Merge branch 'topic/finish_sigs'

cjfields · Jan 10, 2014 · ce066bc · ce066bc
2 parents c97454e + 5c799a3
commit ce066bc
Show file tree

Hide file tree

Showing 14 changed files with 60 additions and 477 deletions.
diff --git a/lib/Biome/Annotation/Collection.pm b/lib/Biome/Annotation/Collection.pm
@@ -1,6 +1,8 @@
 package Biome::Annotation::Collection;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 # though this is an Annotate consumer, we do not allow extra data or object
 # slots (it implements Annotate so we can nest Collections)
@@ -20,23 +22,19 @@ has 'annotation_map' => (
     default   => sub { {} },
 );
 
-sub get_Annotation_keys {
-    keys %{shift->annotation_map};
+method get_Annotation_keys () {
+    keys %{$self->annotation_map};
 }
 
 # may combine with get_Annotation_keys, passing as an option
-sub get_all_Annotation_keys {
-    my ($self, $method) = @_;
-    $method //= 'depth';
+method get_all_Annotation_keys ($method='depth') {
     my @keys;
     for my $key ($self->get_Annotation_keys) {
         push @keys, $key;
     }
 }
 
-sub get_Annotations {
-    my ($self,@keys) = @_;
-
+method get_Annotations (@keys){
     my @anns = ();
     @keys = $self->get_Annotation_keys() unless @keys;
     my $map = $self->annotation_map;
@@ -51,14 +49,13 @@ sub get_Annotations {
     return @anns;
 }
 
-sub get_nested_Annotations {
-    shift->throw_not_implemented;
+method get_nested_Annotations () {
+    $self->throw_not_implemented;
 }
 
 # does this and get_nested_Annotations do the same thing? Seems like some
 # redundancy...
-sub get_all_Annotations {
-    my ($self,@keys) = @_;
+method get_all_Annotations (@keys) {
     my @ann = map {
         $_->does("Biome::Role::CollectAnnotation") ?
             $_->get_all_Annotations(@keys) : $_;
@@ -67,8 +64,7 @@ sub get_all_Annotations {
 }
 
 # does not return nested values, only annotation # contained in this instance
-sub get_num_Annotations {
-    my ($self) = @_;
+method get_num_Annotations () {
     my $count = 0;
     map { $count += scalar @$_ } values %{$self->annotation_map};
     return $count;    
@@ -78,8 +74,7 @@ sub get_num_Annotations {
 
 # As implemented in BioPerl; this doesn't enforce that an incoming instance that
 # Annotates have a matching tagname (key).
-sub add_Annotations {
-    my ($self, $key, $object, $archetype) = @_;
+method add_Annotations ($key, $object?, $archetype?) {
     my $map = $self->annotation_map;
     # if there's no key we use the tagname() as key
     if(ref($key) && $key->does("Biome::Role::Annotate") && (!ref($object))) {
@@ -135,9 +130,7 @@ sub add_Annotations {
 }
 
 # can we remove Annotation by an identifier?
-sub remove_Annotations {
-    my ($self, @keys) = @_;
-
+method remove_Annotations (@keys) {
     @keys = $self->get_Annotation_keys() unless @keys;
     my @anns = $self->get_Annotations(@keys);
     my ($annmap, $typemap) = ($self->annotation_map, $self->type_map);
@@ -149,18 +142,18 @@ sub remove_Annotations {
     return @anns;    
 }
 
-sub flatten_Annotations {
-    shift->throw_not_implemented
+method flatten_Annotations () {
+    $self->throw_not_implemented
 }
 
 # create an iterator and return one at a time...
-sub next_Annotation {
-    shift->throw_not_implemented    
+method next_Annotation () {
+    $self->throw_not_implemented
 }
 
 # create an iterator and return one at a time...
-sub next_Collection {
-    shift->throw_not_implemented    
+method next_Collection () {
+    $self->throw_not_implemented
 }
 
 # Annotate Role
@@ -172,8 +165,8 @@ has '+DEFAULT_CB' => (
     lazy        => 1
     );
 
-sub as_text {
-    shift->throw_not_implemented    
+method as_text () {
+    $self->throw_not_implemented
 }
 
 no Biome;

diff --git a/lib/Biome/Annotation/Comment.pm b/lib/Biome/Annotation/Comment.pm
@@ -2,6 +2,8 @@
 package Biome::Annotation::Comment;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 with 'Biome::Role::Annotate' => {
     'data_slots' => [qw(text type)]
@@ -12,8 +14,7 @@ has '+DEFAULT_CB' => (
     lazy    => 1
     );
 
-sub as_text{
-    my ($self) = @_;
+method as_text () {
     return "Comment: ".$self->text;
 }
 

diff --git a/lib/Biome/Annotation/DBLink.pm b/lib/Biome/Annotation/DBLink.pm
@@ -3,6 +3,8 @@
 package Biome::Annotation::DBLink;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 with qw(Biome::Role::Annotate
         Biome::Role::DatabaseLink
@@ -20,9 +22,7 @@ has '+namespace' => (
     lazy        => 1,
 );
 
-sub as_text{
-    my ($self) = @_;
-
+method as_text () {
     return "Direct database link to ".$self->primary_id
         .($self->version ? ".".$self->version : "")
         .($self->optional_id ? " (".$self->optional_id.")" : "")
@@ -35,9 +35,9 @@ sub as_text{
 #
 #########################################################################
 
-sub _build_display_id {$_[1]}
-sub _build_object_id {shift->primary_id(@_)}
-sub _build_id {shift->display_id(@_)}
+method _build_display_id ($id) { $id }
+method _build_object_id ($id) {$self->primary_id($id)}
+method _build_id ($id) {$self->display_id($id)}
 
 no Biome;
 
@@ -310,4 +310,4 @@ methods. Internal methods are usually preceded with a _
            For DBLink this is the same as database().
  Returns : A scalar
 
-=cut
+=cut
diff --git a/lib/Biome/Annotation/Relation.pm b/lib/Biome/Annotation/Relation.pm
@@ -1,11 +1,12 @@
 package Bio::Annotation::Relation;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 with 'Biome::Role::Annotate';
 
-sub as_text{
-   my ($self) = @_;
+method as_text () {
    return $self->type." to  ".$self->to->id;
 }
 
@@ -220,4 +221,4 @@ The rest of the documentation details each of the object methods. Internal metho
            object or undef, optional)
 
 
-=cut
+=cut
diff --git a/lib/Biome/Annotation/SimpleValue.pm b/lib/Biome/Annotation/SimpleValue.pm
@@ -2,6 +2,8 @@
 package Biome::Annotation::SimpleValue;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 with 'Biome::Role::Annotate' => {
     'data_slots'        => [qw(value term)]
@@ -12,8 +14,7 @@ has '+DEFAULT_CB' => (
     lazy    => 1
     );
 
-sub as_text{
-    my ($self) = @_;
+method as_text () {
     return "Value: ".$self->value;
 }
 
@@ -200,4 +201,4 @@ The rest of the documentation details each of the object methods. Internal metho
  Args    : on set, new value (a L<Bio::Ontology::TermI> compliant
            object or undef, optional)
 
-=cut
+=cut
diff --git a/lib/Biome/Annotation/TagTree.pm b/lib/Biome/Annotation/TagTree.pm
@@ -2,6 +2,9 @@ package Biome::Annotation::TagTree;
 
 use 5.010;
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
+
 use Moose::Util::TypeConstraints;
 use Data::Stag ();
 no if $] >= 5.018, 'warnings',  "experimental::smartmatch";
@@ -44,8 +47,7 @@ has '+DEFAULT_CB' => (
     lazy    => 1
     );
 
-sub as_text {
-    my ($self) = @_;
+method as_text () {
     return "TagTree: " . $self->value;
 }
 
@@ -68,8 +70,7 @@ has 'node' => (
 # TODO: value is not a first-class attribute (it is a method here).
 # Can we shadow 'alias' attributes?
 
-sub value {
-    my ($self, $value) = @_;
+method value ($value?) {
     if (defined $value) {
         $self->node($value); # coercions shoud catch any variants
     }

diff --git a/lib/Biome/Annotation/Target.pm b/lib/Biome/Annotation/Target.pm
@@ -3,6 +3,8 @@
 package Biome::Annotation::Target;
 
 use Biome;
+use namespace::autoclean;
+use Method::Signatures;
 
 extends qw(Biome::Annotation::DBLink);
 
@@ -14,9 +16,7 @@ has '+DEFAULT_CB' => (
     lazy    => 1
 );
 
-sub as_text {
-    my ($self) = @_;
-
+method as_text {
     my $target = $self->target_id || '';
     my $start  = $self->start     || '';
     my $end    = $self->end       || '';
@@ -169,4 +169,4 @@ new value of target_id (to set)
 
 =back
 
-=cut
+=cut