# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: StandAloneFasta.t,v 1.5 2006/11/08 09:48:37 sendu Exp $
#
use strict;
use constant NUMTESTS => 15;
BEGIN { 
    eval { require Test; };
    if( $@ ) {
        use lib 't';
    }
    use Test;
    plan tests => NUMTESTS; 
}
END { 
    foreach( $Test::ntest..NUMTESTS) {
        skip('Fasta or env variables not installed correctly',1);
    }
    unlink('blastreport.out');
        unlink('resultfile');
}
use Bio::Tools::Run::Alignment::StandAloneFasta;
use Bio::SeqIO;
ok(1);
my $verbose = -1;
my $version = '34';
my @params = ( 'b' =>'15', 
               'd' => 0,
               'O' =>'resultfile',
               'm'=>'9',
               "program"=>"fasta$version");
my $factory = Bio::Tools::Run::Alignment::StandAloneFasta->new
    ('-verbose' => $verbose,
     @params);
ok $factory;
my $inputfilename = Bio::Root::IO->catfile("t","data","fasta.fa");
my $fasta_present = $factory->executable();
if( ! $fasta_present ) {
    skip('Fasta  not installed',1);
    exit;
} else { 
    ok($fasta_present);
}
my $lib = Bio::Root::IO->catfile("t","data","fastalib.fa");
$factory->library($lib);
my ($fastareport) = $factory->run($inputfilename);
my $result = $fastareport->next_result;
my $hit    = $result->next_hit();
my $hsp    = $hit->next_hsp();
ok $hsp->algorithm, 'FASTN';
ok $hsp->num_identical, 2982;
ok $hsp->length, 2982;
$factory->program_name('ssearch'.$version);
($fastareport) = $factory->run($inputfilename);
$result = $fastareport->next_result;
$hit    = $result->next_hit();
$hsp    = $hit->next_hsp();
ok $hsp->algorithm, 'SMITH-WATERMAN';
ok $hsp->num_identical, 2982;
ok $hsp->length, 2982;
$factory->program_name('fastx'.$version);
$factory->library(Bio::Root::IO->catfile("t","data","fastaprot.fa"));
($fastareport) = $factory->run($inputfilename);
$result = $fastareport->next_result;
$hit    = $result->next_hit();
$hsp    = $hit->next_hsp();
ok $hsp->algorithm, 'FASTX';
ok $hsp->num_identical, 994;
ok $hsp->length, 994;
my $sio = Bio::SeqIO->new(-file=>$inputfilename,
                          -format=>"fasta");
my $seq = $sio->next_seq;
#test with objects
($fastareport) = $factory->run($seq);
$result = $fastareport->next_result;
$hit    = $result->next_hit();
$hsp    = $hit->next_hsp();
ok $hsp->algorithm, 'FASTX';
ok $hsp->num_identical, 994;
ok $hsp->length, 994;