| line |
true |
false |
branch |
|
163
|
3 |
6 |
if (defined $value) |
|
181
|
3 |
2 |
if (defined $value) |
|
200
|
3 |
52 |
if (defined $value) |
|
219
|
3 |
7 |
if (defined $value) |
|
237
|
4 |
979 |
if (defined $value) |
|
238
|
3 |
1 |
$value ? : |
|
271
|
0 |
355 |
unless defined $clone |
|
272
|
0 |
355 |
if $clone eq '' |
|
273
|
0 |
355 |
unless exists $self->{'_clones'}{$clone} |
|
281
|
0 |
355 |
if (ref $clones{'clone'} eq 'Bio::Map::Clone') |
|
285
|
355 |
0 |
if exists $clones{'type'} |
|
286
|
42 |
313 |
if exists $clones{'markers'} |
|
287
|
355 |
0 |
if exists $clones{'contig'} |
|
288
|
355 |
0 |
if exists $clones{'bands'} |
|
289
|
355 |
0 |
if exists $clones{'gel'} |
|
290
|
0 |
355 |
if exists $clones{'group'} |
|
291
|
11 |
344 |
if exists $clones{'remark'} |
|
293
|
0 |
355 |
if exists $clones{'fp_number'} |
|
294
|
81 |
274 |
if exists $clones{'fpc_remark'} |
|
297
|
5 |
350 |
if exists $clones{'sequence_type'} |
|
299
|
5 |
350 |
if exists $clones{'sequence_status'} |
|
301
|
102 |
253 |
if exists $clones{'matcha'} |
|
302
|
74 |
281 |
if exists $clones{'matche'} |
|
303
|
0 |
355 |
if exists $clones{'matchp'} |
|
306
|
355 |
0 |
if exists $clones{'range'}{'start'} |
|
308
|
355 |
0 |
if exists $clones{'range'}{'end'} |
|
363
|
0 |
15 |
unless defined $marker |
|
364
|
0 |
15 |
if $marker eq '' |
|
365
|
0 |
15 |
unless exists $self->{'_markers'}{$marker} |
|
370
|
0 |
15 |
if ref $mkr{'marker'} eq 'Bio::Map::FPCMarker' |
|
372
|
15 |
0 |
if exists $mkr{'type'} |
|
373
|
15 |
0 |
if exists $mkr{'global'} |
|
374
|
9 |
6 |
if exists $mkr{'framework'} |
|
375
|
15 |
0 |
if exists $mkr{'anchor'} |
|
376
|
15 |
0 |
if exists $mkr{'group'} |
|
377
|
9 |
6 |
if exists $mkr{'subgroup'} |
|
378
|
15 |
0 |
if exists $mkr{'remark'} |
|
383
|
15 |
0 |
if exists $mkr{'posincontig'} |
|
432
|
0 |
11 |
unless defined $contig |
|
433
|
0 |
11 |
if $contig eq '' |
|
434
|
0 |
11 |
unless exists $self->{'_contigs'}{$contig} |
|
441
|
0 |
11 |
if ref $ctg{'contig'} eq 'Bio::Map::Contig' |
|
443
|
11 |
0 |
if exists $ctg{'group'} |
|
444
|
3 |
8 |
if exists $ctg{'subgroup'} |
|
445
|
11 |
0 |
if exists $ctg{'anchor'} |
|
446
|
3 |
8 |
if exists $ctg{'chr_remark'} |
|
447
|
1 |
10 |
if exists $ctg{'usr_remark'} |
|
448
|
1 |
10 |
if exists $ctg{'trace_remark'} |
|
451
|
11 |
0 |
if exists $ctg{'range'}{'start'} |
|
453
|
11 |
0 |
if exists $ctg{'range'}{'end'} |
|
455
|
11 |
0 |
if exists $ctg{'clones'} |
|
456
|
8 |
3 |
if exists $ctg{'markers'} |
|
496
|
0 |
0 |
unless defined $cloneA and defined $cloneB and $self->core_exists |
|
499
|
0 |
0 |
unless defined $tol |
|
513
|
0 |
0 |
if (abs $diff <= $tol) { } |
|
|
0 |
0 |
elsif ($diff < 0) { } |
|
543
|
0 |
0 |
unless defined $cloneA and defined $cloneB and $self->core_exists |
|
555
|
0 |
0 |
unless defined $gellen |
|
556
|
0 |
0 |
unless defined $tol |
|
558
|
0 |
0 |
if ($numbandsA > $numbandsB) { } |
|
608
|
0 |
0 |
unless defined $showall |
|
632
|
0 |
0 |
if ($ctgGroup =~ /\d+|\w/ and $ctgGroup != 0) { } |
|
|
0 |
0 |
elsif ($showall == 1 and not $ctgGroup =~ /\d+/) { } |
|
633
|
0 |
0 |
if ($mrkGroup eq $ctgGroup) { } |
|
|
0 |
0 |
elsif ($showall == 1) { } |
|
634
|
0 |
0 |
if ($mrkFramework == 0) { } |
|
654
|
0 |
0 |
if $ctgGroup =~ /\d+|\w/ |
|
656
|
0 |
0 |
if ($showall == 1) { } |
|
|
0 |
0 |
elsif ($ctgGroup =~ /\d+|\w/ and $ctgGroup ne 0) { } |
|
659
|
0 |
0 |
unless $_contigs{$contig}{'group'} =~ /\d+|\w/ |
|
669
|
0 |
0 |
if $showall == 0 and $ctgGroup =~ /\d+|\w/ and $ctgGroup ne 0 |
|
672
|
0 |
0 |
if ($showall == 1) |
|
708
|
0 |
0 |
if (exists $_clones{$clone}{'contig'}) |
|
711
|
0 |
0 |
if (exists $list{$ctg}) { } |
|
742
|
0 |
0 |
unless defined $style |
|
767
|
0 |
0 |
if ($_contigs{$contig}{'range'}) { } |
|
770
|
0 |
0 |
if ($offset <= 0) { } |
|
792
|
0 |
0 |
if (exists $_clones{$clone}{'range'}) |
|
806
|
0 |
0 |
unless ($contig) |
|
808
|
0 |
0 |
if exists $_clones{$clone}{'markers'} |
|
819
|
0 |
0 |
if ($contig) |
|
821
|
0 |
0 |
if exists $_contigs{$contig}{'markers'} |
|
829
|
0 |
0 |
if (not $style) { } |
|
832
|
0 |
0 |
if (exists $_contigs{$contig}{'range'}) |
|
843
|
0 |
0 |
if (exists $_clones{$clone}{'range'}) |
|
848
|
0 |
0 |
if ($clone =~ /sd1$/) |
|
857
|
0 |
0 |
if scalar @markers |
|
860
|
0 |
0 |
if (exists $_markers{$mkr}{'framework'}) { } |
|
869
|
0 |
0 |
if defined $_clones{$clone}{'contig'} |
|
874
|
0 |
0 |
if (exists $_contigs{$contig}{'markers'}) |
|
884
|
0 |
0 |
if $_markers{$k}{'type'} eq 'eMRK' |
|
886
|
0 |
0 |
if (exists $_markers{$k}{'framework'}) |
|
888
|
0 |
0 |
if $_markers{$k}{'framework'} == 1 |
|
891
|
0 |
0 |
if $_markers{$k}{'framework'} == 0 |
|
902
|
0 |
0 |
if $_clones{$cl}{'contig'} == $contig |
|
921
|
0 |
0 |
unless $chr =~ /\d+|\w+/ |
|
933
|
0 |
0 |
if ($self->group_type eq 'Chromosome') { } |
|
936
|
0 |
0 |
unless $Bio::Map::Physical::a->{'group'} <=> $Bio::Map::Physical::b->{'group'} |
|
942
|
0 |
0 |
unless $Bio::Map::Physical::a->{'group'} cmp $Bio::Map::Physical::b->{'group'} |
|
951
|
0 |
0 |
if ($lastchr eq -1 or $chr->{'group'} ne $lastchr) |
|
952
|
0 |
0 |
if $lastchr eq -1 |
|
960
|
0 |
0 |
if ($chr->{'contig'} != 0) { } |
|
962
|
0 |
0 |
if ($ch->{'group'} eq $chr->{'group'}) |
|
963
|
0 |
0 |
if ($ch->{'contig'} != 0) |
|
965
|
0 |
0 |
if $ch->{'contig'} != 0 |
|
979
|
0 |
0 |
if $chr->{'contig'} == 0 |
|
989
|
0 |
0 |
if $chr->{'group'} ne $lastchr and $chr->{'group'} eq 0 |
|
992
|
0 |
0 |
if $chr->{'contig'} == 0 |
|
996
|
0 |
0 |
if (exists $_contigs{$contig}{'range'}) |
|
1007
|
0 |
0 |
if (exists $_clones{$clone}{'range'}) |
|
1011
|
0 |
0 |
if ($clone =~ /sd1$/) |
|
1022
|
0 |
0 |
if scalar @markers |
|
1025
|
0 |
0 |
if (exists $_markers{$mkr}{'framework'}) { } |
|
1034
|
0 |
0 |
if defined $_clones{$clone}{'contig'} |
|
1039
|
0 |
0 |
if (exists $_contigs{$contig}{'markers'}) |
|
1047
|
0 |
0 |
if $_markers{$k}{'type'} eq 'eMRK' |
|
1049
|
0 |
0 |
if (exists $_markers{$k}{'framework'}) |
|
1051
|
0 |
0 |
if $_markers{$k}{'framework'} == 1 |
|
1054
|
0 |
0 |
if $_markers{$k}{'framework'} == 0 |
|
1067
|
0 |
0 |
if $_clones{$cl}{'contig'} == $contig |
|
1116
|
165 |
0 |
if exists $_markers{$marker}{'clones'} |
|
1131
|
0 |
2657 |
unless $Bio::Map::Physical::a->{'contig'} <=> $Bio::Map::Physical::b->{'contig'} or $Bio::Map::Physical::b->{'start'} <=> $Bio::Map::Physical::a->{'start'} |
|
1137
|
170 |
909 |
if ($ctg != $sortedctgmarker[$i]{'contig'}) { } |
|
|
701 |
208 |
elsif ($sortedctgmarker[$i]{'end'} <= $y) { } |
|
1138
|
165 |
5 |
if ($ctg == -1) { } |
|
1142
|
0 |
5 |
if ($depth > $save_depth) |
|
1163
|
0 |
701 |
if ($x < $sortedctgmarker[$i]{'start'}) |
|
1167
|
593 |
108 |
if ($y > $sortedctgmarker[$i]{'end'}) |
|
1172
|
87 |
121 |
if ($depth > $save_depth) |
|
1184
|
0 |
208 |
if ($stack[$s] < $x) { } |
|
1186
|
0 |
0 |
if $j == -1 |
|
1191
|
23 |
185 |
if $y > $stack[$s] |
|
1192
|
0 |
208 |
if ($stack[$j] == -1) { } |
|
1204
|
324 |
755 |
if ($depth > $save_depth) |
|
1237
|
0 |
0 |
if (exists $_contigs{$contig}{'group'}) |
|
1241
|
0 |
0 |
if exists $_contigs{$contig}{'markers'} |
|
1244
|
0 |
0 |
if $_contigs{$contig}{'group'} =~ /\?/ |
|
1247
|
0 |
0 |
if (exists $_markers{$mkr}{'group'}) |
|
1248
|
0 |
0 |
if ($_markers{$mkr}{'group'} == $chr) |
|
1253
|
0 |
0 |
if $_clones{$clone}{'contig'} == $contig |
|
1269
|
0 |
0 |
if $totalhits != 0 |