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t/Microarray.t  view on Meta::CPAN

#!/usr/bin/perl -w

use strict;

use FindBin;
use Test::More tests=>13;
use Test::Group;
use Test::Differences;
use Test::Deep;
use Test::Image::GD;

#1,2
BEGIN {
	use_ok('Microarray');
	use_ok('Microarray::File::Data');
}

my ($oArray,$oReporter,$oReporter1,$oReporter2,$oReporter3,$oReporter4,$oReporter5,$aReporter_Objects,$aReporter_Names,$hReporters,$file,$aSpots);

my $directory = $FindBin::Bin;

$file = $directory.'/../test_files/quantarray.csv';
begin_skipping_tests "The test-file 'quantarray.csv' could not be found" unless (-s $file);  # skip to end

#3
test "Object creation" => sub {
	ok($oArray = microarray->new('10001',$file),'object creation');
	isa_ok($oArray,'microarray','microarray object');
	$oArray->set_param(min_snr=>2,high_signal=>65000,low_signal=>500,signal_quality=>50);
};

#4
test "Getting and setting params for spot quality assessment criteria" => sub {
    is($oArray->low_signal,'500','low_signal');
    is($oArray->high_signal,'65000','high_signal');
    is($oArray->percen_sat,'10','percen_sat');
    is($oArray->min_snr,'2','min_snr');
    is($oArray->signal_quality,'50','signal_quality');
    is($oArray->min_diameter,'80','min_diameter');
    is($oArray->max_diameter,'150','max_diameter');
    is($oArray->target_diameter,'100','target_diameter'); 
    is($oArray->max_diameter_deviation,'10','max_diameter_deviation');
    is($oArray->normalisation,'yes','normalisation');
    is($oArray->signal_normalisation,'yes','signal_normalisation');
    is($oArray->genetic_data_source,'data_file','genetic_data_source');
};

#5
test "Get reporter data" => sub {
	$oArray->set_reporter_data;
	ok($oReporter = $oArray->get_reporter('RP13-827M24'),'get_reporter'); 
	ok($aReporter_Objects = $oArray->get_reporter_objects,'get_reporter_objects'); 
	ok($aReporter_Names = $oArray->get_reporter_ids,'get_reporter_ids'); 
	ok($hReporters = $oArray->get_all_reporters,'get_all_reporters'); 
	eq_or_diff $hReporters->{ 'RP13-827M24' }, $oReporter, "comparing reporter objects";
};

#6
test "Check reporter objects" => sub {
	ok($oReporter = $oArray->get_reporter('RP13-827M24'),'get_reporter');  # returns a single reporter object
	isa_ok($oReporter, 'array_reporter','get_reporter object');
	ok($aReporter_Objects = $oArray->get_reporter_objects,'get_reporter_objects');  # returns a list of reporter objects
	for my $oRep (@$aReporter_Objects){
		isa_ok($oRep, 'array_reporter','get_reporter_objects objects'); 
	}	
	ok($aReporter_Names = $oArray->get_reporter_ids,'get_reporter_ids');  # returns a list of reporter ids
	for my $id (@$aReporter_Names){
		ok(defined($id), 'get_reporter_ids defined');