# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Assembly.t,v 1.7.2.1 2006/10/02 23:10:39 sendu Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
my $error;
BEGIN {
    # to handle systems with no installed Test module
    # we include the t dir (where a copy of Test.pm is located)
    # as a fallback
    eval { require Test; };
    $error = 0;
    if( $@ ) {
        use lib 't';
    }
    use Test;
    $NUMTESTS = 19;
    plan tests => $NUMTESTS;
    eval { require DB_File };
    if( $@ ) {
                 print STDERR "DB_File not installed. This means the Assembly modules are not available.  Skipping tests.\n";
                 for( 1..$NUMTESTS ) {
                         skip("DB_File not installed",1);
                 }
                 $error = 1; 
    }
}
END {
        foreach ( $Test::ntest..$NUMTESTS) {
                skip('unable to run all of the DB tests',1);
        }
}
if( $error ==  1 ) {
    exit(0);
}
#syntax test
require Bio::Assembly::IO;
require Bio::Assembly::Scaffold;
require Bio::Assembly::Contig;
require Bio::Assembly::ContigAnalysis;
use Data::Dumper;
ok 1;
#
# Testing IO
#
# -file => ">".Bio::Root::IO->catfile("t","data","primaryseq.embl")
ok my $in = Bio::Assembly::IO->new
    (-file=>Bio::Root::IO->catfile
     ("t","data","consed_project","edit_dir","test_project.phrap.out"));
ok my $sc = $in->next_assembly;
#print Dumper $sc;
#
# Testing Scaffold
#
ok $sc->id, "NoName";
ok $sc->id('test'), "test";
ok $sc->annotation;
skip "no annotations in Annotation collection?", $sc->annotation->get_all_annotation_keys, 0;
ok $sc->get_nof_contigs, 1;
ok $sc->get_nof_sequences_in_contigs, 2;
skip "should return a number", $sc->get_nof_singlets, 0;
skip $sc->get_seq_ids, 2;
skip $sc->get_contig_ids, 1;
skip "nothing to test", $sc->get_singlet_ids;
#
# Testing Contig
#
#
# Testing ContigAnalysis
#
#
# Testing Ace 
#
my $aio = Bio::Assembly::IO->new(
    -file=>Bio::Root::IO->catfile
     ("t","data","consed_project","edit_dir","test_project.fasta.screen.ace.2"),
    -format=>'ace',
);
my $assembly = $aio->next_assembly();
my @contigs = $assembly->all_contigs();
my $direction = $contigs[0]->strand;
ok $direction, 1;
my $features =  $contigs[0]->get_features_collection;
my @contig_features = $features->get_all_features;
ok @contig_features, 8;
my @annotations = grep {$_->primary_tag eq 'Annotation'} @contig_features;
ok @annotations, 2;
my $had_tag = 0;
foreach my $an (@annotations) {
        if ($an->has_tag('extra_info')) {
                $had_tag++;
                ok (($an->get_tag_values('extra_info'))[0], "contig extra\ninfo\n");
        }
        elsif ($an->has_tag('comment')){
                $had_tag++;
                ok (($an->get_tag_values('comment'))[0], "contig tag\ncomment\n");
        }
}
ok $had_tag, 2;