diff variant_effect_predictor/Bio/Annotation/DBLink.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Annotation/DBLink.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,352 @@
+# $Id: DBLink.pm,v 1.12 2002/10/23 18:07:49 lapp Exp $
+#
+# BioPerl module for Bio::Annotation::Link
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Annotation::DBLink - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+   $link1 = new Bio::Annotation::DBLink(-database => 'TSC',
+                                        -primary_id => 'TSC0000030'
+					);
+
+   #or 
+
+   $link2 = new Bio::Annotation::DBLink();
+   $link2->database('dbSNP');
+   $link2->primary_id('2367');
+
+   # DBLink is-a Bio::AnnotationI object, can be added to annotation
+   # collections, e.g. the one on features or seqs
+   $feat->annotation->add_Annotation('dblink', $link2);
+
+
+=head1 DESCRIPTION
+
+Provides an object which represents a link from one object to something
+in another database without prescribing what is in the other database
+
+=head1 AUTHOR - Ewan Birney
+
+Ewan Birney - [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Annotation::DBLink;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::AnnotationI;
+use Bio::IdentifiableI;
+
+@ISA = qw(Bio::Root::Root Bio::AnnotationI Bio::IdentifiableI);
+
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+
+  my ($database, $primary_id, $optional_id, $comment, $tag, $ns, $auth, $v) =
+      $self->_rearrange([qw(DATABASE
+			    PRIMARY_ID
+			    OPTIONAL_ID
+			    COMMENT
+			    TAGNAME
+			    NAMESPACE
+			    AUTHORITY
+			    VERSION
+			    )], @args);
+  
+  $database    && $self->database($database);
+  $primary_id  && $self->primary_id($primary_id);
+  $optional_id && $self->optional_id($optional_id);
+  $comment     && $self->comment($comment);
+  $tag         && $self->tagname($tag);
+  # Bio::IdentifiableI parameters:
+  $ns          && $self->namespace($ns); # this will override $database
+  $auth        && $self->authority($auth);
+  defined($v)  && $self->version($v);
+
+  return $self;
+}
+
+=head1 AnnotationI implementing functions
+
+=cut
+
+
+=head2 as_text
+
+ Title   : as_text
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub as_text{
+   my ($self) = @_;
+
+   return "Direct database link to ".$self->primary_id." in database ".$self->database;
+}
+
+=head2 hash_tree
+
+ Title   : hash_tree
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub hash_tree{
+   my ($self) = @_;
+   
+   my $h = {};
+   $h->{'database'}   = $self->database;
+   $h->{'primary_id'} = $self->primary_id;
+   if( defined $self->optional_id ) {
+       $h->{'optional_id'} = $self->optional_id;
+   }
+   if( defined $self->comment ) {
+       # we know that comments have hash_tree methods
+       $h->{'comment'} = $self->comment;
+   }
+
+   return $h;
+}
+
+=head2 tagname
+
+ Title   : tagname
+ Usage   : $obj->tagname($newval)
+ Function: Get/set the tagname for this annotation value.
+
+           Setting this is optional. If set, it obviates the need to
+           provide a tag to Bio::AnnotationCollectionI when adding
+           this object. When obtaining an AnnotationI object from the
+           collection, the collection will set the value to the tag
+           under which it was stored unless the object has a tag
+           stored already.
+
+ Example : 
+ Returns : value of tagname (a scalar)
+ Args    : new value (a scalar, optional)
+
+
+=cut
+
+sub tagname{
+    my ($self,$value) = @_;
+    if( defined $value) {
+	$self->{'tagname'} = $value;
+    }
+    return $self->{'tagname'};
+}
+
+=head1 Specific accessors for DBLinks
+
+=cut
+
+=head2 database
+
+ Title   : database
+ Usage   : $self->database($newval)
+ Function: set/get on the database string. Databases are just
+           a string here which can then be interpretted elsewhere
+ Example : 
+ Returns : value of database
+ Args    : newvalue (optional)
+
+=cut
+
+sub database{
+   my ($self,$value) = @_;
+
+   if( defined $value) {
+      $self->{'database'} = $value;
+    }
+    return $self->{'database'};
+
+}
+
+=head2 primary_id
+
+ Title   : primary_id
+ Usage   : $self->primary_id($newval)
+ Function: set/get on the primary id (a string)
+           The primary id is the main identifier used for this object in 
+           the database. Good examples would be accession numbers. The id
+           is meant to be the main, stable identifier for this object
+ Example : 
+ Returns : value of primary_id
+ Args    : newvalue (optional)
+
+=cut
+
+sub primary_id{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'primary_id'} = $value;
+    }
+    return $self->{'primary_id'};
+
+}
+
+=head2 optional_id
+
+ Title   : optional_id
+ Usage   : $self->optional_id($newval)
+ Function: get/set for the optional_id (a string)
+
+           optional id is a slot for people to use as they wish. The
+           main issue is that some databases do not have a clean
+           single string identifier scheme. It is hoped that the
+           primary_id can behave like a reasonably sane "single string
+           identifier" of objects, and people can use/abuse optional
+           ids to their heart's content to provide precise mappings.
+
+ Example : 
+ Returns : value of optional_id
+ Args    : newvalue (optional)
+
+=cut
+
+#'
+
+sub optional_id{
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'optional_id'} = $value;
+    }
+    return $self->{'optional_id'};
+
+}
+
+=head2 comment
+
+ Title   : comment
+ Usage   : $self->comment($newval)
+ Function: get/set of comments (comment object)
+           Sets or gets comments of this dblink, which is sometimes relevant
+ Example : 
+ Returns : value of comment (Bio::Annotation::Comment)
+ Args    : newvalue (optional)
+
+=cut
+
+sub comment {
+   my ($self,$value) = @_;
+   if( defined $value) {
+      $self->{'comment'} = $value;
+    }
+    return $self->{'comment'};
+}
+
+=head1 Methods for Bio::IdentifiableI compliance
+
+=head2 object_id
+
+ Title   : object_id
+ Usage   : $string    = $obj->object_id()
+ Function: a string which represents the stable primary identifier
+           in this namespace of this object. For DNA sequences this
+           is its accession_number, similarly for protein sequences
+
+           This is aliased to primary_id().
+ Returns : A scalar
+
+
+=cut
+
+sub object_id {
+    return shift->primary_id(@_);
+}
+
+=head2 version
+
+ Title   : version
+ Usage   : $version    = $obj->version()
+ Function: a number which differentiates between versions of
+           the same object. Higher numbers are considered to be
+           later and more relevant, but a single object described
+           the same identifier should represent the same concept
+
+ Returns : A number
+
+=cut
+
+sub version{
+    my ($self,$value) = @_;
+    if( defined $value) {
+	$self->{'_version'} = $value;
+    }
+    return $self->{'_version'};
+}
+
+
+=head2 authority
+
+ Title   : authority
+ Usage   : $authority    = $obj->authority()
+ Function: a string which represents the organisation which
+           granted the namespace, written as the DNS name for  
+           organisation (eg, wormbase.org)
+
+ Returns : A scalar
+
+=cut
+
+sub authority {
+    my ($obj,$value) = @_;
+    if( defined $value) {
+	$obj->{'authority'} = $value;
+    }
+    return $obj->{'authority'};
+}
+
+=head2 namespace
+
+ Title   : namespace
+ Usage   : $string    = $obj->namespace()
+ Function: A string representing the name space this identifier
+           is valid in, often the database name or the name
+           describing the collection 
+
+           For DBLink this is the same as database().
+ Returns : A scalar
+
+
+=cut
+
+sub namespace{
+    return shift->database(@_);
+}
+
+1;