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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: SeqDiff.t,v 1.5 2001/01/25 22:13:40 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 39;
}
use Bio::Variation::SeqDiff;
use Bio::Variation::DNAMutation;
ok 1;
my ($obj, $mm, $aa, $dna, $m);
ok $obj = Bio::Variation::SeqDiff -> new;
ok $obj->id('id');
ok $obj->id, 'id';
ok $obj->sysname('sysname');
ok $obj->sysname, 'sysname';
$obj->trivname('trivname');
ok $obj->trivname eq 'trivname';
ok $obj->chromosome('chr');
ok $obj->chromosome, 'chr';
ok $obj->description('desc');
ok $obj->description, 'desc';
ok $obj->numbering('numbering');
ok $obj->numbering, 'numbering';
ok $obj->offset(100);
ok $obj->offset, 100;
ok $obj->dna_ori('gctgctgatcgatcgtagctagctag');
ok $obj->dna_ori, 'gctgctgatcgatcgtagctagctag';
ok $obj->dna_mut('gctgctgatcggtcgtagctagctag');
ok $obj->dna_mut, 'gctgctgatcggtcgtagctagctag';
ok $obj->rna_ori('gctgctgatcgatcgtagctagctag');
ok $obj->rna_ori, 'gctgctgatcgatcgtagctagctag';
$obj->rna_mut('gctgctgatcgatcgtagctagctag');
ok $obj->rna_mut, 'gctgctgatcgatcgtagctagctag';
ok $obj->aa_ori('MHYTRD');
ok $obj->aa_ori, 'MHYTRD';
ok $obj->aa_mut('MHGTRD');
ok $obj->aa_mut, 'MHGTRD';
ok $m = Bio::Variation::DNAMutation->new;
ok $obj->add_Variant($m);
foreach $mm ( $obj->each_Variant ) {
$mm->primary_tag('a');
ok $mm->isa('Bio::Variation::VariantI');
}
ok $obj->gene_symbol('fos');
ok $obj->gene_symbol, 'fos';
ok $obj->rna_offset(10);
ok $obj->rna_offset == 10;
ok $obj->rna_id('transcript#3');
ok $obj->rna_id, 'transcript#3';
ok $dna = $obj->seqobj('dna_ori');
ok $dna->isa('Bio::PrimarySeq');
$obj->aa_mut('');
$aa = $obj->seqobj('aa_mut');
ok not defined $aa;
eval {
$dna = $obj->seqobj('dna_ri');
};
ok $@;
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