# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Sopma.t,v 1.1 2003/07/23 
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $ERROR $METAERROR);
$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 = 15;
        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");
        $ERROR = 1;
        }
        # check this is available, set error flag if not.
        eval {
                require Bio::Seq::Meta::Array;
        };
        if ($@) {
                warn ("Bio::Seq::Meta::Array not installed - will skip tests using meta sequences");
                $METAERROR = 1;
        }
}
END {
        foreach ( $Test::ntest..$NUMTESTS) {
                skip('unable to run all of the Sopma tests',1);
        }
}
exit 0 if $ERROR ==  1;
use Data::Dumper;
use Bio::PrimarySeq;
require Bio::Tools::Analysis::Protein::Sopma;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
my $seq = Bio::PrimarySeq->new(
  -seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
  -display_id => 'test2');
ok $tool = Bio::Tools::Analysis::Protein::Sopma->new( -seq=>$seq,
                                                      -window_width => 15);
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->[0]{'helix'}, '104');
        ok my @res = $tool->result('Bio::SeqFeatureI');
        ok my $meta = $tool->result('meta', "ww15");
        ok $tool->window_width(21);
        ok $tool->clear();
        ok $tool->run;
        ok my $meta2 = $tool->result('meta', "ww21");
        if (!$METAERROR) { 
                # if Bio::Seq::Meta::Array available
                # meta sequence contains data...
                # but not available thru method call...??
                ok ($meta->named_submeta_text('Sopma_helix|ww15',1,2), '104 195');
                ok ($meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS');
        }
} else {
        for ( $Test::ntest..$NUMTESTS) {
                skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
        }
}