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# -*-Perl-*- Test Harness script for Bioperl
# $Id: SiteMatrix.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 14);
use_ok('Bio::Matrix::PSM::SiteMatrix');
}
my $score;
my $A='a0501';
my $C='014a0';
my $G='01103';
my $T='08006';
my $eval=0.0001;
my %param=(pA=>$A,pC=>$C,pG=>$G,pT=>$T,e_val=>$eval, correction =>0);
ok my $matrix=Bio::Matrix::PSM::SiteMatrix->new(%param);
#Simple methods here
is $matrix->IUPAC,'ABVCD';
is $matrix->consensus,'ATACT';
is $matrix->width,5;
is $matrix->curpos,0;
is $matrix->get_string('A'),$A;
my %x= (base=>'A',pA=>1,pC=>0,pG=>0,pT=>0,prob=>10,rel=>0,
lA=>undef,lC=>undef,lG=>undef,lT=>undef);
my %pos = $matrix->next_pos;
my ($all) = 1;
while(my ($k,$v) = each %x ) {
my $r =$pos{$k};
if( ! defined $v && ! defined $r) {
} elsif($pos{$k} ne $v ) {
$all = 0;
last;
}
}
ok($all);
is $matrix->curpos,1;
ok $matrix->e_val(0.0001);
is $matrix->e_val,0.0001;
#Now some PSM specific methods like regexp and matrix info
is $matrix->regexp,'[Aa][CcGgTtBb][AaCcGgVv][Cc][AaGgTtDd]';
my @x=(1,0,0.5,0,0.1);
is_deeply [$matrix->get_array('A')], \@x;
@x=qw([Aa] [CcGgTtBb] [AaCcGgVv] [Cc] [AaGgTtDd]);
is_deeply [$matrix->regexp_array], \@x;
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