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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: NetPhos.t,v 1.5 2003/11/13 15:18:00 radams Exp $
# 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);
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 = 14;
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 {
foreach ( $Test::ntest..$NUMTESTS) {
skip('unable to run all of the tests depending on web access',1);
}
}
exit 0 if $ERROR == 1;
use Data::Dumper;
require Bio::Tools::Analysis::Protein::NetPhos;
use Bio::PrimarySeq;
require Bio::WebAgent;
ok 1;
my $verbose = 0;
$verbose = 1 if $DEBUG;
ok my $tool = Bio::WebAgent->new(-verbose =>$verbose);
ok $tool->sleep;
ok $tool->delay(1), 1;
ok $tool->sleep;
ok $tool->timeout(120); # LWP::UserAgent method
ok $tool->url('http://a.b.c/'), 'http://a.b.c/';
my $seq = Bio::PrimarySeq->new(-id=>'bioperl',
-seq=>'ABCDEFGHIJKLLKJFHSAKNDJFPSINCSJNDSKNSN');
ok $tool = Bio::Tools::Analysis::Protein::NetPhos->new(-verbose =>$verbose);
ok $tool->run ( {seq=>$seq, threshold=>0.9} );
exit if $tool->status eq 'TERMINATED_BY_ERROR';
ok my @res = $tool->result('Bio::SeqFeatureI');
#new tests her in v 1.2
ok my $raw = $tool->result('');
ok my $parsed = $tool->result('parsed');
ok($parsed->[0][1], '0.934');
if (scalar @res > 0) {
ok 1;
} else {
skip('No network access - could not connect to NetPhos server', 1);
}
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