# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Scansite.t,v 1.1 2003/11/18 
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($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 = 12;
        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");
                $ERROR = 1;
        }
}
END {
        if ($DEBUG) {
                foreach ( $Test::ntest..$NUMTESTS) {
                        skip('unable to run all of the Scansite tests',1);
                }
        } else {
                foreach ( $Test::ntest..$NUMTESTS) {
                        skip('set env BIOPERLDEBUG to run tests over web',1);
                }
        }
}
exit 0 if $ERROR ==  1;
use Data::Dumper;
require Bio::Tools::Analysis::Protein::Scansite;
use Bio::SeqIO;
use Bio::PrimarySeq;
require Bio::WebAgent;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
my $seqio=new Bio::SeqIO( -verbose => $verbose,
                  -format => 'swiss',
                  -file   => Bio::Root::IO->catfile('t','data', 'swiss.dat'));
my $seq = $seqio->next_seq();
ok $tool = Bio::Tools::Analysis::Protein::Scansite->new( 
                                        -seq=>$seq->primary_seq);
ok $tool->stringency('Low');
ok $tool->stringency(), 'Low';
ok $tool->protein_id(), $tool->seq->display_id();
exit unless $DEBUG;
ok $tool->run ();
exit if $tool->status eq 'TERMINATED_BY_ERROR';
ok my $raw = $tool->result('');
print $raw if $verbose;
ok my $parsed = $tool->result('parsed');
ok $parsed->[0]{'site'}, 'T101';
ok my @res = $tool->result('Bio::SeqFeatureI');
ok $res[0]->start, 101;