SeqFeature::Annotated tests

bioperl · Mar 5, 2012 · c334576 · c334576
1 parent 8f07a6d
commit c334576
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Showing 2 changed files with 54 additions and 44 deletions.
diff --git a/Bio/SeqFeature/Annotated.pm b/Bio/SeqFeature/Annotated.pm
@@ -312,6 +312,7 @@ sub from_feature {
             $self->add_Annotation($key,$val)
         }
     }
+    return 1;
 }
 #given a key and its values, make the values into
 #Bio::Annotation::\w+ objects

diff --git a/t/SeqFeature/SeqFeatAnnotated.t → t/SeqFeature/Annotated.t b/t/SeqFeature/SeqFeatAnnotated.t → t/SeqFeature/Annotated.t
@@ -7,44 +7,50 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 34, 
-	       -requires_modules => [qw(URI::Escape Graph::Directed)],
-	       -requires_networking => 1
-	);
-
-	use_ok('Bio::SeqFeature::Generic');
-	use_ok('Bio::SeqFeature::Annotated');
+    test_begin(
+        -tests => 40, 
+        -requires_modules => [qw(URI::Escape Graph::Directed)],
+        -requires_networking => 1
+    );
+
+    use_ok('Bio::SeqFeature::Generic');
+    use_ok('Bio::SeqFeature::Annotated');
 }
 
-my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
-					  -end => 5,
-					  -strand => "+",
-					  -frame => 2,
-					  -type => 'nucleotide_motif',
-					  -phase => 2,
-					  -score => 12,
-					  -source => 'program_b',
-					  -display_name => 'test.annot',
-					  -seq_id => 'test.displayname' );
+my ($sfa, $sfa2, $sfa3, $loc, $sfg, $sfaa);
+
 
-ok (defined $sfa);
-my $loc = $sfa->location;
-ok $loc->isa("Bio::Location::Simple");    
+ok $sfa = Bio::SeqFeature::Annotated->new(
+    -start => 1,
+    -end => 5,
+    -strand => '+',
+    -frame => 2,
+    -type => 'nucleotide_motif',
+    -phase => 2,
+    -score => 12,
+    -source => 'program_b',
+    -display_name => 'test.annot',
+    -seq_id => 'test.displayname',
+);
+ok $loc = $sfa->location;
+ok $loc->isa('Bio::Location::Simple');
 ok $sfa->display_name eq 'test.annot';
 
-#test bsfa::from_feature
-my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
-					  -end => 440,
-					  -strand => 1,
-					  -primary => 'nucleotide_motif',
-					  -source  => 'program_a',
-					  -tag => {
-					  silly => 20,
-					  new => 1
-					  }
-					  );
-my $sfa2;
-$sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
+
+# Test bsfa::from_feature
+$sfg = Bio::SeqFeature::Generic->new (
+    -start => 400,
+    -end => 440,
+    -strand => 1,
+    -primary => 'nucleotide_motif',
+    -source  => 'program_a',
+    -tag => {
+        silly => 20,
+        new => 1
+    }
+);
+
+ok $sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
 
 is $sfa2->type->name,'nucleotide_motif';
 is $sfa2->primary_tag, 'nucleotide_motif';
@@ -55,7 +61,8 @@ is $sfa2->start,400;
 is $sfa2->end,440;
 is $sfa2->get_Annotations('silly')->value,20;
 is $sfa2->get_Annotations('new')->value,1;
-my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
+
+ok $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
 is $sfaa->type->name,'nucleotide_motif';
 is $sfaa->primary_tag, 'nucleotide_motif';
 is $sfaa->source->display_text,'program_b';
@@ -65,16 +72,18 @@ is $sfaa->start,1;
 is $sfaa->end,5;
 is $sfaa->score,12;
 
-my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
-					-end => 5,
-					-strand => "+",
-					-frame => 2,
-					-phase => 2,
-					-score => 12,
-					-display_name => 'test.annot',
-					-seq_id => 'test.displayname' );
-$sfa3->from_feature($sfg);
+ok $sfa3 = Bio::SeqFeature::Annotated->new(
+    -start => 1,
+    -end => 5,
+    -strand => '+',
+    -frame => 2,
+    -phase => 2,
+    -score => 12,
+    -display_name => 'test.annot',
+    -seq_id => 'test.displayname',
+);
 
+ok $sfa3->from_feature($sfg);
 is $sfa3->type->name,'nucleotide_motif', 'type->name';
 is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
 is $sfa3->source->display_text,'program_a';
@@ -90,7 +99,7 @@ is $sfa3->get_Annotations('new')->value,1;
 # By popular vote there is no operator overloading, so this needs to be
 # resolved
 is $sfa3->score(), 12; 
-$sfa3->score(11);
+ok $sfa3->score(11);
 is $sfa3->score(), 11; 
 $sfa3->score(0);
 is $sfa3->score(), 0;	# test that setting to 0 no longer is overriddent to set score to '.' (fixed in Bio::SeqFeature::Annotated version 1.3.7)