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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Sopma.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 16,
-requires_modules => [qw(IO::String LWP::UserAgent)]);
use_ok('Bio::PrimarySeq');
use_ok('Bio::Tools::Analysis::Protein::Sopma');
}
my $verbose = test_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,
#-verbose => $verbose,
-window_width => 15);
SKIP: {
test_skip(-tests => 12, -requires_networking => 1);
ok $tool->run();
skip "Tool was terminated by some error: problem connecting to server?", 11 if $tool->status eq 'TERMINATED_BY_ERROR';
ok my $raw = $tool->result('');
ok my $parsed = $tool->result('parsed');
is ($parsed->[0]{'helix'}, '102');
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");
SKIP: {
test_skip(-tests => 2, -requires_module => 'Bio::Seq::Meta::Array');
is $meta->named_submeta_text('Sopma_helix|ww15',1,2), '102 195';
is $meta->seq, 'MSADQRWRQDSQDSFGDSFDGDPPPPPPPPFGDSFGDGFSDRSRQDQRS';
}
}
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