added supporting feature test

modules/t/gene.t

@@ -4,7 +4,7 @@ use warnings;
 
 BEGIN { $| = 1;  
 	use Test;
-	plan tests => 22;
+	plan tests => 26;
 }
 
 use MultiTestDB;
@@ -13,7 +13,8 @@ use TestUtils qw ( debug );
 use Bio::EnsEMBL::Gene;
 
 # switch on the debug prints
-my $verbose = 0;
+
+our $verbose = 0;
 
 debug( "Startup test" );
 ok(1);
@@ -58,11 +59,16 @@ ok( scalar @$links == 6 );
 
 # now create a new gene ...
 
-my $slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end( "20",30264615, 30265615 );
+
+my $sa = $db->get_SliceAdaptor();
+
+my $slice = $sa->fetch_by_chr_start_end( "20", 30_249_935, 31_254_640 );
+
 debug( "Slice from SliceAdaptor" );
 ok($slice);
 
 my $analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("ensembl");
+my $f_analysis = $db->get_AnalysisAdaptor->fetch_by_logic_name("Vertrna");
 debug( "Analysis from AnalysisAdaptor" );
 ok($analysis);
 
@@ -82,26 +88,106 @@ my $translation2 = Bio::EnsEMBL::Translation->new();
 ok($gene);
 
 
-$ex1->start(5);
-$ex1->end(10);
+$ex1->start( 13586 );
+$ex1->end( 13735 );
 $ex1->phase(0);
 $ex1->end_phase( 0 );
 $ex1->contig( $slice );
 $ex1->strand(1);
 $ex1->analysis($analysis);
 
-$ex2->start(15);
-$ex2->end(23);
+my @feats;
+my $fp = new Bio::EnsEMBL::FeaturePair;
+
+$fp->start(13586);
+$fp->end  (13705);
+$fp->strand(1);
+$fp->score(10);
+$fp->contig($slice);
+$fp->hstart(100);
+$fp->hend    (219);
+$fp->hstrand (1);
+$fp->hseqname('dummy-hid');
+
+push(@feats,$fp);
+
+
+$fp = new Bio::EnsEMBL::FeaturePair;
+$fp->start(13707);
+$fp->end  (13735);
+$fp->strand(1);
+$fp->score(10);
+$fp->contig($slice);
+$fp->seqname(1);
+
+$fp->hstart  (220);
+$fp->hend    (248);
+$fp->hstrand (1);
+$fp->hseqname('dummy-hid');
+push(@feats,$fp);
+
+#
+#
+# 2 Test DnaDnaAlignFeature::new(-features)
+#
+my $dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new( -features => \@feats );
+$dnaf->analysis( $f_analysis );
+
+$ex1->add_supporting_features( $dnaf );
+
+
+
+$ex2->start(201372);
+$ex2->end(201571);
 $ex2->phase(0);
-$ex2->end_phase( 0 );
+$ex2->end_phase( -1 );
 $ex2->contig( $slice );
 $ex2->strand(1);
 $ex2->analysis($analysis);
 
-$ex3->start(28);
-$ex3->end(33);
-$ex3->phase(0);
-$ex3->end_phase( 0 );
+@feats = ();
+$fp = new Bio::EnsEMBL::FeaturePair;
+
+$fp->start(201372);
+$fp->end  (201471);
+$fp->strand(1);
+$fp->score(10);
+$fp->contig($slice);
+$fp->hstart(100);
+$fp->hend    (199);
+$fp->hstrand (1);
+$fp->hseqname('dummy-hid');
+
+push(@feats,$fp);
+
+
+$fp = new Bio::EnsEMBL::FeaturePair;
+$fp->start(201472);
+$fp->end  (201571);
+$fp->strand(1);
+$fp->score(10);
+$fp->contig($slice);
+$fp->seqname(1);
+
+$fp->hstart  (201);
+$fp->hend    (300);
+$fp->hstrand (1);
+$fp->hseqname('dummy-hid');
+push(@feats,$fp);
+
+#
+#
+# 2 Test DnaDnaAlignFeature::new(-features)
+#
+$dnaf = Bio::EnsEMBL::DnaDnaAlignFeature->new( -features => \@feats );
+$dnaf->analysis( $f_analysis );
+
+$ex2->add_supporting_features( $dnaf );
+
+$ex3->start(210600);
+$ex3->end(210800);
+$ex3->phase(-1);
+$ex3->end_phase( -1 );
 $ex3->contig( $slice );
 $ex3->strand(1);
 $ex3->analysis($analysis);
@@ -111,7 +197,7 @@ $transcript1->add_Exon($ex2);
 $translation1->start_Exon($ex1);
 $translation1->end_Exon($ex2);
 $translation1->start(1);
-$translation1->end(9);
+$translation1->end(150);
 $transcript1->translation($translation1);
 
 
@@ -119,9 +205,9 @@ $transcript2->add_Exon($ex1);
 $transcript2->add_Exon($ex2);
 $transcript2->add_Exon($ex3);
 $translation2->start_Exon($ex1);
-$translation2->end_Exon($ex3);
+$translation2->end_Exon($ex2);
 $translation2->start(1);
-$translation2->end(6);
+$translation2->end(180);
 $transcript2->translation($translation2);
 
 debug( "Transcripts created" );
@@ -136,8 +222,14 @@ $gene->analysis($analysis);
 debug( "Getting all the Transcripts/Exons from new Gene" );
 
 my $count = 0;
+my $translates  = 1;
 
 foreach my $tr( @{$gene->get_all_Transcripts()} ) {
+  if( $tr->translate()->seq() =~ /\*./ ) {
+    $translates = 0;
+    debug( "Translate failed.".$tr->translate()->seq() );
+  }
+
   foreach my $exon ( @{$tr->get_all_Exons()} ) {
     debug( "  Exon start: ". $exon->start());
     debug( "  Exon end:   ". $exon->end() );
@@ -147,11 +239,12 @@ foreach my $tr( @{$gene->get_all_Transcripts()} ) {
 }
 
 ok($count == 5);
+ok( $translates );
 
 ok( scalar(@{$gene->get_all_Exons()} ) == 3);
 
 $gene->transform();
-$multi->hide( "core", "gene", "transcript", "exon", "exon_transcript", "gene_description", "translation", "gene_stable_id", "transcript_stable_id", "exon_stable_id", "translation_stable_id" );
+$multi->hide( "core", "gene", "transcript", "exon", "exon_transcript", "gene_description", "translation", "gene_stable_id", "transcript_stable_id", "exon_stable_id", "translation_stable_id", "supporting_feature", "dna_align_feature" );
 
 my $gene_ad = $db->get_GeneAdaptor();
 debug( "Storing the gene" );
@@ -159,9 +252,7 @@ $gene_ad->store($gene);
 
 ok(1);
 
-my $new_slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end( "20",30263615, 30265615 );
-
-my $genes = $new_slice->get_all_Genes();
+my $genes = $slice->get_all_Genes();
 
 
 
@@ -181,9 +272,11 @@ foreach my $tr( @{$gene_out->get_all_Transcripts()} ) {
 
 my $exons = $gene_out->get_all_Transcripts()->[0]->get_all_Exons();
 
-ok($exons->[0]->start==1005);
-ok($exons->[1]->strand==1);
-ok($exons->[1]->phase==0);
+ok( $exons->[0]->start == 13586 );
+
+
+ok( $exons->[1]->strand == 1 );
+ok( $exons->[1]->phase == 0 );
 
 
 
@@ -204,7 +297,26 @@ foreach my $trans( @{$gene_out->get_all_Transcripts()} ){
 ok($translate == 1);
 
 my $t = $gene_out->get_all_Transcripts()->[1];
+
 my $e = $t->get_all_Exons()->[0];
+my $se = $e->get_all_supporting_features();
+
+debug( "Got ".scalar( @$se )." supporting features." );
+ok( scalar( @$se ) == 2 );
+
+my $se_start = $se->[0]->start() < $se->[1]->start() ? 
+  $se->[0]->start() : $se->[1]->start();
+
+my $se_end = $se->[0]->end() > $se->[1]->end() ? 
+  $se->[0]->end() : $se->[1]->end();
+
+
+debug( "Supporting start $se_start, end $se_end" );
+debug( "Exon start ".$e->start()." end ".$e->end() );
+
+ok( $se_start == $e->start() );
+ok( $se_end == $e->end() );
+
 
 my $pep1 = $t->translate()->seq();