From cd432f4c2bf67baf080e2c5651b6719e50317c64 Mon Sep 17 00:00:00 2001
From: Florent Angly <florent.angly@gmail.com>
Date: Tue, 6 Mar 2012 07:29:32 +1000
Subject: [PATCH] SeqFeature::Annotated tests

---
 Bio/SeqFeature/Annotated.pm |   1 +
 t/SeqFeature/Annotated.t    | 106 ++++++++++++++++++++++++++++++++++++
 2 files changed, 107 insertions(+)
 create mode 100644 t/SeqFeature/Annotated.t

diff --git a/Bio/SeqFeature/Annotated.pm b/Bio/SeqFeature/Annotated.pm
index 9061679..9e5dd61 100644
--- 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/Annotated.t b/t/SeqFeature/Annotated.t
new file mode 100644
index 0000000..6a25099
--- /dev/null
+++ b/t/SeqFeature/Annotated.t
@@ -0,0 +1,106 @@
+# -*-Perl-*- Test Harness script for Bioperl
+# $Id$
+
+use strict;
+
+BEGIN { 
+    use lib '.';
+    use Bio::Root::Test;
+    
+    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, $sfa2, $sfa3, $loc, $sfg, $sfaa);
+
+
+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 $sfa->display_name eq 'test.annot';
+
+
+# Test bsfa::from_feature
+$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';
+is $sfa2->source->display_text,'program_a';
+is $sfa2->source_tag,'program_a';
+is $sfa2->strand,1;
+is $sfa2->start,400;
+is $sfa2->end,440;
+is $sfa2->get_Annotations('silly')->value,20;
+is $sfa2->get_Annotations('new')->value,1;
+
+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';
+is $sfaa->source_tag,'program_b';
+is $sfaa->strand,1;
+is $sfaa->start,1;
+is $sfaa->end,5;
+is $sfaa->score,12;
+
+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';
+is $sfa3->source_tag,'program_a';
+is $sfa3->strand,1;
+is $sfa3->start,400;
+is $sfa3->end,440;
+is $sfa3->get_Annotations('silly')->value,20;
+is $sfa3->get_Annotations('new')->value,1;
+
+# Note there is an API conflict with SeqFeature::Generic, where score is a
+# simple scalar, and here it is a Bio::Annotation::SimpleValue
+# By popular vote there is no operator overloading, so this needs to be
+# resolved
+is $sfa3->score(), 12; 
+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)
+