Added a test for ProteinAlignFeatureAdaptor and altered the dnaalignfeature...

Added a test for ProteinAlignFeatureAdaptor and altered the dnaalignfeature test to work with the alterd base align
feature

modules/t/dnaalignfeature.t

@@ -39,6 +39,7 @@ $feature1->start(5);
 $feature1->end  (7);
 $feature1->strand(1);
 $feature1->score(10);
+$feature1->seqname(1);
 #$feature1->analysis($self->analysis);
 
 $feature2 = new Bio::EnsEMBL::SeqFeature();
@@ -46,7 +47,7 @@ $feature2->start  (105);
 $feature2->end    (107);
 $feature2->strand (1);
 $feature2->score  (10);
-
+$feature2->seqname('dummy-hid');
 $fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
 				    -feature2 => $feature2);
 
@@ -58,6 +59,7 @@ $feature1->start(10);
 $feature1->end  (14);
 $feature1->strand(1);
 $feature1->score(10);
+$feature1->seqname(1);
 #$feature1->analysis($self->analysis);
 
 $feature2 = new Bio::EnsEMBL::SeqFeature();
@@ -65,7 +67,7 @@ $feature2->start  (106);
 $feature2->end    (110);
 $feature2->strand (1);
 $feature2->score  (10);
-
+$feature2->seqname('dummy-hid');
 $fp2 = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
 				    -feature2 => $feature2);
 

modules/t/proteinalignfeature.t

+
+ use lib 't';
+
+BEGIN { $| = 1;  
+	use Test;
+	plan tests => 7;
+}
+
+my $loaded = 0;
+END {print "not ok 1\n" unless $loaded;}
+
+use EnsTestDB;
+use Bio::EnsEMBL::DBLoader;
+
+
+
+$loaded = 1;
+
+ok(1);
+
+# Database will be dropped when this
+# object goes out of scope
+my $ens_test = EnsTestDB->new;
+
+$ens_test->do_sql_file("t/minidatabase.dump");
+
+ok($ens_test);
+
+my @feats;
+
+my $db = $ens_test->get_DBSQL_Obj;
+
+$pep_f_ad = $db->get_ProteinAlignFeatureAdaptor();
+
+my $feature1 = new Bio::EnsEMBL::SeqFeature();
+$feature1->start(50);
+$feature1->end(115);
+$feature1->strand(-1);
+$feature1->score(41);
+$feature1->seqname(1);
+$feature1->percent_id(100);
+
+my $feature2 = new Bio::EnsEMBL::SeqFeature();
+$feature2->start(5);
+$feature2->end(26);
+$feature2->seqname('dummy-hid');
+$feature2->score(41);
+$feature2->strand(1);
+$feature2->percent_id(100);
+
+$fp = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,
+				    -feature2 => $feature2);
+
+
+
+push(@feats, $fp);
+
+
+$feature1 = new Bio::EnsEMBL::SeqFeature();
+$feature1->start(07);
+$feature1->end(39);
+$feature1->strand(-1);
+$feature1->score(41);
+$feature1->seqname(1);
+$feature1->percent_id(100);
+
+$feature2 = new Bio::EnsEMBL::SeqFeature();
+$feature2->start(27);
+$feature2->end(37);
+$feature2->seqname('dummy-hid');
+$feature2->score(41);
+$feature2->strand(1);
+$feature2->percent_id(100);
+
+$fp2 = new Bio::EnsEMBL::FeaturePair(-feature1 => $feature1,		
+				     -feature2 => $feature2);			
+
+	
+push(@feats, $fp2);
+
+$pepf = Bio::EnsEMBL::DnaPepAlignFeature->new( -features => \@feats );
+
+$pepf->analysis($db->get_AnalysisAdaptor->fetch_by_logic_name("dummy-blast"));
+
+ok($pepf);
+
+$pep_f_ad->store(1, $pepf);
+
+ok(1);
+
+($outf) = $pep_f_ad->fetch_by_contig_id(1);
+
+ok($outf);  
+
+
+ok($outf->start == 07);
+ok($outf->end == 115);
+