|
391
|
1086 |
0 |
2039 |
not defined $type or $type eq 'hsp' |
|
|
1086 |
0 |
2039 |
not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
395
|
1099 |
11 |
2015 |
defined $value or not defined $previous |
|
416
|
0 |
3 |
607 |
defined $value or not defined $previous |
|
440
|
0 |
1 |
617 |
defined $value or not defined $previous |
|
466
|
0 |
3 |
6902 |
defined $value or not defined $previous |
|
493
|
0 |
0 |
8 |
defined $value or not defined $previous |
|
520
|
0 |
2 |
7 |
defined $value or not defined $previous |
|
847
|
94 |
0 |
0 |
$t eq 's' or $t eq 'h' |
|
964
|
1331 |
0 |
5608 |
not $self->{'_finished_new'} or $self->{'_making_qff'} |
|
995
|
0 |
0 |
4408 |
not $self->{'_finished_new'} or $self->{'_making_sff'} |
|
1021
|
19 |
0 |
0 |
not defined $self->{'SIGNIFICANCE'} or defined $val |
|
1157
|
589 |
168 |
29845 |
$mchar eq '+' or $mchar eq '.' |
|
|
560 |
24811 |
4474 |
$mchar eq ':' or $mchar ne ' ' |
|
1481
|
22 |
3 |
1145 |
$algo =~ /^(?:FAST|BLAST)(?:X|Y|XY)/io or $algo =~ /^P?GENEWISE/io |
|
|
126 |
103 |
916 |
$algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/io or $algo =~ /^(BLAST|FAST|SW)N/io |
|
|
229 |
57 |
859 |
$algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/io or $algo =~ /^(BLAST|FAST|SW)N/io or $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SSEARCH|SMITH\-WATERMAN|SIM4$/ |
|
1505
|
0 |
602 |
256 |
$stranded eq 'q' || $stranded eq 'b' |
|
1506
|
15 |
602 |
241 |
$stranded eq 'h' || $stranded eq 's' || $stranded eq 'b' |
|
1551
|
1176 |
0 |
0 |
$self->{'_sim1'} || 'Bio::SeqFeature::Similarity'->new |
|
1576
|
0 |
0 |
623 |
$dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0 |
|
1624
|
0 |
562 |
0 |
$self->{'_sim2'} || 'Bio::SeqFeature::Similarity'->new |
|
1647
|
0 |
0 |
132 |
$dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0 |
|
1764
|
0 |
42 |
0 |
$self->{'PERCENT_IDENTITY'} || $self->frac_identical('total') * 100 |