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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 18);
use_ok('Bio::Tools::Run::Alignment::DBA');
use_ok('Bio::SimpleAlign');
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
}
my $verbose = -1;
my @params = ('matchA' => 0.75, 'matchB' => '0.55','dymem'=>'linear');
my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 14);
isa_ok $factory,'Bio::Tools::Run::Alignment::DBA';
my $bequiet = 1;
$factory->quiet($bequiet); # Suppress clustal messages to terminal
#test with one file with 2 sequences
my $inputfilename_1a = test_input_file("dba1a.fa");
my $inputfilename_1b = test_input_file("dba1b.fa");
my $inputfilename2 = test_input_file("dba2.fa");
my $aln;
my @hsps = $factory->align($inputfilename2);
isa_ok($hsps[0],"Bio::Search::HSP::GenericHSP");
is($hsps[0]->query->start,4);
is($hsps[0]->query->end,209);
is($hsps[0]->gaps,6);
#test with 2 files of 1 sequence each
my @files = ($inputfilename_1a,$inputfilename_1b);
@hsps = $factory->align(\@files);
is($hsps[0]->query->start,3);
is($hsps[0]->query->end,88);
is($hsps[0]->gaps,0);
is($hsps[1]->hit->start,90);
is($hsps[1]->hit->end,195);
is($hsps[1]->gaps,0);
#test with an array of 2 PrimarySeqI objects
my $str = Bio::SeqIO->new(-file=> test_input_file("dba2.fa"), '-format' => 'Fasta');
my @seq_array =();
while ( my $seq = $str->next_seq() ) {
push (@seq_array, $seq) ;
}
@hsps = $factory->align(\@seq_array);
is($hsps[0]->query->start,4);
is($hsps[0]->query->end,209);
is($hsps[0]->gaps,6);
}