Annotation.t

use v6;

BEGIN {
    @*INC.push('./lib');
}

use Test;
plan 158;
eval_lives_ok('Bio::Annotation::Collection');
eval_lives_ok('Bio::Annotation::DBLink');
eval_lives_ok('Bio::Annotation::Comment');
eval_lives_ok('Bio::Annotation::Reference');
eval_lives_ok('Bio::Annotation::Target');
eval_lives_ok('Bio::Annotation::AnnotationFactory');
eval_lives_ok('Bio::Annotation::StructuredValue');
eval_lives_ok('Bio::Annotation::TagTree');
eval_lives_ok('Bio::Annotation::Tree');
eval_lives_ok('Bio::Seq');
eval_lives_ok('Bio::SimpleAlign');
eval_lives_ok('Bio::Cluster::UniGene');
eval_lives_ok('Bio::Annotation::SimpleValue','Can load Bio::Annotation::SimpleValue');

use Bio::Annotation::SimpleValue;

#simple value
my $simple = Bio::Annotation::SimpleValue.new(tagname => 'colour',
					       value   => '1',
					      );

# isa_ok($simple, 'Bio::AnnotationI');
is $simple.display_text, 1;
is $simple.as_text, 'Value: 1';
is $simple.value, 1;
is $simple.tagname, 'colour';
is $simple.tag_term, Any;

is $simple.value(0), 0;
is $simple.value, 0;
is $simple.display_text, 0;

# link

#my $link1 = Bio::Annotation::DBLink.new(database => 'TSC',
#					 primary_id => 'TSC0000030',
#					);
# isa_ok($link1,'Bio::AnnotationI');
# is $link1.database(), 'TSC';
# is $link1.primary_id(), 'TSC0000030';
# is $link1.as_text, 'Direct database link to TSC0000030 in database TSC';
# my $ac = Bio::Annotation::Collection.new();
# isa_ok($ac,'Bio::AnnotationCollectionI');

# $ac.add_Annotation('dblink',$link1);
# $ac.add_Annotation('dblink',
# 		    Bio::Annotation::DBLink.new(database => 'TSC',
# 						 primary_id => 'HUM_FABV'));

# my $comment = Bio::Annotation::Comment.new( text => 'sometext');
# is $comment.text, 'sometext';
# is $comment.as_text, 'Comment: sometext';
# $ac.add_Annotation('comment', $comment);



# my $target = Bio::Annotation::Target.new(target_id  => 'F321966.1',
# 					  start      => 1,
# 					  end        => 200,
# 					  strand     => 1,
# 					 );
# isa_ok($target,'Bio::AnnotationI');
# ok $ac.add_Annotation('target', $target);


# my $ref = Bio::Annotation::Reference.new( authors  => 'author line',
# 					   title    => 'title line',
# 					   location => 'location line',
# 					   start    => 12);
# isa_ok($ref,'Bio::AnnotationI');
# is $ref.authors, 'author line';
# is $ref.title,  'title line';
# is $ref.location, 'location line';
# is $ref.start, 12;
# is $ref.database, 'MEDLINE';
# is $ref.as_text, 'Reference: title line';
# $ac.add_Annotation('reference', $ref);


# my $n = 0;
# foreach my $link ( $ac.get_Annotations('dblink') ) {
#     is $link.database, 'TSC';
#     is $link.tagname(), 'dblink';
#     $n++;
# }
# is ($n, 2);

# $n = 0;
# my @keys = $ac.get_all_annotation_keys();
# is (scalar(@keys), 4);
# foreach my $ann ( $ac.get_Annotations() ) {
#     shift(@keys) if ($n > 0) && ($ann.tagname ne $keys[0]);
#     is $ann.tagname(), $keys[0];
#     $n++;
# }
# is ($n, 5);

# $ac.add_Annotation($link1);

# $n = 0;
# foreach my $link ( $ac.get_Annotations('dblink') ) {
#     is $link.tagname(), 'dblink';
#     $n++;
# }
# is ($n, 3);

# # annotation of structured simple values (like swissprot''is GN line)
# my $ann = Bio::Annotation::StructuredValue.new();
# isa_ok($ann, "Bio::AnnotationI");

# $ann.add_value([-1], "val1");
# is ($ann.value(), "val1");
# $ann.value("compat test");
# is ($ann.value(), "compat test");
# $ann.add_value([-1], "val2");
# is ($ann.value(joins => [" AND "]), "compat test AND val2");
# $ann.add_value([0], "val1");
# is ($ann.value(joins => [" AND "]), "val1 AND val2");
# $ann.add_value([-1,-1], "val3", "val4");
# $ann.add_value([-1,-1], "val5", "val6");
# $ann.add_value([-1,-1], "val7");
# is ($ann.value(joins => [" AND "]), "val1 AND val2 AND (val3 AND val4) AND (val5 AND val6) AND val7");
# is ($ann.value(joins => [" AND ", " OR "]), "val1 AND val2 AND (val3 OR val4) AND (val5 OR val6) AND val7");

# $n = 1;
# foreach ($ann.get_all_values()) {
#     is ($_, "val".$n++);
# }

# # nested collections
# my $nested_ac = Bio::Annotation::Collection.new();
# $nested_ac.add_Annotation('nested', $ac);

# is (scalar($nested_ac.get_Annotations()), 1);
# ($ac) = $nested_ac.get_Annotations();
# isa_ok($ac, "Bio::AnnotationCollectionI");
# is (scalar($nested_ac.get_all_Annotations()), 6);
# $nested_ac.add_Annotation('gene names', $ann);
# is (scalar($nested_ac.get_Annotations()), 2);
# is (scalar($nested_ac.get_all_Annotations()), 7);
# is (scalar($nested_ac.get_Annotations('dblink')), 0);
# my @anns = $nested_ac.get_Annotations('gene names');
# isa_ok($anns[0], "Bio::Annotation::StructuredValue");
# @anns = map { $_.get_Annotations('dblink');
# 	  } $nested_ac.get_Annotations('nested');
# is (scalar(@anns), 3);
# is (scalar($nested_ac.flatten_Annotations()), 2);
# is (scalar($nested_ac.get_Annotations()), 7);
# is (scalar($nested_ac.get_all_Annotations()), 7);

# SKIP: {
#   test_skip(-tests => 7, -requires_modules => [qw(Graph::Directed Bio::Annotation::OntologyTerm)]);
#   use_ok('Bio::Annotation::OntologyTerm');
#   # OntologyTerm annotation
#   my $termann = Bio::Annotation::OntologyTerm.new(label => 'test case',
# 						   identifier => 'Ann:00001',
# 						   ontology => 'dumpster');
#   isa_ok($termann.term,'Bio::Ontology::Term');
#   is ($termann.term.name, 'test case');
#   is ($termann.term.identifier, 'Ann:00001');
#   is ($termann.tagname, 'dumpster');
#   is ($termann.ontology.name, 'dumpster');
#   is ($termann.as_text, "dumpster|test case|");
# }

# # AnnotatableI
# my $seq = Bio::Seq.new();
# isa_ok($seq,"Bio::AnnotatableI");
# SKIP: {
# 	test_skip(-requires_modules => [qw(Bio::SeqFeature::Annotated URI::Escape)],
# 			  -tests => 4);
# 	my $fea = Bio::SeqFeature::Annotated.new();
# 	isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
# 	isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
# 	$fea = Bio::SeqFeature::Generic.new();
# 	isa_ok($fea, "Bio::SeqFeatureI",'isa SeqFeatureI');
# 	isa_ok($fea, "Bio::AnnotatableI",'isa AnnotatableI');
# }
# my $clu = Bio::Cluster::UniGene.new();
# isa_ok($clu, "Bio::AnnotatableI");
# my $aln = Bio::SimpleAlign.new();
# isa_ok($clu,"Bio::AnnotatableI");

# # tests for Bio::Annotation::AnnotationFactory

# my $factory = Bio::Annotation::AnnotationFactory.new;
# isa_ok($factory, 'Bio::Factory::ObjectFactoryI');

# # defaults to SimpleValue
# $ann = $factory.create_object(value => 'peroxisome',
# 			       tagname => 'cellular component');
# isa_ok($ann, 'Bio::Annotation::SimpleValue');

# $factory.type('Bio::Annotation::OntologyTerm');

# $ann = $factory.create_object(name => 'peroxisome',
# 			       tagname => 'cellular component');
# ok(defined $ann);
# isa_ok($ann, 'Bio::Annotation::OntologyTerm');

# # unset type()
# $factory.type(undef);
# $ann = $factory.create_object(text => 'this is a comment');
# ok(defined $ann,'Bio::Annotation::Comment');

# isa_ok($ann,'Bio::Annotation::Comment');

# ok $factory.type('Bio::Annotation::Comment');
# $ann = $factory.create_object(text => 'this is a comment');
# ok(defined $ann,'Bio::Annotation::Comment');
# isa_ok($ann,'Bio::Annotation::Comment');

# # factory guessing the type: Comment
# $factory = Bio::Annotation::AnnotationFactory.new();
# $ann = $factory.create_object(text => 'this is a comment');
# ok(defined $ann,'Bio::Annotation::Comment');
# isa_ok($ann,'Bio::Annotation::Comment');

# # factory guessing the type: Target
# $factory = Bio::Annotation::AnnotationFactory.new();
# $ann = $factory.create_object(target_id => 'F1234',
# 			       start     => 1,
# 			       end       => 10 );
# ok defined $ann;
# isa_ok($ann,'Bio::Annotation::Target');

# # factory guessing the type: OntologyTerm
# $factory = Bio::Annotation::AnnotationFactory.new();
# ok(defined ($ann = $factory.create_object(name => 'peroxisome',
# 					   tagname => 'cellular component')));
# like(ref $ann, qr(Bio::Annotation::OntologyTerm));

# # tree
# my $tree_filename = test_input_file('longnames.dnd');
# my $tree = Bio::TreeIO.new(file=>$tree_filename).next_tree();
# my $ann_tree = Bio::Annotation::Tree.new(
# 					  tagname  => 'tree',
# 					  tree_obj => $tree,
# 					 );

# isa_ok($ann_tree, 'Bio::AnnotationI');
# $ann_tree.tree_id('test');
# is $ann_tree.tree_id(), 'test', "tree_id()";
# $ann_tree.tagname('tree'); 
# is $ann_tree.tagname(), 'tree', "tagname()";
# my $aln_filename = test_input_file('longnames.aln');
# use Bio::AlignIO;
# $aln = Bio::AlignIO.new(file  => $aln_filename,
# 			 format=>'clustalw').next_aln();
# isa_ok($aln, 'Bio::AnnotatableI');
# $ac = Bio::Annotation::Collection.new();
# $ac.add_Annotation('tree',$ann_tree);
# $aln.annotation($ac);
# for my $treeblock ( $aln.annotation.get_Annotations('tree') ) {
#   my $treeref = $treeblock.tree();
#   my @nodes = sort { defined $a.id &&
# 		       defined $b.id &&
# 			 $a.id cmp $b.id } $treeref.get_nodes();
#   is $nodes[12].id, '183.m01790', "add tree to AlignI";
#   my $str;
#   for my $seq ($aln.each_seq_with_id($nodes[12].id)) {
#     $str = $seq.subseq(1,20);
#   }
#   is( $str, "MDDKELEIPVEHSTAFGQLV", "get seq from node id");
# }

# # factory guessing the type: Tree
# $factory = Bio::Annotation::AnnotationFactory.new();
# $ann = $factory.create_object(tree_obj => $tree);
# ok defined $ann;
# isa_ok($ann,'Bio::Annotation::Tree');

# #tagtree
# my $struct = [ 'genenames' => [
# 			       ['genename' => [
# 					       [ 'Name' => 'CALM1' ],
# 					       ['Synonyms'=> 'CAM1'],
# 					       ['Synonyms'=> 'CALM'],
# 					       ['Synonyms'=> 'CAM' ] ] ],
# 			       ['genename'=> [
# 					      [ 'Name'=> 'CALM2' ],
# 					      [ 'Synonyms'=> 'CAM2'],
# 					      [ 'Synonyms'=> 'CAMB'] ] ],
# 			       [ 'genename'=> [
# 					       [ 'Name'=> 'CALM3' ],
# 					       [ 'Synonyms'=> 'CAM3' ],
# 					       [ 'Synonyms'=> 'CAMC' ] ] ]
# 			      ] ];

# my $ann_struct = Bio::Annotation::TagTree.new(tagname => 'gn',
# 					       value => $struct);

# isa_ok($ann_struct, 'Bio::AnnotationI');
# my $val = $ann_struct.value;
# like($val, qr/Name: CALM1/,'default itext');

# # roundtrip
# my $ann_struct2 = Bio::Annotation::TagTree.new(tagname => 'gn',
# 						value => $val);
# is($ann_struct2.value, $val,'roundtrip');

# # formats 
# like($ann_struct2.value, qr/Name: CALM1/,'itext');
# $ann_struct2.tagformat('sxpr');
# like($ann_struct2.value, qr/\(Name "CALM1"\)/,'spxr');
# $ann_struct2.tagformat('indent');
# like($ann_struct2.value, qr/Name "CALM1"/,'indent');

# SKIP: {
#     eval {require XML::Parser::PerlSAX};
#     skip ("XML::Parser::PerlSAX rquired for XML",1) if $@;
#     $ann_struct2.tagformat('xml');
#     like($ann_struct2.value, qr/<Name>CALM1<\/Name>/,'xml');
# }

# # grab Data::Stag nodes, use Data::Stag methods
# my @nodes = $ann_struct2.children;
# for my $node (@nodes) {
#     isa_ok($node, 'Data::Stag::StagI');
#     is($node.element, 'genename');
#     # add tag-value data to node
#     $node.set('foo', 'bar');
#     # check output
#     like($node.itext, qr/foo:\s+bar/,'child changes');
# }

# $ann_struct2.tagformat('itext');
# like($ann_struct2.value, qr/foo:\s+bar/,'child changes in parent node');

# # pass in a Data::Stag node to value()
# $ann_struct = Bio::Annotation::TagTree.new(tagname => 'mytags');
# like($ann_struct.value, qr/^\s+:\s+$/xms, 'no tags');
# like($ann_struct.value, qr/^\s+:\s+$/xms,'before Stag node');
# $ann_struct.value($nodes[0]);
# like($ann_struct.value, qr/Name: CALM1/,'after Stag node');
# is(ref $ann_struct.node, ref $nodes[0], 'both stag nodes');
# isnt($ann_struct.node, $nodes[0], 'different instances');

# # pass in another TagTree to value()
# $ann_struct = Bio::Annotation::TagTree.new(tagname => 'mytags');
# like($ann_struct.value, qr/^\s+:\s+$/xms,'before TagTree');
# $ann_struct.value($ann_struct2);
# like($ann_struct.value, qr/Name: CALM2/,'after TagTree');
# is(ref $ann_struct.node, ref $ann_struct2.node, 'both stag nodes');
# isnt($ann_struct.node, $ann_struct2.node, 'different instances');

# # replace the Data::Stag node in the annotation (no copy)
# $ann_struct = Bio::Annotation::TagTree.new(tagname => 'mytags');
# like($ann_struct.value, qr/^\s+:\s+$/xms,'before TagTree');
# $ann_struct.node($nodes[1]);
# like($ann_struct.value, qr/Name: CALM2/,'after TagTree');
# is(ref $ann_struct.node, ref $ann_struct2.node, 'stag nodes');
# is($ann_struct.node, $nodes[1], 'same instance');
# # replace the Data::Stag node in the annotation (use duplicate)
# $ann_struct = Bio::Annotation::TagTree.new(tagname => 'mytags');
# like($ann_struct.value, qr/^\s+:\s+$/xms,'before TagTree');
# $ann_struct.node($nodes[1],'copy');
# like($ann_struct.value, qr/Name: CALM2/,'after TagTree');
# is(ref $ann_struct.node, ref $ann_struct2.node, 'stag nodes');
# isnt($ann_struct.node, $nodes[1], 'different instance');

# #check insertion in to collection
# $ann_struct = Bio::Annotation::TagTree.new(value => $struct);
# $ac = Bio::Annotation::Collection.new();

# $ac.add_Annotation('genenames',$ann_struct);
# my $ct = 0;
# for my $tagtree ( $ac.get_Annotations('genenames') ) {
#   isa_ok($tagtree, 'Bio::AnnotationI');
#   for my $node ($tagtree.children) {
#     isa_ok($node, 'Data::Stag::StagI');
#     like($node.itext, qr/Name:\s+CALM/,'child changes');
#     $ct++;
#   }
# }
# is($ct,3);

# # factory guessing the type: TagTree
# $factory = Bio::Annotation::AnnotationFactory.new();
# $ann = $factory.create_object(value => $struct);
# ok defined $ann;
# isa_ok($ann,'Bio::Annotation::TagTree');

done();