| line |
true |
false |
branch |
|
192
|
705 |
626 |
if defined $self->{'VERBOSE'} |
|
193
|
0 |
1331 |
if (exists $self->{'GAP_SYMBOL'}) { } |
|
198
|
0 |
0 |
if CORE::length $self->{'GAP_SYMBOL'} != 1 |
|
206
|
0 |
1331 |
unless (defined $self->{'QUERY_LENGTH'} and defined $self->{'HIT_LENGTH'}) |
|
218
|
105 |
208 |
unless (defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'}) |
|
221
|
209 |
104 |
$type =~ /sbjct|hit|tot/i ? : |
|
244
|
0 |
7397 |
if (defined $value or not defined $previous) |
|
245
|
0 |
0 |
unless defined $value |
|
266
|
0 |
63 |
if (defined $value) |
|
285
|
0 |
170 |
if (defined $value) |
|
311
|
105 |
497 |
unless ($self->{'_did_prefrac'}) |
|
315
|
602 |
0 |
if defined $type |
|
316
|
0 |
602 |
if defined $type and $type =~ /subject|sbjct/ |
|
318
|
85 |
517 |
if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
321
|
313 |
289 |
if (defined $value or not defined $previous) |
|
322
|
0 |
313 |
unless defined $value |
|
323
|
208 |
105 |
if ($type eq 'hit' or $type eq 'query') |
|
353
|
0 |
440 |
unless ($self->{'_did_prefrac'}) |
|
357
|
434 |
6 |
if defined $type |
|
358
|
0 |
440 |
if defined $type and $type =~ /subject|sbjct/ |
|
359
|
4 |
430 |
if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
362
|
313 |
127 |
if (defined $value or not defined $previous) |
|
363
|
0 |
313 |
unless defined $value |
|
386
|
378 |
2747 |
unless ($self->{'_did_pregaps'}) |
|
390
|
2039 |
1086 |
if defined $type |
|
391
|
0 |
2039 |
if not defined $type or $type eq 'hsp' or not $type =~ /query|hit|subject|sbjct|total/ |
|
393
|
38 |
3087 |
if $type =~ /sbjct|subject/ |
|
395
|
1110 |
2015 |
if (defined $value or not defined $previous) |
|
396
|
11 |
1099 |
unless defined $value |
|
416
|
3 |
607 |
if (defined $value or not defined $previous) |
|
417
|
3 |
0 |
unless defined $value |
|
440
|
1 |
617 |
if (defined $value or not defined $previous) |
|
441
|
1 |
0 |
unless defined $value |
|
466
|
3 |
6902 |
if (defined $value or not defined $previous) |
|
467
|
3 |
0 |
unless defined $value |
|
493
|
0 |
8 |
if (defined $value or not defined $previous) |
|
494
|
0 |
0 |
unless defined $value |
|
520
|
2 |
7 |
if (defined $value or not defined $previous) |
|
521
|
2 |
0 |
unless defined $value |
|
552
|
675 |
3164 |
unless defined $type |
|
555
|
1615 |
2224 |
if ($type =~ /^q/i) { } |
|
|
989 |
1235 |
elsif ($type =~ /^(hit|subject|sbjct)/) { } |
|
561
|
105 |
1130 |
if (defined $v) |
|
595
|
42 |
42 |
unless ($self->{'_did_prepi'}) |
|
635
|
0 |
610 |
unless (defined $val) |
|
644
|
284 |
326 |
if ($val =~ /^q/i) { } |
|
|
326 |
0 |
elsif ($val =~ /^hi|^s/i) { } |
|
|
0 |
0 |
elsif ($val =~ /^list|array/i) { } |
|
|
0 |
0 |
elsif ($val =~ /^\d+$/) { } |
|
657
|
0 |
0 |
wantarray ? : |
|
707
|
16 |
3 |
$q_nm ? : |
|
718
|
19 |
0 |
$s_nm ? : |
|
739
|
1 |
1913 |
unless ($self->{'_did_presimilar'}) |
|
743
|
0 |
1914 |
if (defined $value) |
|
763
|
437 |
1486 |
unless ($self->{'_did_presimilar'}) |
|
767
|
0 |
1923 |
if (defined $value) |
|
785
|
0 |
4514 |
if (defined $value) |
|
845
|
94 |
100 |
if $seqType eq 'hit' |
|
847
|
100 |
94 |
if ($t eq 'q') { } |
|
|
94 |
0 |
elsif ($t eq 's' or $t eq 'h') { } |
|
858
|
8 |
186 |
if ($t eq 'c') { } |
|
|
0 |
186 |
elsif ($t eq 'i') { } |
|
|
18 |
168 |
elsif ($t eq 'n') { } |
|
|
10 |
158 |
elsif ($t eq 'm') { } |
|
|
150 |
8 |
elsif ($t eq 'g') { } |
|
|
8 |
0 |
elsif ($t eq 'f') { } |
|
859
|
0 |
8 |
if ($class =~ /conserved\-not\-identical/) { } |
|
884
|
150 |
44 |
if ($class eq '_gap') { } |
|
|
8 |
36 |
elsif ($class eq '_conservedall') { } |
|
907
|
48 |
146 |
if $collapse |
|
909
|
48 |
146 |
$collapse ? : |
|
936
|
1 |
1 |
$self->{'_sbjct_offset'} == 3 ? : |
|
|
2 |
2 |
$self->{'_query_offset'} == 3 ? : |
|
|
2 |
4 |
$self->{'_query_offset'} == 3 && $self->{'_sbjct_offset'} == 3 ? : |
|
956
|
1167 |
4423 |
unless ($self->{'_created_qff'}) |
|
964
|
1331 |
5608 |
if (not $self->{'_finished_new'} or $self->{'_making_qff'}) |
|
965
|
0 |
1331 |
if $self->{'_sim1'} |
|
969
|
9 |
5599 |
unless ($self->{'_created_qff'}) |
|
987
|
550 |
3840 |
unless ($self->{'_created_sff'}) |
|
995
|
0 |
4408 |
if (not $self->{'_finished_new'} or $self->{'_making_sff'}) |
|
996
|
0 |
0 |
if $self->{'_sim2'} |
|
1000
|
12 |
4396 |
unless ($self->{'_created_sff'}) |
|
1021
|
19 |
0 |
if (not defined $self->{'SIGNIFICANCE'} or defined $val) |
|
1022
|
0 |
8 |
defined $self->pvalue ? : |
|
|
11 |
8 |
defined $self->evalue ? : |
|
|
0 |
19 |
defined $val ? : |
|
1045
|
2 |
585 |
if ($type =~ /^q/i and defined $self->{'QUERY_STRAND'}) { } |
|
|
2 |
862 |
elsif ($type =~ /^(hit|subject|sbjct)/i and defined $self->{'HIT_STRAND'}) { } |
|
1089
|
132 |
73 |
unless $self->{'_sequenceschanged'} |
|
1097
|
18 |
55 |
$qdir <= 0 ? : |
|
1099
|
14 |
59 |
$sdir <= 0 ? : |
|
1104
|
4 |
69 |
if ($prog =~ /FAST|SSEARCH|SMITH-WATERMAN/i) |
|
1112
|
4 |
0 |
if ($seqString =~ /^(\s+)?(.*?)\s*$/) |
|
1113
|
3 |
1 |
$1 ? : |
|
1139
|
2 |
71 |
unless (defined $self->{'_sbjct_offset'} and defined $self->{'_query_offset'}) |
|
1150
|
30602 |
0 |
$pos < CORE::length $qseq ? : |
|
|
30602 |
0 |
$pos < CORE::length $sseq ? : |
|
1157
|
757 |
29845 |
if ($mchar eq '+' or $mchar eq '.') { } |
|
|
25371 |
4474 |
elsif ($mchar eq ':' or $mchar ne ' ') { } |
|
|
4474 |
0 |
elsif ($mchar eq ' ') { } |
|
1166
|
2 |
4472 |
$qchar eq '\\' ? : |
|
|
0 |
4474 |
$qchar eq '/' ? : |
|
1169
|
0 |
4474 |
$schar eq '\\' ? : |
|
|
0 |
4474 |
$schar eq '/' ? : |
|
1172
|
2 |
4472 |
if ($qfs) { } |
|
|
0 |
4472 |
elsif ($sfs) { } |
|
|
512 |
3960 |
elsif ($qchar eq $self->{'GAP_SYMBOL'}) { } |
|
|
491 |
3469 |
elsif ($schar eq $self->{'GAP_SYMBOL'}) { } |
|
1218
|
3981 |
493 |
unless ($sgap) |
|
1221
|
3960 |
514 |
unless ($qgap) |
|
1237
|
30088 |
514 |
unless $qgap |
|
1238
|
30109 |
493 |
unless $sgap |
|
1247
|
68 |
39 |
if ($prog =~ /^(?:PSI)?T(BLAST|FAST)(N|X|Y)/io) { } |
|
|
3 |
36 |
elsif ($prog =~ /^(BLAST|FAST)(X|Y|XY)/io) { } |
|
1249
|
67 |
1 |
if ($1 eq 'BLAST' and $2 eq 'X') |
|
1266
|
0 |
113 |
if (@_) |
|
1268
|
10 |
103 |
defined $self->{'N'} ? : |
|
1281
|
758 |
901 |
if $seqType eq 'hit' |
|
1284
|
840 |
819 |
if ($seqType eq 'query') { } |
|
1311
|
0 |
54 |
if @_ |
|
1330
|
0 |
12 |
if @_ |
|
1350
|
0 |
6 |
if @_ |
|
1406
|
0 |
8 |
if defined $arg |
|
1408
|
7 |
1 |
unless (defined $self->{'_cigar_string'}) |
|
1431
|
0 |
7 |
unless (scalar @qchars == scalar @hchars) |
|
1442
|
1837 |
80 |
if ($qchar ne $self->{'GAP_SYMBOL'} and $hchar ne $self->{'GAP_SYMBOL'}) { } |
|
|
13 |
67 |
elsif ($qchar eq $self->{'GAP_SYMBOL'}) { } |
|
|
67 |
0 |
elsif ($hchar eq $self->{'GAP_SYMBOL'}) { } |
|
1462
|
1835 |
89 |
if ($self->{'_state_for_cigar_string'} eq $new_state) { } |
|
1466
|
55 |
34 |
unless $self->{'_count_for_cigar_string'} == 1 |
|
1481
|
7 |
1170 |
if ($algo =~ /^(?:PSI)?T(?:BLAST|FAST|SW)[NY]/io) { } |
|
|
25 |
1145 |
elsif ($algo =~ /^(?:FAST|BLAST)(?:X|Y|XY)/io or $algo =~ /^P?GENEWISE/io) { } |
|
|
286 |
859 |
elsif ($algo =~ /^T(BLAST|FAST|SW)(X|Y|XY)/io or $algo =~ /^(BLAST|FAST|SW)N/io or $algo =~ /^WABA|AXT|BLAT|BLASTZ|PSL|MEGABLAST|EXONERATE|SW|SSEARCH|SMITH\-WATERMAN|SIM4$/) { } |
|
|
1 |
858 |
elsif ($algo =~ /^RPS-BLAST/) { } |
|
1490
|
126 |
160 |
if ($2) |
|
1497
|
0 |
1 |
if ($algo =~ /^RPS-BLAST\(BLASTX\)/) |
|
1505
|
602 |
256 |
$stranded eq 'q' || $stranded eq 'b' ? : |
|
1506
|
617 |
241 |
$stranded eq 'h' || $stranded eq 's' || $stranded eq 'b' ? : |
|
1520
|
1133 |
43 |
unless (defined $self->{'_query_factor'}) |
|
1525
|
0 |
1176 |
unless (defined $qe and defined $qs) |
|
1528
|
1106 |
70 |
if ($qe > $qs) { } |
|
1529
|
843 |
263 |
if ($queryfactor) { } |
|
1537
|
70 |
0 |
if ($queryfactor) { } |
|
1562
|
14 |
1162 |
if $self->can('meta') |
|
1567
|
603 |
573 |
if (defined $strand and not defined $qframe and $queryfactor) { } |
|
|
263 |
310 |
elsif (not defined $strand) { } |
|
1574
|
1176 |
0 |
if ($qframe =~ /^([+-])?([0-3])/) { } |
|
1576
|
0 |
623 |
if ($qframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0) |
|
1579
|
623 |
553 |
$2 != 0 ? : |
|
1598
|
44 |
518 |
unless (defined $self->{'_hit_factor'}) |
|
1603
|
0 |
562 |
unless (defined $he and defined $hs) |
|
1606
|
455 |
107 |
if ($he > $hs) { } |
|
1607
|
199 |
256 |
if ($hitfactor) { } |
|
1615
|
106 |
1 |
if ($hitfactor) { } |
|
1635
|
15 |
547 |
if $self->can('meta') |
|
1638
|
3 |
559 |
if (defined $strand and not defined $hframe and $hitfactor) { } |
|
|
257 |
302 |
elsif (not defined $strand) { } |
|
1645
|
562 |
0 |
if ($hframe =~ /^([+-])?([0-3])/) { } |
|
1647
|
0 |
132 |
if ($hframe and $dir eq '-' && $strand >= 0 || $dir eq '+' && $strand <= 0) |
|
1650
|
132 |
430 |
$2 != 0 ? : |
|
1670
|
0 |
438 |
unless (defined $identical) |
|
1671
|
0 |
0 |
if (not defined $percent_id) { } |
|
1680
|
0 |
438 |
unless (defined $conserved) |
|
1682
|
0 |
0 |
unless $self->{'ALGORITHM'} =~ /^((FAST|BLAST)N)|EXONERATE|SIM4|AXT|PSL|BLAT|BLASTZ|WABA/io |
|
1704
|
105 |
0 |
if ($hsp_len) |
|
1710
|
104 |
1 |
if ($hit_len) |
|
1715
|
104 |
1 |
if ($query_len) |
|
1736
|
0 |
378 |
if (defined $query_gaps) { } |
|
|
363 |
15 |
elsif (defined $query_seq) { } |
|
1739
|
0 |
294 |
$self->algorithm eq 'ERPIN' ? : |
|
|
69 |
294 |
defined $self->{'_query_offset'} ? : |
|
1745
|
0 |
378 |
if (defined $hit_gaps) { } |
|
|
358 |
20 |
elsif (defined $hit_seq) { } |
|
1748
|
2 |
288 |
$self->algorithm eq 'ERPIN' ? : |
|
|
68 |
290 |
defined $self->{'_sbjct_offset'} ? : |
|
1754
|
329 |
49 |
unless (defined $gaps) |
|
1764
|
42 |
0 |
if $self->{'HSP_LENGTH'} > 0 |