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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 27);
use_ok('Bio::Variation::Allele');
use_ok('Bio::Variation::AAChange');
use_ok('Bio::Variation::RNAChange');
}
ok my $obj = Bio::Variation::AAChange->new();
isa_ok $obj, 'Bio::Variation::AAChange';
$obj->start(3);
is $obj->start, 3;
$obj->end(3);
is $obj->end, 3;
$obj->length(3);
is $obj->length, 3;
$obj->strand('1');
is $obj->strand, '1';
is $obj->primary_tag, 'Variation';
$obj->source_tag('source');
is $obj->source_tag, 'source';
$obj->frame(2);
is $obj->frame,2;
$obj->score(2);
is $obj->score, 2;
$obj->isMutation(1);
ok $obj->isMutation;
my $a1 = Bio::Variation::Allele->new(-seq => 'V');
$obj->allele_ori($a1);
is $obj->allele_ori->seq, 'V';
my $a2 = Bio::Variation::Allele->new('-seq' => 'A');
$obj->add_Allele($a2);
is $obj->allele_mut->seq, 'A';
is $obj->similarity_score, 0;
$obj->upStreamSeq('upStreamSeq');
is $obj->upStreamSeq, 'upStreamSeq';
$obj->dnStreamSeq('dnStreamSeq');
is $obj->dnStreamSeq, 'dnStreamSeq' ;
is $obj->label, 'substitution, conservative';
$obj->status('proven');
is $obj->status, 'proven';
$obj->proof('experimental');
is $obj->proof, 'experimental';
$obj->region('region');
is $obj->region, 'region';
$obj->region_value('region_value');
is $obj->region_value, 'region_value';
$obj->numbering('coding');
is $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);
is $obj->trivname, 'V3A', "Trivial name is [". $obj->trivname. "]";
$obj->mut_number(2);
is $obj->mut_number, 2;
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