written tests for affy features, now write classes to make them pass

modules/t/affy.t

+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::AffyFeature;
+use Bio::EnsEMBL::AffyProbe;
+use Bio::EnsEMBL::AffyArray;
+
+use Bio::EnsEMBL::Test::TestUtils qw( test_getter_setter debug );
+
+BEGIN { $| = 1;
+	use Test;
+	plan tests => 18;
+}
+
+
+our $verbose = 0;
+verbose('WARNING');
+
+
+#
+# Affy arrays dont have to have anythong more than a name, 
+# but it should be possible to have some other information on them
+#
+
+my $another_array = undef;
+
+my $affy_array = Bio::EnsEMBL::AffyArray->new 
+  (
+     -name => "Affy-1",
+     -setsize => 11,
+     -included_in => $another_array,
+     -probecount => 4443
+);
+
+ok( ref( $affy_array ) && $affy_array->isa( "Bio::EnsEMBL::AffyArray" ));
+
+#
+# What Affy arryas should be able to do
+#
+
+ok( test_getter_setter( $affy_array, "dbID", 3 ));
+ok( test_getter_setter( $affy_array, "adaptor", undef ));
+ok( test_getter_setter( $affy_array, "name", "Some name" ));
+ok( test_getter_setter( $affy_array, "setsize", 11 ));
+
+# possibly do the following with database connection
+my $probes = $affy_array->get_all_AffyProbes();
+ok( 
+
+#
+# Create an AffyProbe
+#
+
+my $affy_probe = Bio::EnsEMBL::AffyProbe->new
+(
+  -arrayname => "AFFY-1",
+  -probename => "123-145",
+  -probeset => "affy_probeset"
+);
+
+my $affy_probe = Bio::EnsEMBL::AffyProbe->new
+(
+  -array => $affy_array,
+  -probename => "123-145",
+  -probeset => "affy_probeset"
+);
+
+ok( ref( $affy_probe ) && $affy_probe->isa( "Bio::EnsEMBL::AffyProbe" ));
+
+my $merge_probe = Bio::EnsEMBL::AffyProbe->new
+(
+  -arraynames => [ "Affy-1", "Affy-2", "Affy-3" ],
+  -probenames => [ "123-145", "23,24,56", "someplace" ],
+  -probeset => "affy_probeset"
+)
+
+ok( ref( $merge_probe ) && $merge_probe->isa( "Bio::EnsEMBL::AffyProbe" ));
+
+
+
+
+#
+# What probes need to be able to do
+#
+
+ok( test_getter_setter( $merge_probe, "dbID", 1 ));
+ok( test_getter_setter( $merge_probe, "adaptor", {} ));
+ok( test_getter_setter( $merge_probe, "probeset", "Affy_probeset" ));
+
+
+# This is expected to access the database
+my $features = $affy_probe->get_all_AffyFeatures();
+
+ok( ref( $features ) eq "ARRAY" );
+ok( $features->[0] && $features->[0]->isa( "Bio::EnsEMBL::AffyFeature" ));
+
+my $arrays = $affy_probe->get_all_AffyArrays();
+ok( ref( $arrays ) eq "ARRAY" );
+ok( $arrays->[0] && $arrays->[0]->isa( "Bio::EnsEMBL::AffyArray" ));
+
+
+# expected to construct full probenames from Chipname, setname and probename
+my $full_probenames = $merge_probe->get_complete_names();
+ok( ref( $full_probenames ) eq 'ARRAY' );
+ok( $full_probenames->[0] && ( $full_probenames->[0] =~ /affy_probeset/ ));
+ 
+my $full_probename = $merge_probe->get_complete_name( $affy_array );
+ok( $full_probename =~ /affy_probeset/ && $full_probename =~ /$affy_array->name()/ );
+
+my $probenames = $merge_probe->get_probenames();
+my $probename = $merge_probe->get_probename( $affy_array );
+
+
+#
+# When we implement storing this should be implemented as well
+# for starters we are not creating these objects, but load the database with probes ...
+
+$affy_probe->add_array_name( $affy_array, $probename );
+
+
+#
+# Create an affy feature
+#
+
+my $coord_system = Bio::EnsEMBL::CoordSystem->new
+   ( -name => "chromosome",
+     -version => '' );
+
+my $slice = Bio::EnsEMBL::Slice->new
+   ( 
+     -seq_region_name => '1',
+     -coord_system => $coord_system,
+     -start => 1,
+     -end => 50,
+     -seq_region_length => 200_000_000
+);
+     
+my $affy_feature = Bio::EnsEMBL::AffyFeature->new
+   (
+     -probe => $affy_probe,
+     -slice => $slice,
+     -start => 1,
+     -end => 10,
+     -strand => -1,
+     -probeset => "affy_probeset"	
+);
+
+ok( ref( $affy_feature ) && $affy_feature->isa( "Bio::EnsEMBL::AffyFeature"));
+
+1;