# -*-Perl-*- Test Harness script for Bioperl
# $Id$

use strict;

BEGIN {
    use lib '.';
    use Bio::Root::Test;
    
    test_begin(-tests => 39);
	
    use_ok('Bio::SeqEvolution::Factory');
    use_ok('Bio::PrimarySeq');
}

#
# point mutations
#

ok my $evolve = Bio::SeqEvolution::Factory->new (-verbose => 1);
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';

ok $evolve = Bio::SeqEvolution::DNAPoint->new (-verbose => 2);
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 3,
                                             -type => 'Bio::SeqEvolution::DNAPoint');
isa_ok $evolve, 'Bio::SeqEvolution::DNAPoint';


my $seq = Bio::PrimarySeq->new(-id=>'test',
                              -seq=>'aaacccgggtta'
                             );

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -foo => 'bar',
                                              -rate => 5,
                                              -seq => $seq
                                             );

is $evolve->seq->id, 'test';
is $evolve->rate, 5,               'get rate()';
is $evolve->rate(2), 2,            'get and set rate()';


is $evolve->identity(80), 80, 'identity()';
is $evolve->identity(undef), undef, 'identity()';

is $evolve->pam, undef, 'pam()';
is $evolve->pam(80), 80, 'pam()';

is $evolve->mutation_count, undef, 'mutation_count()';
is $evolve->mutation_count(5), 5, , 'mutation_count()';



is $evolve->seq_type, 'Bio::PrimarySeq', 'seq_type()';
is $evolve->seq_type('Bio::Seq'), 'Bio::Seq', 'seq_type()';

ok my $newseq = $evolve->next_seq, 'next_seq()';

foreach ( $evolve->each_mutation('string')) {
    ok $_;
}
is $evolve->each_mutation, 5, 'each_mutation()';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -identity => 50     ###
                                             );
ok $newseq = $evolve->next_seq;
cmp_ok $evolve->get_alignment_identity, '<=', 50, "get_alignment_identity()";

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -pam => 50     ###
                                             );
ok $newseq = $evolve->next_seq;
is $evolve->get_mutation_counter, 6, 'get_mutation_counter()';
$newseq = $evolve->next_seq;
is $evolve->get_sequence_counter, 2, 'get_sequence_counter()';
ok $evolve->reset_sequence_counter(), 'reset_sequence_counter()';
is $evolve->get_sequence_counter, 0, 'get_sequence_counter() == 0';

ok $evolve = Bio::SeqEvolution::Factory->new (-verbose => 0,
                                              -rate => 5,
                                              -seq => $seq,
                                              -pam => 50
                                             );

ok $newseq = $evolve->next_seq;
# ok $evolve->get_alignment_identity <= 50, "get_alignment_identity()";
isa_ok $evolve->get_alignmet, 'Bio::SimpleAlign';


#
#print "-----------------------------------------\n";
#print $evolve->{'_ori_locatableseq'}->seq, "\n";
#print $evolve->{'_mut_locatableseq'}->seq, "\n";
#print $evolve->{'_align'}->overall_percentage_identity, "\n";
#print $evolve->get_mutation_counter, "\n";
#print "-----------------------------------------\n";
#


#
# indels
#

#use Bio::SeqEvolution::DNAIndel;
#ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
#                                               -mutation_count => 3,
#                                               -rate => 1,
#                                               -seq => $seq
#                                             );
#
#
#
#ok $newseq = $evolve->next_seq;
#ok $evolve->get_mutation_counter, 3;
##print Dumper $evolve;
#
#foreach ( $evolve->each_mutation) {
##    print Dumper $_;
##    print $_->sysname, "\n";
#    ok $_->sysname;
#}
#
#
#ok $evolve = Bio::SeqEvolution::DNAIndel->new (-verbose => 0,
#                                               -duplication => 1,
##                                               -identity =>50,
#                                               -mutation_count => 3,
#                                               -rate => 1,
#                                               -seq => $seq
#                                             );
##$evolve->{'_mut_string'} = $evolve->{'_ori_string'};
#
##ok $newseq = $evolve->mutate(12);
#ok $newseq = $evolve->next_seq;
##print Dumper $evolve;
##print $evolve->{'_ori_locatableseq'}->seq, "\n";
##print $evolve->{'_mut_locatableseq'}->seq, "\n";
#
#print "-----------------------------------------\n";
#print $evolve->{'_ori_locatableseq'}->seq, "\n";
#print $evolve->{'_mut_locatableseq'}->seq, "\n";
#print $evolve->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#
#
##
## mixer, simulation
##
#
#
#ok my $evolve2 = Bio::SeqEvolution::Factory->new (-verbose => 0,
#                                                  -rate => 2,
#                                                  -seq => $seq,
#                                                  -set_mutated_seq => $newseq,
##                                                  -identity => 50
#                                                  -mutation_count => 1     ###
#                                             );
#ok $evolve2->seq_type('Bio::LocatableSeq');
#
#print "=-----------------------------------------\n";
#print $evolve2->{'_ori_locatableseq'}->seq, "\n";
#print $evolve2->{'_mut_locatableseq'}->seq, "\n";
#print $evolve2->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#
#ok $newseq = $evolve2->next_seq;
#
#
#print "-----------------------------------------\n";
#print $evolve2->{'_ori_locatableseq'}->seq, "\n";
#print $evolve2->{'_mut_locatableseq'}->seq, "\n";
#print $evolve2->{'_align'}->overall_percentage_identity, "\n";
#print "-----------------------------------------\n";
#