# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: HNN.t,v 1.1 2003/07/23 
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG);
BEGIN {
        $NUMTESTS = 13;
        $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
         
        eval {require Test::More;};
        if ($@) {
                use lib 't/lib';
        }
        use Test::More;
         
        eval {
                require IO::String; 
                require LWP::UserAgent;
        };
        if ($@) {
                plan skip_all => 'IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests';
        }
        else {
                plan tests => $NUMTESTS;
        }
         
        use_ok("Bio::Seq");
        use_ok("Bio::Tools::Analysis::Protein::HNN");
}
#       eval {require Bio::Seq::Meta::Array;};
#       "Bio::Seq::Meta::Array not installed - will skip tests using meta sequences"
my $verbose = $DEBUG;
my $seq = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
                        -display_id => 'test2');
ok my $tool = Bio::Tools::Analysis::Protein::HNN->new(-seq=>$seq->primary_seq);
SKIP: {
        skip "Skipping tests which require remote servers, set BIOPERLDEBUG=1 to test", 10 unless $DEBUG;
    ok $tool->run();
        skip "Skipping tests since we got terminated by a server error", 9 if $tool->status eq 'TERMINATED_BY_ERROR';
    ok my $raw = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    is $parsed->[0]{'coil'}, '1000';
    my @res = $tool->result('Bio::SeqFeatureI');
    if (scalar @res > 0) {
                ok 1;
    }
        else {
                skip 'No results - could not connect to HNN server?', 6;
    }
     
    ok my $meta = $tool->result('meta');
    ok my $seqobj = Bio::Seq->new(-primary_seq => $meta, display_id=>"a");
    ok $seqobj->add_SeqFeature($tool->result('Bio::SeqFeatureI'));
     
    eval {require Bio::Seq::Meta::Array;};
        skip "Bio::Seq::Meta::Array not installed - will skip tests using meta sequences", 2 if $@;
        is $meta->named_submeta_text('HNN_helix',1,2), '0 111';
        is $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS';
}