| line |
true |
false |
branch |
|
84
|
0 |
6 |
unless (ref $inputfeatures eq 'HASH') |
|
93
|
0 |
6 |
unless (ref $DNA eq 'Bio::LiveSeq::DNA') |
|
105
|
6 |
0 |
if (ref $Transcripts[0] eq 'Bio::LiveSeq::Transcript') { } |
|
114
|
6 |
0 |
if (ref $i eq 'Bio::LiveSeq::Transcript' and $DNA->valid($start) and $DNA->valid($end)) { } |
|
119
|
6 |
0 |
unless ($minstart) |
|
120
|
6 |
0 |
unless ($maxend) |
|
121
|
0 |
6 |
if ($i->strand != $strand) |
|
125
|
0 |
6 |
if ($strand == 1 and $start < $minstart or $strand == -1 and $start > $minstart) |
|
126
|
0 |
6 |
if ($strand == 1 and $end > $maxend or $strand == -1 and $end < $maxend) |
|
130
|
6 |
0 |
if (defined $features->{'Translations'}) |
|
132
|
1 |
5 |
if (defined $features->{'Exons'}) |
|
134
|
1 |
5 |
if (defined $features->{'Introns'}) |
|
136
|
0 |
6 |
if (defined $features->{'Repeat_Units'}) |
|
138
|
0 |
6 |
if (defined $features->{'Repeat_Regions'}) |
|
140
|
5 |
1 |
if (defined $features->{'Prim_Transcripts'}) |
|
144
|
6 |
0 |
if (@Translations) |
|
147
|
0 |
6 |
unless (ref $i eq 'Bio::LiveSeq::Translation' and $DNA->valid($start) and $DNA->valid($end)) |
|
153
|
1 |
5 |
if (@Exons) |
|
156
|
0 |
9 |
unless (ref $i eq 'Bio::LiveSeq::Exon' and $DNA->valid($start) and $DNA->valid($end)) |
|
160
|
0 |
9 |
if ($i->strand != $strand) |
|
164
|
0 |
9 |
if ($strand == 1 and $start < $minstart or $strand == -1 and $start > $minstart) |
|
165
|
0 |
9 |
if ($strand == 1 and $end > $maxend or $strand == -1 and $end < $maxend) |
|
168
|
1 |
5 |
if (@Introns) |
|
171
|
0 |
8 |
unless (ref $i eq 'Bio::LiveSeq::Intron' and $DNA->valid($start) and $DNA->valid($end)) |
|
177
|
0 |
6 |
if (@Repeat_Units) |
|
180
|
0 |
0 |
unless (ref $i eq 'Bio::LiveSeq::Repeat_Unit' and $DNA->valid($start) and $DNA->valid($end)) |
|
186
|
0 |
6 |
if (@Repeat_Regions) |
|
189
|
0 |
0 |
unless (ref $i eq 'Bio::LiveSeq::Repeat_Region' and $DNA->valid($start) and $DNA->valid($end)) |
|
195
|
5 |
1 |
if (@Prim_Transcripts) |
|
198
|
0 |
7 |
unless (ref $i eq 'Bio::LiveSeq::Prim_Transcript' and $DNA->valid($start) and $DNA->valid($end)) |
|
202
|
0 |
7 |
if ($i->strand != $strand) |
|
206
|
5 |
2 |
if ($strand == 1 and $start < $minstart or $strand == -1 and $start > $minstart) |
|
207
|
5 |
2 |
if ($strand == 1 and $end > $maxend or $strand == -1 and $end < $maxend) |
|
220
|
19 |
6 |
unless ($key eq 'DNA') |
|
238
|
6 |
0 |
if (defined $upbound) { } |
|
239
|
0 |
6 |
unless ($DNA->valid($upbound)) |
|
246
|
6 |
0 |
if (defined $downbound) { } |
|
247
|
0 |
6 |
unless ($DNA->valid($downbound)) |
|
276
|
0 |
1 |
if (defined $value) |
|
279
|
1 |
0 |
if (exists $self->{'name'}) { } |
|
358
|
1 |
6 |
if (index(ref $value, 'LiveSeq') != -1) { } |
|
|
1 |
5 |
elsif (index(ref $value, 'ARRAY') != -1) { } |
|
|
2 |
3 |
elsif (index(ref $value, 'HASH') != -1) { } |