# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 152);
use_ok('Bio::Annotation::Collection');
use_ok('Bio::Annotation::DBLink');
use_ok('Bio::Annotation::Comment');
use_ok('Bio::Annotation::Reference');
use_ok('Bio::Annotation::SimpleValue');
use_ok('Bio::Annotation::Target');
use_ok('Bio::Annotation::AnnotationFactory');
use_ok('Bio::Annotation::StructuredValue');
use_ok('Bio::Annotation::TagTree');
use_ok('Bio::Annotation::Tree');
}
my $DEBUG = test_debug();
#simple value
my $simple = Bio::Annotation::SimpleValue->new(-tagname => 'colour',
-value => '1',
);
isa_ok($simple, 'Bio::AnnotationI');
is $simple->display_text, 1;
is $simple->value, 1;
is $simple->tagname, 'colour';
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(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
use Bio::Seq;
my $seq = Bio::Seq->new();
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');
}
# 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()";
use Bio::AlignIO;
my $aln = Bio::AlignIO->new(-file => test_input_file('longnames.aln'),
-format=>'clustalw')->next_aln();
$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, 26);
is $nodes[12]->id, 'Skud_Contig1703.7', "add tree to AlignI";
my $str;
for my $seq ($aln->each_seq_with_id($nodes[12]->id)) {
$str = $seq->subseq(1,20);
}
is( $str, "-------------MPFAQIV", "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');