# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: MitoProt.t,v 1.1 2003/07/26 
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $ERROR);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
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 = 8;
        plan tests => $NUMTESTS;
        eval {
                require IO::String; 
                require LWP::UserAgent;
        };
        if( $@ ) {
                warn("IO::String or LWP::UserAgent not installed. This means that the module is not usable. Skipping tests\n");
                $ERROR = 1;
        }
}
END {
        foreach ( $Test::ntest..$NUMTESTS) {
                skip('unable to complete MitoProt tests, skipping',1);
        }
}
exit 0 if $ERROR ==  1;
use Data::Dumper;
require Bio::Tools::Analysis::Protein::Mitoprot;
use Bio::PrimarySeq;
require Bio::WebAgent;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
my $seq = Bio::PrimarySeq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDSFFGSDFDGDS'.
                               'DFGSDFGSDGDFGSDFGDSFGDGFSDRSRQDQRS',
                               -display_id => 'test2');
ok $tool = Bio::Tools::Analysis::Protein::Mitoprot->new( -seq=>$seq);
if( $DEBUG ) { 
    ok $tool->run ();
    exit if $tool->status eq 'TERMINATED_BY_ERROR';
    ok my $raw = $tool->result('');
    ok my $parsed = $tool->result('parsed');
    ok ($parsed->{'charge'}, -13);
    ok my @res = $tool->result('Bio::SeqFeatureI');
} else { 
    for ( $Test::ntest..$NUMTESTS) {
        skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
    }
}