added some regression tests

modules/t/exon.t

@@ -3,15 +3,16 @@ use strict;
 
 BEGIN { $| = 1;  
 	use Test ;
-	plan tests => 9;
+	plan tests => 18;
 }
 
 my $loaded = 0;
 END {print "not ok 1\n" unless $loaded;}
 
 use MultiTestDB;
+use TestUtils qw(debug test_getter_setter);
 
-my $verbose = 1;
+our $verbose = 0; #set to 1 to turn on debug printouts
 
 $loaded = 1;
 my $multi = MultiTestDB->new();
@@ -34,28 +35,49 @@ ok($exonad);
 my $exon = Bio::EnsEMBL::Exon->new();
 
 
+$exon->start(31_200);
+ok(&test_getter_setter($exon, 'start', 200));
 
-$exon->start(10);
-ok($exon->start == 10);
-
-$exon->end(20);
-ok($exon->end == 20);
+$exon->end(31_400);
+ok(&test_getter_setter($exon, 'end', 400));
 
 $exon->strand(1);
-ok($exon->strand == 1);
+ok(&test_getter_setter($exon, 'strand', -1));
 
 $exon->phase(0);
-ok($exon->phase == 0);
+ok(&test_getter_setter($exon, 'phase', -1));
 
 $exon->contig( $contig );
+ok(&test_getter_setter($exon, 'contig', $contig));
+
 # should try to store (!)
 $exon->end_phase( -1 );
+ok(&test_getter_setter($exon, 'end_phase', 1));
 
 $multi->hide( "core", "exon" );
 
+
+#
+# find supporting evidence for the exon
+#
+my @evidence = ();
+my @fs = ();
+push @fs, @{$db->get_DnaAlignFeatureAdaptor->fetch_all_by_RawContig($contig)};
+push @fs, @{$db->get_ProteinAlignFeatureAdaptor->fetch_all_by_RawContig($contig)};
+
+while(my $f = shift @fs) {
+  #debug("feature at: " . $f->start . "-" . $f->end);
+  next if $f->start > $exon->end || $f->end < $exon->start;
+  push(@evidence, $f);
+}
+
+my $count = scalar(@evidence);
+debug("adding $count supporting features");
+$exon->add_supporting_features(@evidence);
+
 $exonad->store($exon);
 
-ok($exon->dbID() == 1);
+ok($exon->dbID() == 1 && $exon->adaptor == $exonad);
 
 # now test fetch_by_dbID
 
@@ -63,14 +85,44 @@ my $newexon = $exonad->fetch_by_dbID($exon->dbID);
 
 ok($newexon);
 
-$multi->restore();
 
+#
+# Test transform to empty Slice
+#
+my $slice = new Bio::EnsEMBL::Slice(-empty => 1, 
+				    -adaptor => $db->get_SliceAdaptor);
+$exon = $newexon->transform($slice);
+
+debug("exon chr start  = " . $exon->start);
+debug("exon chr end    = " . $exon->end);
+debug("exon chr strand = " . $exon->strand); 
+ok($exon->start == 30_961_059 && $exon->end == 30_961_259 && $exon->strand==1);
+
+
+#
+# Test transform to another slice
+#
+my $slice = $db->get_SliceAdaptor->fetch_by_chr_start_end($slice->chr_name, 
+						   $exon->start - 10,
+						   $exon->end + 10);
+$exon = $exon->transform($slice);
+debug("exon chr start  = " . $exon->start);
+debug("exon chr end    = " . $exon->end);
+debug("exon chr strand = " . $exon->strand); 
+ok($exon->start == 11 && $exon->end == 211 && $exon->strand==1);
+
+
+#
+# Test Transform back to Raw Contig
+#
+$exon = $exon->transform;
+ok($exon->start == 31_200);
+ok($exon->end   == 31_400);
+ok($exon->strand == 1);
+ok($exon->contig->name eq $exon->contig->name);
 
-sub debug {
-  my $txt = shift;
-  if( $verbose ) {
-    print STDERR $txt,"\n";
-  }
-}
+#regression test, supporting evidence was lost post transform before...
+ok(scalar(@{$exon->get_all_supporting_features} == $count));
 
+$multi->restore();