# -*-Perl-*-
## Bioperl Test Harness Script for Modules


use strict;
BEGIN {
    use Bio::Root::Test;
    test_begin(-tests => 89);
	use_ok('Bio::Tools::Run::Alignment::Exonerate');
}

my $verbose = test_debug() || -1;

my $query= test_input_file("exonerate_cdna.fa");
my $target= test_input_file("exonerate_genomic.fa");
my $targetrev= test_input_file("exonerate_genomic_rev.fa");

my $run = Bio::Tools::Run::Alignment::Exonerate->new(-verbose  => $verbose,
						     arguments=>'--model est2genome --bestn 1');
SKIP: {
	test_skip(-requires_executable => $run, -tests => 88);

	isa_ok $run, 'Bio::Tools::Run::Alignment::Exonerate';
	ok $run->version;
	
	my $searchio= $run->run($query,$target);
	isa_ok $searchio, "Bio::SearchIO";
	my @expect = ( [qw(29   268     4 242)],# target-start t-end query-start q-end
			   [qw(526  646   243 363)],
			   [qw(964 1056   364 456)],
			   [qw(1770 1923  457 610)],
			   [qw(2250 2479  611 840 )],
			   [qw(2565 2687  841 963)],
			   [qw(2769 3074  964 1279)] );
	RESULT: while(my $result = $searchio->next_result){
	  while( my $hit = $result->next_hit ) {
	#      ok($hit->start('hit'), 29);
	#      ok($hit->end('hit'), 3074);
		  my $i = 0;
		while( my $hsp = $hit->next_hsp ) {	
		is ($hsp->hit->strand, 1);
		is ($hsp->query->strand, 1);
		is ($hsp->hit->start,$expect[$i]->[0]);
		is ($hsp->hit->end,$expect[$i]->[1]);
		is ($hsp->query->start,$expect[$i]->[2]);
		is ($hsp->query->end,$expect[$i]->[3]);	
		$i++;
		if( $verbose > 0 ) {
			warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
			warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
		}
		}
		  last; # only show a single HIT
	  }
	  last;
	}
	
	
	$searchio= $run->run($query,$targetrev);
	isa_ok $searchio,"Bio::SearchIO";
	my @expectrev;
	if ($run->version >= 2 ) { # latest 2.0.0 version
		@expectrev = ( # target-start t-end query-start q-end
			   [qw(2834 3073  4 242)],
			   [qw(2456 2576  243 363)],
			   [qw(2046 2138  364 456)],
			   [qw(1179 1332  457 610)],
			   [qw(623 852    611 840)],
			   [qw(415  537   841 963)],
			   [qw(28   333   964 1279)]
		);
	} else { # version 1.4.0 presumably
		@expectrev = ( # target-start t-end query-start q-end
			   [qw(28   333   964 1279)],
			   [qw(415  537   841 963)],
			   [qw(623 852    611 840)],
			   [qw(1179 1332  457 610)],
			   [qw(2046 2138  364  456)],
			   [qw(2456 2576  243 363)],
			   [qw(2834 3073  4 242)]
		);
	
	}
	RESULT: while(my $result = $searchio->next_result){
		while( my $hit = $result->next_hit ) {
		  my $i = 0;
		while( my $hsp = $hit->next_hsp ) {	
		is ($hsp->hit->strand, -1);
		is ($hsp->query->strand, 1);
		is ($hsp->hit->start,$expectrev[$i]->[0]);
		is ($hsp->hit->end,$expectrev[$i]->[1]);
		is ($hsp->query->start,$expectrev[$i]->[2]);
		is ($hsp->query->end,$expectrev[$i]->[3]);	
		$i++;
		if( $verbose > 0 ) {
			warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
			warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
		}
		}
		  last; # only show a single HIT
	  }
	  last;
	}
}