BEGIN {
if
( $@ ) {
}
plan
tests
=> 25;
}
my
$obj
= Bio::Variation::AAChange -> new;
ok(1);
ok
defined
$obj
;
ok
ref
(
$obj
),
'Bio::Variation::AAChange'
;
$obj
->start(3);
ok
$obj
->start, 3;
$obj
->end(3);
ok
$obj
->end, 3;
$obj
->
length
(3);
ok
$obj
->
length
, 3;
$obj
->strand(
'1'
);
ok
$obj
->strand,
'1'
;
ok
$obj
->primary_tag,
'Variation'
;
$obj
->source_tag(
'source'
);
ok
$obj
->source_tag,
'source'
;
$obj
->frame(2);
ok
$obj
->frame,2;
$obj
->score(2);
ok
$obj
->score, 2;
$obj
->isMutation(1);
ok
$obj
->isMutation;
my
$a1
= Bio::Variation::Allele->new(
-seq
=>
'V'
);
$obj
->allele_ori(
$a1
);
ok
$obj
->allele_ori->seq,
'V'
;
my
$a2
= Bio::Variation::Allele->new(
'-seq'
=>
'A'
);
$obj
->add_Allele(
$a2
);
ok
$obj
->allele_mut->seq,
'A'
;
ok
$obj
->similarity_score, 0;
$obj
->upStreamSeq(
'upStreamSeq'
);
ok
$obj
->upStreamSeq,
'upStreamSeq'
;
$obj
->dnStreamSeq(
'dnStreamSeq'
);
ok
$obj
->dnStreamSeq,
'dnStreamSeq'
;
ok
$obj
->label,
'substitution, conservative'
;
$obj
->status(
'proven'
);
ok
$obj
->status,
'proven'
;
$obj
->proof(
'experimental'
);
ok
$obj
->proof,
'experimental'
;
$obj
->region(
'region'
);
ok
$obj
->region,
'region'
;
$obj
->region_value(
'region_value'
);
ok
$obj
->region_value,
'region_value'
;
$obj
->numbering(
'coding'
);
ok
$obj
->numbering,
'coding'
;
my
$obj2
= Bio::Variation::RNAChange -> new(
-start
=> 7,
-end
=> 7,
-cds_end
=> 100,
-codon_pos
=> 1,
-upStreamSeq
=>
'acgcgcgcgc'
,
-dnStreamSeq
=>
'acgcgcgcgc'
);
$obj2
->label(
'missense'
);
$obj
->RNAChange(
$obj2
);
ok
$obj
->trivname,
'V3A'
,
"Trivial name is !"
.
$obj
->trivname.
"!\n"
;
$obj
->mut_number(2);
ok
$obj
->mut_number, 2;