| line |
true |
false |
branch |
|
147
|
3494 |
101 |
if defined $query_len |
|
149
|
0 |
3595 |
if (not defined $name) { } |
|
155
|
2377 |
1218 |
if defined $acc |
|
156
|
0 |
3595 |
if defined $locus |
|
157
|
3505 |
90 |
if defined $desc |
|
158
|
876 |
2719 |
if defined $length |
|
159
|
3533 |
62 |
if defined $algo |
|
160
|
3506 |
89 |
if defined $signif |
|
161
|
1235 |
2360 |
if defined $score |
|
162
|
1546 |
2049 |
if defined $bits |
|
163
|
3533 |
62 |
if defined $rank |
|
164
|
3533 |
62 |
if defined $hsp_factory |
|
165
|
8 |
3587 |
if defined $gi |
|
166
|
0 |
3595 |
if defined $iter |
|
167
|
0 |
3595 |
if defined $found |
|
169
|
1 |
3594 |
if (defined $p) |
|
174
|
3534 |
61 |
if (defined $hsps) { } |
|
175
|
0 |
3534 |
if (not ref($hsps) =~ /array/i) { } |
|
183
|
1526 |
2008 |
if $hspcount == 0 |
|
206
|
0 |
3435 |
if (not defined $hsp or ref $hsp ne 'HASH' and not $hsp->isa('Bio::Search::HSP::HSPI')) |
|
212
|
2832 |
603 |
if (ref $hsp eq 'HASH') |
|
230
|
3533 |
728 |
if (@_) |
|
251
|
3656 |
1461 |
if (defined $value or not defined $previous) |
|
252
|
0 |
3656 |
unless defined $value |
|
271
|
2377 |
575 |
if (defined $value or not defined $previous) |
|
272
|
0 |
2377 |
unless defined $value |
|
291
|
3510 |
159 |
if (defined $value or not defined $previous) |
|
292
|
5 |
3505 |
unless defined $value |
|
311
|
954 |
184 |
if (defined $value or not defined $previous) |
|
312
|
17 |
937 |
unless defined $value |
|
336
|
3533 |
1128 |
if (defined $value or not defined $previous) |
|
337
|
0 |
3533 |
unless defined $value |
|
358
|
1235 |
101 |
if (defined $value) { } |
|
|
53 |
48 |
elsif (not defined $previous) { } |
|
362
|
0 |
53 |
unless (defined $self->{'_hsps'}[0]) |
|
368
|
52 |
1 |
if (defined(($self->hsps)[0]->score)) { } |
|
|
1 |
0 |
elsif (defined(($self->hsps)[0]->bits)) { } |
|
403
|
3506 |
181 |
if (defined $value) { } |
|
|
4 |
177 |
elsif (not defined $previous) { } |
|
406
|
0 |
4 |
unless (defined $self->{'_hsps'}[0]) |
|
433
|
1546 |
150 |
if (defined $value) { } |
|
|
90 |
60 |
elsif (not defined $previous) { } |
|
437
|
0 |
90 |
unless (defined $self->{'_hsps'}[0]) |
|
460
|
0 |
347 |
unless defined $self->{'_iterator'} |
|
463
|
90 |
257 |
unless defined $self->{'_hsps'} and $self->{'_iterator'} <= scalar @{$self->{'_hsps'};} |
|
467
|
142 |
51 |
if (ref $hsp eq 'HASH') |
|
496
|
476 |
2895 |
unless $self->{'_hashes'} |
|
502
|
415 |
2954 |
unless $self->{'_hsps'} |
|
|
0 |
2 |
unless $self->{'_hsps'} |
|
|
3369 |
2 |
wantarray ? : |
|
520
|
0 |
139 |
unless ($self->{'_hsps'}) |
|
566
|
9 |
0 |
if (@_) |
|
567
|
0 |
9 |
unless $self->{'_ambiguous_aln'} |
|
578
|
0 |
10 |
if (@_) |
|
579
|
0 |
10 |
defined $self->{'_overlap'} ? : |
|
613
|
0 |
0 |
if (not defined $self->{'_n'}) { } |
|
614
|
0 |
0 |
if ($self->hsp) |
|
659
|
2 |
1 |
unless (defined $val) |
|
666
|
3 |
0 |
if not $fmt or $fmt =~ /^raw/i |
|
668
|
0 |
0 |
if $fmt =~ /^exp/i |
|
669
|
0 |
0 |
if $fmt =~ /^parts/i |
|
698
|
0 |
48 |
unless (ref $self->{'_hsps'}) |
|
704
|
48 |
0 |
if $option =~ /best|first|1/i |
|
705
|
0 |
0 |
if $option =~ /worst|last/i |
|
743
|
0 |
32 |
if $seqType eq 'hit' |
|
749
|
13 |
19 |
if ($seqType eq 'sbjct') { } |
|
789
|
38 |
410 |
if $seqType eq 'hit' |
|
792
|
270 |
178 |
if (defined $num) |
|
796
|
0 |
178 |
unless ($self->{'_hsps'}) |
|
802
|
0 |
178 |
unless $self->tiled_hsps |
|
807
|
0 |
178 |
unless ($data) |
|
851
|
0 |
0 |
wantarray ? : |
|
852
|
20 |
96 |
if $seqType eq 'hit' |
|
854
|
0 |
116 |
unless ($self->{'_hsps'}) |
|
856
|
0 |
0 |
wantarray ? : |
|
860
|
0 |
116 |
unless $self->tiled_hsps |
|
864
|
116 |
0 |
if (defined $num) { } |
|
|
0 |
0 |
elsif ($seqType =~ /list|array/i) { } |
|
|
0 |
0 |
elsif ($seqType eq 'total') { } |
|
865
|
0 |
116 |
unless $seqType eq 'sbjct' or $seqType eq 'query' |
|
890
|
0 |
124 |
unless ($self->{'_hsps'}) |
|
892
|
0 |
0 |
wantarray ? : |
|
895
|
2 |
122 |
unless $self->tiled_hsps |
|
897
|
14 |
110 |
if (not $arg1) { } |
|
903
|
46 |
64 |
if (defined $arg2) { } |
|
|
45 |
19 |
elsif ($arg1 =~ /^id/i) { } |
|
950
|
0 |
24 |
unless ($self->{'_hsps'}) |
|
952
|
0 |
0 |
wantarray ? : |
|
955
|
0 |
3 |
wantarray ? : |
|
956
|
10 |
14 |
if $seqType eq 'hit' |
|
958
|
20 |
4 |
if (defined $num) |
|
964
|
3 |
1 |
if ($self->num_hsps == 1) { } |
|
971
|
1 |
0 |
unless (defined $self->{'_queryStart'}) |
|
976
|
3 |
3 |
if (not defined $earliest_query_start or $this_query_start < $earliest_query_start) |
|
981
|
3 |
3 |
if (not defined $earliest_sbjct_start or $this_sbjct_start < $earliest_sbjct_start) |
|
990
|
0 |
1 |
if ($seqType =~ /list|array/i) { } |
|
1027
|
0 |
24 |
unless ($self->{'_hsps'}) |
|
1028
|
0 |
0 |
wantarray ? : |
|
1031
|
0 |
3 |
wantarray ? : |
|
1032
|
10 |
14 |
if $seqType eq 'hit' |
|
1034
|
20 |
4 |
if (defined $num) |
|
1040
|
3 |
1 |
if ($self->num_hsps == 1) { } |
|
1047
|
1 |
0 |
unless (defined $self->{'_queryStop'}) |
|
1052
|
4 |
2 |
if (not defined $latest_query_end or $this_query_end > $latest_query_end) |
|
1057
|
2 |
4 |
if (not defined $latest_sbjct_end or $this_sbjct_end > $latest_sbjct_end) |
|
1066
|
0 |
1 |
if ($seqType =~ /list|array/i) { } |
|
1095
|
0 |
0 |
if $seqType eq 'hit' |
|
1152
|
5 |
36 |
if $seqType eq 'hit' |
|
1157
|
0 |
41 |
unless ($self->{'_hsps'}) |
|
1163
|
28 |
13 |
unless $self->tiled_hsps |
|
1171
|
0 |
41 |
if $ratio_rounded == 1 and $ratio < 1 |
|
1228
|
5 |
10 |
if $seqType eq 'hit' |
|
1233
|
0 |
15 |
unless ($self->{'_hsps'}) |
|
1239
|
0 |
15 |
unless $self->tiled_hsps |
|
1247
|
0 |
15 |
if $ratio_rounded == 1 and $ratio < 1 |
|
1277
|
0 |
19 |
unless ($self->{'_hsps'}) |
|
1283
|
17 |
2 |
unless $self->tiled_hsps |
|
1286
|
3 |
16 |
if $qry_len == 0 |
|
1315
|
0 |
13 |
unless ($self->{'_hsps'}) |
|
1321
|
0 |
13 |
unless $self->tiled_hsps |
|
1324
|
3 |
10 |
if $sbjct_len == 0 |
|
1371
|
0 |
0 |
unless ($self->{'_hsps'}) |
|
1377
|
0 |
0 |
unless $self->tiled_hsps |
|
1380
|
0 |
0 |
$num < 0 ? : |
|
1407
|
0 |
0 |
unless ($self->{'_hsps'}) |
|
1413
|
0 |
0 |
unless $self->tiled_hsps |
|
1416
|
0 |
0 |
$num < 0 ? : |
|
1453
|
0 |
0 |
if $seqType eq 'hit' |
|
1462
|
0 |
0 |
if (@inds) |
|
1467
|
0 |
0 |
$collapse ? : |
|
1480
|
0 |
20 |
unless ($self->{'_hsps'}) |
|
1482
|
0 |
0 |
wantarray ? : |
|
1486
|
0 |
20 |
unless $self->tiled_hsps |
|
1488
|
0 |
0 |
wantarray ? : |
|
1489
|
10 |
10 |
if $seqType eq 'hit' |
|
1493
|
20 |
0 |
if (defined $strnd) |
|
1494
|
0 |
20 |
unless $seqType eq 'sbjct' or $seqType eq 'query' |
|
1501
|
0 |
0 |
if ($self->num_hsps == 1) { } |
|
|
0 |
0 |
elsif (defined $self->{'_strand_query'}) { } |
|
1524
|
0 |
0 |
if ($seqType =~ /list|array/i) { } |
|
|
0 |
0 |
elsif ($seqType eq 'query') { } |
|
1542
|
0 |
10 |
unless ($self->{'_hsps'}) |
|
1548
|
0 |
10 |
unless $self->tiled_hsps |
|
1550
|
10 |
0 |
if (defined $frm) |
|
1558
|
0 |
0 |
if (not defined $self->{'_frame'}) { } |
|
1580
|
3520 |
3 |
if @_ |
|
1597
|
1 |
0 |
if (defined $value or not defined $previous) |
|
1598
|
1 |
0 |
unless (defined $value) |
|
1599
|
1 |
0 |
if ($self->{'_name'} =~ /(gb|emb|dbj|ref)\|(.*)\|(.*)/) { } |
|
1628
|
1 |
0 |
if (defined $desc) |
|
1632
|
2 |
0 |
if ($id =~ /(gb|emb|dbj|sp|pdb|bbs|ref|tp[gde])\|(.*)\|(.*)/) { } |
|
|
0 |
0 |
elsif ($id =~ /(pir|prf|pat|gnl)\|(.*)\|(.*)/) { } |
|
|
0 |
0 |
elsif ($id =~ /(gim|gi|bbm|bbs|lcl)\|(\d*)/) { } |
|
|
0 |
0 |
elsif ($id =~ /(oth)\|(.*)\|(.*)\|(.*)/) { } |
|
1672
|
48 |
536 |
if @_ |
|
1690
|
3547 |
18 |
if (defined $value or not defined $previous) |
|
1691
|
3 |
3544 |
unless defined $value |
|
1713
|
0 |
10 |
if (defined $value) { } |
|
1716
|
10 |
0 |
$self->name =~ /^gi\|(\d+)/ ? : |
|
1746
|
0 |
0 |
if ($coderef) { } |
|
1747
|
0 |
0 |
unless ref $coderef eq 'CODE' |
|
1758
|
0 |
0 |
if ($@) { } |
|
1784
|
0 |
0 |
if (defined $value) |
|
1819
|
0 |
0 |
if @_ |