| line |
true |
false |
branch |
|
277
|
0 |
4 |
unless $seq->isa('Bio::PrimarySeqI') |
|
279
|
0 |
4 |
unless $seq->alphabet eq 'protein' |
|
282
|
1 |
3 |
if (defined $stop) |
|
283
|
0 |
1 |
if length $stop != 1 |
|
291
|
87 |
0 |
if $THREECODE{$aa} |
|
294
|
2 |
2 |
if $sep |
|
320
|
0 |
3 |
unless $seq->isa('Bio::PrimarySeqI') |
|
322
|
0 |
3 |
unless $seq->alphabet eq 'protein' |
|
325
|
0 |
3 |
if (defined $stop) |
|
326
|
0 |
0 |
if length $stop != 1 |
|
330
|
0 |
3 |
if (defined $unknown) |
|
331
|
0 |
0 |
if length $unknown != 1 |
|
341
|
88 |
1 |
if $ONECODE{$aa3} |
|
363
|
0 |
3 |
unless $seq->can('translate') |
|
426
|
204 |
206 |
if (not $code) { } |
|
|
1 |
205 |
elsif ($code == 1) { } |
|
|
205 |
0 |
elsif ($code == 2) { } |
|
429
|
4692 |
816 |
unless $c =~ /[BZX\*]/ |
|
437
|
23 |
4 |
unless $c =~ /(Asx|Glx|Xaa|Ter)/ |
|
480
|
0 |
3 |
unless $seq->isa('Bio::PrimarySeqI') |
|
485
|
0 |
3 |
unless $mutations[0]->isa('Bio::LiveSeq::Mutation') |
|
492
|
0 |
4 |
unless $mutation->pos - 1 <= $seq->length |
|
521
|
0 |
4 |
unless $seq->isa('Bio::PrimarySeqI') |
|
528
|
0 |
5 |
unless $catseq->isa('Bio::PrimarySeqI') |
|
534
|
1 |
4 |
unless $catseq->alphabet eq $seq->alphabet |
|
548
|
3 |
1 |
if ($seq->isa('Bio::AnnotatableI') and $catseq->isa('Bio::AnnotatableI')) |
|
561
|
3 |
1 |
if ($seq->isa('Bio::SeqI') and $catseq->isa('Bio::SeqI')) |
|
587
|
0 |
1 |
unless $seq->isa('Bio::SeqI') |
|
611
|
3 |
0 |
if $_->overlaps($truncrange) |
|
647
|
0 |
6 |
unless @_ == 3 or @_ == 4 |
|
650
|
0 |
6 |
unless &blessed($seq) and $seq->isa('Bio::PrimarySeqI') |
|
654
|
0 |
6 |
if $left < 1 |
|
655
|
0 |
6 |
if ($right > $seq->length) |
|
665
|
0 |
6 |
unless ($left_seq and $right_seq) |
|
677
|
2 |
4 |
if ($opts_ref->{'clone_obj'}) { } |
|
685
|
4 |
0 |
if ($product->isa('Bio::SeqI') and $seq->isa('Bio::SeqI')) |
|
688
|
19 |
7 |
if $adjfeat |
|
736
|
0 |
3 |
unless @_ == 3 or @_ == 4 |
|
739
|
0 |
3 |
unless &blessed($recipient) and $recipient->isa('Bio::PrimarySeqI') |
|
744
|
0 |
3 |
unless &blessed($fragment) and $fragment->isa('Bio::PrimarySeqI') |
|
749
|
0 |
3 |
unless $recipient->alphabet eq $fragment->alphabet |
|
756
|
0 |
3 |
if ($insert_pos < 0 or $insert_pos > $recipient->length) |
|
763
|
0 |
3 |
if ($fragment->can('is_circular') and $fragment->is_circular) |
|
767
|
0 |
3 |
unless ($recipient->seq) |
|
773
|
3 |
0 |
$insert_pos > 0 ? : |
|
778
|
3 |
0 |
$insert_pos < $recipient->length ? : |
|
789
|
1 |
2 |
if ($opts_ref->{'clone_obj'}) { } |
|
794
|
2 |
0 |
if defined $fragment->desc |
|
796
|
2 |
0 |
if defined $recipient->desc |
|
814
|
3 |
0 |
if ($product->isa('Bio::AnnotatableI') and $fragment->isa('Bio::AnnotatableI')) |
|
825
|
3 |
0 |
if ($product->isa('Bio::SeqI')) |
|
828
|
3 |
0 |
if ($fragment->isa('Bio::SeqI')) |
|
831
|
3 |
0 |
if $adjfeat |
|
836
|
3 |
0 |
if ($recipient->isa('Bio::SeqI')) |
|
841
|
15 |
2 |
if $adjfeat |
|
910
|
0 |
3 |
unless $recipient |
|
911
|
0 |
3 |
unless $fragment |
|
912
|
0 |
3 |
unless defined $left |
|
916
|
0 |
3 |
unless &blessed($fragment) and $fragment->isa('Bio::PrimarySeqI') |
|
921
|
3 |
0 |
if $flip |
|
924
|
1 |
2 |
if $clone_obj |
|
931
|
0 |
3 |
if ($right == $left + 1) { } |
|
939
|
1 |
2 |
if $@ |
|
941
|
0 |
2 |
if $@ |
|
971
|
0 |
38 |
unless $feat->isa('Bio::SeqFeatureI') |
|
976
|
0 |
38 |
unless defined $left and defined $right |
|
979
|
0 |
38 |
if ($left > $right) |
|
980
|
0 |
0 |
if ($feat->can('is_circular') and $feat->is_circular) { } |
|
1003
|
6 |
6 |
if $adjsubfeat |
|
1009
|
13 |
25 |
if $deletion->contains($_) |
|
1013
|
25 |
0 |
$_->can('start_pos_type') ? : |
|
1015
|
25 |
0 |
$_->can('end_pos_type') ? : |
|
1017
|
4 |
21 |
if ($start < $deletion->start and $end > $deletion->end) { } |
|
|
8 |
13 |
elsif ($_->start < $deletion->start and $_->end >= $deletion->start) { } |
|
|
5 |
8 |
elsif ($_->start <= $deletion->end and $_->end > $deletion->end) { } |
|
|
4 |
4 |
elsif ($start >= $deletion->end) { } |
|
1038
|
0 |
8 |
if ($feat->strand) |
|
1039
|
0 |
0 |
$feat->strand == 1 ? : |
|
1053
|
2 |
3 |
if ($feat->strand) { } |
|
1054
|
0 |
2 |
$feat->strand == 1 ? : |
|
1074
|
0 |
25 |
unless @newcoords |
|
1095
|
17 |
21 |
if ($note) |
|
1102
|
25 |
13 |
$loc ? : |
|
1133
|
0 |
22 |
unless $feat->isa('Bio::SeqFeatureI') |
|
1138
|
0 |
22 |
unless defined $insert_pos |
|
1139
|
0 |
22 |
unless defined $insert_len |
|
1153
|
2 |
20 |
if $_->location_type eq 'IN-BETWEEN' and $_->start == $insert_pos |
|
1157
|
20 |
0 |
$_->can('start_pos_type') ? : |
|
1159
|
20 |
0 |
$_->can('end_pos_type') ? : |
|
1161
|
3 |
17 |
if ($start <= $insert_pos and $end > $insert_pos) { } |
|
|
8 |
9 |
elsif ($start > $insert_pos) { } |
|
1190
|
0 |
20 |
unless @newcoords |
|
1213
|
3 |
19 |
if ($note) |
|
1220
|
20 |
2 |
$loc ? : |
|
1242
|
7 |
112 |
if (@locs > 1) { } |
|
|
97 |
15 |
elsif (@locs == 1) { } |
|
1279
|
0 |
59 |
unless @_ == 3 |
|
1280
|
0 |
59 |
unless ref $coords_ref eq 'ARRAY' |
|
1288
|
66 |
0 |
if ($type ne 'IN-BETWEEN') { } |
|
1295
|
58 |
8 |
if $start_type |
|
1296
|
58 |
8 |
if $end_type |
|
1326
|
3 |
0 |
if $out_seq_obj->can('remove_SeqFeatures') |
|
1327
|
0 |
3 |
if (&blessed(scalar $out_seq_obj->seq) and $out_seq_obj->seq->isa('Bio::PrimarySeq')) { } |
|
1353
|
0 |
6 |
if $attr and ref $attr ne 'HASH' |
|
1357
|
4 |
2 |
if ($in_seq_obj->can_call_new) { } |
|
1378
|
4 |
0 |
if ($out_seq_obj->isa('Bio::AnnotatableI') and $in_seq_obj->isa('Bio::AnnotatableI')) |
|
1410
|
0 |
8 |
unless $feat->isa('Bio::SeqFeatureI') |
|
1425
|
0 |
16 |
if $_ < 0 |
|
1427
|
2 |
14 |
if ($add + $_ < 1) { } |
|
|
1 |
13 |
elsif (defined $length and $add + $_ > $length) { } |
|
1452
|
8 |
0 |
$loc ? : |
|
1471
|
0 |
5 |
unless $seq->isa('Bio::SeqI') |
|
1516
|
0 |
6 |
unless $feat->isa('Bio::SeqFeatureI') |
|
1529
|
5 |
1 |
if ($_->strand == -1) { } |
|
|
1 |
0 |
elsif ($_->strand == 1) { } |
|
1537
|
0 |
6 |
if $_->end_pos_type eq 'AFTER' |
|
1538
|
0 |
6 |
if $_->end_pos_type eq 'BEFORE' |
|
1540
|
0 |
6 |
if $_->start_pos_type eq 'AFTER' |
|
1541
|
1 |
5 |
if $_->start_pos_type eq 'BEFORE' |
|
1559
|
6 |
0 |
$loc ? : |
|
1567
|
0 |
12 |
if ($type eq 'BETWEEN' or $type eq 'WITHIN') { } |
|
1573
|
1 |
11 |
if $type eq 'BEFORE' and substr($coord, 0, 1) ne '>' |
|
1575
|
0 |
12 |
if $type eq 'AFTER' and substr($coord, 0, 1) ne '<' |
|
1610
|
0 |
1 |
unless $seq->isa('Bio::PrimarySeqI') |
|
1616
|
0 |
1 |
unless $sim =~ /^[+\d.]+$/ and $sim <= 100 |
|
1620
|
0 |
1 |
unless $sim > 25 |
|
1625
|
0 |
1 |
if $seq->alphabet eq 'protein' |
|
1662
|
3 |
1 |
if ($choose < $transition) { } |
|
|
1 |
0 |
elsif ($choose < $first_transversion) { } |
|
1692
|
40 |
10 |
if substr($oriseq, $i, 1) eq substr($seq, $i, 1) |