# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Domcut.t,v 1.1 2003/07/23 
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $DEBUG $ERROR $METAERROR);
use lib '../';
$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 = 25;
    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 complete all Domcut tests',1);
        }
}
exit 0 if $ERROR ==  1;
use Data::Dumper;
use Bio::PrimarySeq;
require Bio::Tools::Analysis::Protein::Domcut;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
######## test using PrimarySeq object ##############
my $seq = Bio::PrimarySeq->new(-seq        => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS',
                                                       -display_id => 'test2');
ok $tool = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$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->[23]{'score'}, '-0.209');
    my @res       = $tool->result('Bio::SeqFeatureI');
    if (scalar @res > 0) {
        ok 1;
    } else {
        skip('No network access - could not connect to Domcut server', 1);
    }
    ok my $meta = $tool->result('meta');
     
    if (!$METAERROR) { #if Bio::Seq::Meta::Array available
        ok($meta->named_submeta_text('Domcut', 1,2), "0.068 0.053");
        ok ($meta->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQPPPPPPPPPPPPPDQRS");
    }
     
     
########## test using Bio::Seq object ##############
    ok my $tool2 = Bio::WebAgent->new(-verbose =>$verbose);
     
    ok my $seq2  = Bio::Seq->new(-seq => 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS',
                                 -display_id => 'test2');
     
    ok $tool2 = Bio::Tools::Analysis::Protein::Domcut->new( -seq=>$seq2->primary_seq);
    ok $tool2->run ();
     
    ok my $parsed2 = $tool2->result('parsed');
    ok ($parsed2->[23]{'score'}, '-0.209');
     
    @res = $tool2->result('Bio::SeqFeatureI');
    if (scalar @res > 0) {
        ok 1;
    } else {
        skip('No network access - could not connect to Domcut server', 1);
    }
    ok my $meta2 = $tool2->result('meta');
     
    if (!$METAERROR) { #if Bio::Seq::Meta::Array available
        ok($meta2->named_submeta_text('Domcut', 1,2), "0.068 0.053");
        ok ($meta2->seq, "MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS");
    }
    ok my $seq4 = new Bio::Seq;
    ok $seq2->primary_seq($meta2);
    ok $seq2->add_SeqFeature(@res);
    ok $seq2->primary_seq->named_submeta_text('Domcut', 1,2);
} else { 
    for ( $Test::ntest..$NUMTESTS) {
        skip("Skipping tests which require remote servers - set env variable BIOPERLDEBUG to test",1);
    }
}