| line |
true |
false |
branch |
|
203
|
108 |
183 |
if $src |
|
204
|
7 |
284 |
if defined $score |
|
213
|
8 |
283 |
if $id |
|
214
|
8 |
283 |
if $acc |
|
215
|
8 |
283 |
if $desc |
|
216
|
9 |
282 |
if $coll |
|
218
|
0 |
291 |
if ($sa) |
|
219
|
0 |
0 |
unless $coll |
|
224
|
1 |
290 |
if ($feats and ref $feats eq 'ARRAY') |
|
229
|
0 |
291 |
if $con |
|
230
|
8 |
283 |
if $cmeta |
|
232
|
9 |
282 |
if ($seqs and ref $seqs eq 'ARRAY') |
|
276
|
0 |
2420 |
unless ($seq) |
|
279
|
0 |
2420 |
unless (ref $seq and $seq->isa('Bio::LocatableSeq')) |
|
282
|
2417 |
3 |
unless defined $order |
|
285
|
1 |
2419 |
if ($order < 0) |
|
299
|
0 |
2419 |
if ($self->{'_seq'}{$name}) { } |
|
300
|
0 |
0 |
unless $self->verbose < 0 |
|
306
|
0 |
2419 |
if ($ordh->{$order}) |
|
312
|
0 |
0 |
$_[1] - $_[0] == 1 ? : |
|
320
|
2400 |
19 |
unless (exists $self->{'_start_end_lists'}{$id}) |
|
352
|
0 |
13 |
unless ref $seq and $seq->isa('Bio::LocatableSeq') |
|
358
|
0 |
13 |
unless (exists $self->{'_seq'}{$name}) |
|
366
|
13 |
0 |
if (exists $self->{'_start_end_lists'}{$id}) { } |
|
371
|
13 |
0 |
if (do {
$$self{'_start_end_lists'}{$id}
}->[$i] eq $seq) |
|
376
|
13 |
0 |
if ($found) { } |
|
420
|
11 |
4 |
if exists $duplicate{$seq->display_id} |
|
429
|
1 |
27 |
if exists $duplicate{$seq2->display_id} |
|
437
|
4329 |
2058 |
if ($one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] and $one[$k] eq $two[$k]) |
|
441
|
6320 |
67 |
if ($one[$k] ne '.' and $one[$k] ne '-' and defined $two[$k] and $two[$k] ne '.' and $two[$k] ne '-') |
|
448
|
27 |
0 |
unless $res == 0 |
|
452
|
12 |
15 |
if ($ratio > $perc) |
|
453
|
0 |
12 |
if $self->verbose > 0 |
|
517
|
0 |
1 |
unless open my $listfh, '<', $list |
|
521
|
0 |
6 |
unless &_in_aln($name, \@ids) |
|
557
|
1 |
1 |
if ($seqid =~ /^\d+$/) { } |
|
559
|
0 |
1 |
if $seqid <= 1 or $seqid > $self->num_sequences |
|
561
|
0 |
1 |
unless &_in_aln($seqid, \@ids) |
|
566
|
2 |
10 |
if ($is_num and $pos == $seqid or $seqid eq $seq[$i]->display_id) { } |
|
579
|
7 |
17 |
if $str eq $_ |
|
619
|
0 |
15 |
if $str =~ /^[atcgn-]+$/i |
|
639
|
4 |
11 |
if ($seen) { } |
|
655
|
0 |
11 |
if $str2 =~ /^[atcg\-\?]+$/i |
|
670
|
0 |
1 |
wantarray ? : |
|
678
|
1 |
14 |
if @array == 0 |
|
684
|
1867 |
22382 |
if $char1[$i] eq '?' |
|
685
|
642 |
21740 |
if $char2[$i] eq '?' |
|
686
|
14469 |
7271 |
if $char1[$i] ne $char2[$i] |
|
688
|
4 |
55 |
if $diff == 0 |
|
701
|
343 |
26 |
$array[$i] eq $sym1 ? : |
|
705
|
526 |
26 |
$array[$i] eq $sym1 ? : |
|
736
|
56107 |
13 |
if (exists $self->{'_seq'}{$self->{'_order'}{$order}}) |
|
776
|
0 |
97 |
if ($aname eq $bname) { } |
|
806
|
0 |
89 |
unless defined $id |
|
811
|
89 |
0 |
if (exists $self->{'_start_end_lists'}{$id}) |
|
834
|
0 |
258 |
unless $pos =~ /^\d+$/ and $pos > 0 |
|
836
|
0 |
258 |
unless $pos <= $self->num_sequences |
|
856
|
0 |
18 |
unless (defined $name) |
|
861
|
18 |
26 |
if ($seq->id eq $name) |
|
906
|
0 |
0 |
unless $arg{'-pos'} |
|
911
|
0 |
0 |
if defined $arg{'-mask'} |
|
915
|
0 |
0 |
if $consensus_string =~ /^[^?]/ |
|
924
|
0 |
0 |
if $consensus_string =~ /[^?]$/ |
|
972
|
0 |
1 |
unless $start =~ /^\d+$/ and $start > 0 |
|
974
|
0 |
1 |
unless $end =~ /^\d+$/ and $end > 0 |
|
976
|
0 |
1 |
unless $start <= $end |
|
1015
|
1 |
7 |
unless ($pos[0] =~ /^\d+$/) |
|
1017
|
1 |
0 |
if ($sortcmd eq 'nosort') { } |
|
1026
|
0 |
32 |
unless /^\d+$/ and $_ > 0 and $_ <= $end |
|
1030
|
7 |
1 |
unless $nosort |
|
1086
|
0 |
31 |
unless $start =~ /^\d+$/ and $start > 0 |
|
1088
|
0 |
31 |
unless $end =~ /^\d+$/ and $end > 0 |
|
1090
|
0 |
31 |
unless $start <= $end |
|
1092
|
1 |
30 |
if $start > $self->length |
|
1098
|
0 |
107 |
$seq->isa('Bio::Seq::MetaI') ? : |
|
1112
|
0 |
107 |
if $end > $seq->length |
|
1119
|
24 |
83 |
if (exists $self->{'_mask_char'}) |
|
1125
|
52 |
55 |
if ($start > 1) { } |
|
1128
|
38 |
14 |
if (not defined $seq->strand) { } |
|
|
1 |
13 |
elsif ($seq->strand < 0) { } |
|
1136
|
2 |
53 |
if (defined $seq->strand and $seq->strand < 0) { } |
|
1142
|
0 |
107 |
if ($new_seq->isa('Bio::Seq::MetaI')) |
|
1149
|
106 |
1 |
if ($new_seq->start and $new_seq->end >= $new_seq->start) { } |
|
1152
|
1 |
0 |
if ($keep_gap_only) { } |
|
1161
|
0 |
30 |
if ($cons_meta) |
|
1190
|
0 |
4 |
unless @args |
|
1193
|
1 |
3 |
if ($args[0][0] =~ /^[a-z_]+$/i) { } |
|
|
3 |
0 |
elsif ($args[0][0] =~ /^\d+$/) { } |
|
1224
|
2 |
4 |
if ($all_gaps_columns) { } |
|
1248
|
5 |
1 |
$#remove >= 0 ? : |
|
1271
|
0 |
658 |
unless $sequence |
|
1273
|
627 |
31 |
$start > 0 ? : |
|
1274
|
32 |
626 |
$end + 1 >= CORE::length $sequence ? : |
|
1277
|
42 |
616 |
unless (defined $new_seq->start) |
|
1278
|
31 |
11 |
if ($start == 0) { } |
|
1284
|
5 |
6 |
if ($start_adjust) |
|
1291
|
32 |
626 |
if ($end + 1 >= CORE::length $orig) { } |
|
1300
|
1 |
41 |
if ($new_seq->end < $new_seq->start) |
|
1307
|
42 |
0 |
if $sequence |
|
1323
|
0 |
1 |
if grep {$_ eq 'gaps';} @{$type;} |
|
1324
|
0 |
1 |
if grep /all_gaps_columns/, @{$type;} |
|
1341
|
1 |
0 |
if ($del_char) |
|
1356
|
1 |
0 |
$#remove >= 0 ? : |
|
1357
|
0 |
1 |
if $gap |
|
1358
|
0 |
1 |
if $all_gaps_columns |
|
1384
|
3 |
0 |
$#remove >= 0 ? : |
|
1454
|
0 |
4 |
unless defined $from and defined $to |
|
1519
|
28 |
104 |
if ($seq[$x] eq $consensus[$x]) { } |
|
|
84 |
20 |
elsif ($seq[$x] ne $gapchar) { } |
|
1530
|
4 |
0 |
if do {
$cigars{$name}
}->[0] + 1 < do {
$cigars{$name}
}->[1] |
|
1533
|
4 |
0 |
if ${$cigars{$name};}[$#{$cigars{$name};} - 1] + 1 < ${$cigars{$name};}[$#{$cigars{$name};}] |
|
1535
|
4 |
24 |
if (${$cigars{$name};}[$x - 1] + 1 < do {
$cigars{$name}
}->[$x] and ${$cigars{$name};}[$x + 1] > do {
$cigars{$name}
}->[$x] + 1) |
|
1545
|
8 |
28 |
if (do {
$cigars{$name}
}->[$x] == ${$cigars{$name};}[$x - 1] + 1 and do {
$cigars{$name}
}->[$x] == ${$cigars{$name};}[$x + 1] - 1) |
|
1592
|
6 |
63 |
unless defined $alphabet |
|
1601
|
6 |
3132 |
unless (defined $refchar) |
|
1602
|
6 |
0 |
if $pos == $self->length |
|
1610
|
0 |
26906 |
if $pos >= scalar @$seq |
|
1611
|
99 |
24512 |
if $seq->[$pos] eq '-' or $seq->[$pos] eq '.' or $seq->[$pos] eq ' ' |
|
1613
|
26906 |
0 |
if defined $seq->[$pos] |
|
1618
|
758 |
2374 |
if ($dash) { } |
|
|
1721 |
653 |
elsif (@colresidues == 1) { } |
|
|
472 |
181 |
elsif ($alphabet eq 'protein') { } |
|
1639
|
3744 |
196 |
if scalar @$cols != scalar @colresidues |
|
1642
|
0 |
453 |
if $cols->[$_] ne $colresidues[$_] |
|
1678
|
217 |
1756 |
exists $gap_hsh{$pos} ? : |
|
1706
|
1 |
21 |
if (exists $gap_hsh{$pos} and $gap_hsh{$pos} == scalar @seqs) { } |
|
1769
|
1 |
0 |
if $match =~ /[\^.$|()\[\]]/ |
|
1773
|
0 |
1 |
unless scalar @seqs > 1 |
|
1782
|
524 |
196 |
if defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ and $refseq[$i] eq $varseq[$i] |
|
1814
|
0 |
5 |
unless scalar @seqs > 1 |
|
1822
|
13780 |
6002 |
if defined $refseq[$i] and $refseq[$i] =~ /[A-Za-z\*]/ || $refseq[$i] =~ /$gapchar/ and $varseq[$i] eq $match |
|
1856
|
72 |
70 |
if (defined $name) |
|
1876
|
8 |
8 |
if (defined $acc) |
|
1896
|
13 |
12 |
if (defined $name) |
|
1918
|
22 |
10 |
if (defined $char) |
|
1919
|
0 |
22 |
if CORE::length $char > 1 |
|
1941
|
9 |
9 |
if (defined $char) |
|
1942
|
0 |
9 |
if CORE::length $char > 1 |
|
1963
|
51 |
11191 |
if (defined $char or not defined $self->{'_gap_char'}) |
|
1964
|
26 |
25 |
unless defined $char |
|
1965
|
0 |
51 |
if CORE::length $char > 1 |
|
1986
|
3 |
2 |
unless ($self->{'_symbols'}) |
|
1992
|
5 |
0 |
unless ($includeextra) |
|
1995
|
7 |
8 |
if defined $char |
|
2018
|
17 |
9 |
if @_ |
|
2087
|
2472 |
2426 |
if ($hash{$key} > $count and $hash{$key} >= $threshold) |
|
2103
|
0 |
22078 |
if $letter eq '' |
|
2104
|
4744 |
17334 |
if $letter eq $gapchar or $letter =~ /\./ |
|
2136
|
0 |
2 |
if $seq->alphabet eq 'protein' |
|
2158
|
1 |
9 |
if ($string =~ /N/) |
|
2159
|
0 |
1 |
$string =~ /\W/ ? : |
|
2162
|
2 |
7 |
if $string =~ /^\W+$/ |
|
2165
|
0 |
7 |
if ($string =~ /U/) |
|
2173
|
0 |
7 |
if ($string =~ /[VDHB]/) |
|
2180
|
1 |
6 |
if ($string =~ /[SKYRWM]/) |
|
2191
|
5 |
2 |
if ($string =~ /A/) { } |
|
|
0 |
2 |
elsif ($string =~ /C/) { } |
|
|
0 |
2 |
elsif ($string =~ /G/) { } |
|
|
2 |
0 |
elsif ($string =~ /T/) { } |
|
2193
|
0 |
5 |
if ($string =~ /G/) { } |
|
|
0 |
5 |
elsif ($string =~ /C/) { } |
|
|
2 |
3 |
elsif ($string =~ /T/) { } |
|
2195
|
0 |
0 |
if ($string =~ /C/) { } |
|
|
0 |
0 |
elsif ($string =~ /T/) { } |
|
2197
|
0 |
0 |
if ($string =~ /T/) |
|
2205
|
0 |
0 |
if ($string =~ /T/) |
|
2213
|
0 |
0 |
if ($string =~ /T/) { } |
|
|
0 |
0 |
elsif ($string =~ /G/) { } |
|
2215
|
0 |
0 |
if ($string =~ /G/) |
|
2223
|
0 |
0 |
if ($string =~ /C/) { } |
|
|
0 |
0 |
elsif ($string =~ /T/) { } |
|
2232
|
0 |
7 |
if $rna and $char eq 'T' |
|
2233
|
1 |
6 |
if $string =~ /\W/ |
|
2253
|
0 |
56 |
if ($meta and not ref $meta && $meta->isa('Bio::Seq::MetaI')) |
|
2256
|
17 |
39 |
if $meta |
|
2278
|
58 |
200 |
if ($length == -1) |
|
2284
|
0 |
200 |
if ($temp != $length) |
|
2285
|
0 |
0 |
if $report |
|
2324
|
2231 |
6303 |
if ($temp > $length) |
|
2366
|
52 |
70 |
if ($len > $maxname) |
|
2393
|
6 |
11 |
unless $seq->isa('Bio::Seq::MetaI') |
|
2396
|
0 |
0 |
if ($len > $maxname) |
|
2404
|
1 |
1 |
unless $meta |
|
2407
|
1 |
0 |
if ($len > $maxname) |
|
2480
|
0 |
9 |
unless ($self->is_flush) |
|
2498
|
7077 |
503 |
if (exists $countHashes[$column]{$char}) |
|
2515
|
9 |
0 |
$divisor > 0 ? : |
|
2558
|
0 |
22 |
if $length_measure and not exists $enum{$length_measure} |
|
2561
|
0 |
22 |
unless ($self->is_flush) |
|
2578
|
17139 |
769 |
if (exists $alphabet{$char}) |
|
2581
|
12795 |
4344 |
if (defined $countHashes[$column]{$char}) { } |
|
2587
|
851 |
16288 |
if ($countHashes[$column]{$char} == $nof_seqs) |
|
2596
|
32 |
68 |
if ($length_measure eq 'short' or $length_measure eq 'long') |
|
2598
|
16 |
16 |
if ($length_measure eq 'short') { } |
|
|
16 |
0 |
elsif ($length_measure eq 'long') { } |
|
2599
|
5 |
11 |
if (not defined $len or $seq_len < $len) |
|
2603
|
2 |
14 |
if (not defined $len or $seq_len > $len) |
|
2611
|
20 |
2 |
if ($length_measure eq 'align') |
|
2669
|
0 |
27 |
unless $self->{'_start_end_lists'}{$name} |
|
2670
|
0 |
27 |
unless $resnumber |
|
2675
|
0 |
27 |
if $@ |
|
2705
|
0 |
550 |
unless defined $self->{'_seq'}{$name} |
|
2707
|
112 |
438 |
if ($disname and $name) { } |
|
|
48 |
390 |
elsif (defined $self->{'_dis_name'}{$name}) { } |
|
2753
|
0 |
16 |
if (defined $name and $name eq $seq->id) { } |
|
2825
|
111 |
12 |
if (defined $value) |
|
2889
|
0 |
14 |
unless defined $name{$seq->id} |
|
2986
|
0 |
14 |
unless $a1 and $a2 and $ref |
|
2988
|
7 |
7 |
if $delim |
|
2994
|
0 |
14 |
unless ($refseq and $allele1 and $allele2) |
|
3005
|
182 |
28 |
$compres eq $res1 && $compres eq $res2 ? : |
|
3033
|
0 |
4 |
unless not defined $filter_cb or ref $filter_cb eq 'CODE' |
|
3036
|
2 |
2 |
unless (defined $self->{'_as_feat'}) |
|
3039
|
0 |
4 |
if ($filter_cb) |
|
3060
|
2 |
7 |
unless $self->{'_as_feat'} |
|
3062
|
0 |
9 |
if (scalar @feat > 1) |
|
3074
|
0 |
9 |
if $feat eq 'EXPAND' |
|
3076
|
0 |
9 |
unless ($feat->isa('Bio::SeqFeatureI')) |
|
3100
|
0 |
0 |
unless $self->{'_as_feat'} |
|
3119
|
2 |
0 |
if (defined $self->{'_as_feat'}) { } |
|
3159
|
46 |
41 |
if (defined $value) { } |
|
|
21 |
20 |
elsif (not defined $obj->{'_annotation'}) { } |
|
3160
|
0 |
46 |
unless $value->isa('Bio::AnnotationCollectionI') |
|
3240
|
0 |
6 |
unless (defined $mask_char) |
|
3242
|
0 |
6 |
unless $start =~ /^\d+$/ and $start > 0 and $start <= $self->length |
|
3245
|
0 |
6 |
unless $end =~ /^\d+$/ and $end > 0 and $end <= $self->length |
|
3248
|
0 |
6 |
unless $start <= $end |
|
3250
|
0 |
6 |
unless CORE::length $mask_char == 1 and not $mask_char =~ /$nonres/ |