diff variant_effect_predictor/Bio/Structure/Model.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Structure/Model.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,294 @@
+# $Id: Model.pm,v 1.6 2002/10/22 07:38:44 lapp Exp $
+#
+# bioperl module for Bio::Structure::Model
+#
+# Cared for by Kris Boulez <[e-mail]>
+#
+# Copyright Kris Boulez
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Structure::Model - Bioperl structure Object, describes a Model
+
+=head1 SYNOPSIS
+
+  #add synopsis here
+
+=head1 DESCRIPTION
+
+This object stores a Bio::Structure::Chain
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]             - General discussion
+  http://bio.perl.org/MailList.html - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Kris Boulez
+
+Email [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::Structure::Model;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::Structure::Entry;
+use Bio::Structure::Chain;
+@ISA = qw(Bio::Root::Root);
+
+
+=head2 new()
+
+ Title   : new()
+ Usage   : $struc = Bio::Structure::Model->new( 
+                                           -id  => 'human_id',
+                                           );
+
+ Function: Returns a new Bio::Structure::Model object from basic 
+	constructors. Probably most called from Bio::Structure::IO.
+ Returns : a new Bio::Structure::Model object
+
+=cut
+
+
+
+sub new {
+    my ($class, @args) = @_;
+    my $self = $class->SUPER::new(@args);
+
+    my($id, $chain, $residue ) =
+        $self->_rearrange([qw(
+			      ID
+			      CHAIN
+			      RESIDUE
+                              )],
+                          @args);
+
+    $id      && $self->id($id);
+
+    $chain && $self->throw("you have to add chain via an Entry object\n");
+
+    $residue && $self->throw("you have to add residues via an Entry object\n");
+
+    return $self;
+}
+
+
+
+=head2 chain()
+
+ Title   : chain
+ Usage   : 
+ Function: will eventually allow parent/child navigation not via an Entry object
+ Returns : 
+ Args    : 
+
+=cut
+
+sub chain {
+	my ($self,$value) = @_;
+
+	$self->throw("go via an Entry object\n");
+}
+
+
+=head2 add_chain()
+
+ Title   : add_chain
+ Usage   : 
+ Function:  will eventually allow parent/child navigation not via an Entry object
+ Returns : 
+ Args    : 
+
+=cut
+
+sub add_chain {
+	my ($self,$value) = @_;
+
+	$self->throw("go via an Entry object for now\n");
+}
+
+=head2 entry()
+
+ Title   : entry
+ Usage   : 
+ Function:  will eventually allow parent/child navigation not via an Entry object
+ Returns : 
+ Args    : 
+
+=cut
+
+sub entry {
+	my($self) = @_;
+
+	$self->throw("Model::entry go via an Entry object please\n");
+}
+
+
+=head2 id()
+
+ Title   : id
+ Usage   : $model->id("model 5")
+ Function: Gets/sets the ID for this model
+ Returns : the ID
+ Args    : the ID
+
+=cut
+
+sub id {
+	my ($self, $value) = @_;;
+	if (defined $value) {
+		$self->{'id'} = $value;
+	}
+	return $self->{'id'};
+}
+
+=head2 residue()
+
+ Title   : residue
+ Usage   : 
+ Function:  will eventually allow parent/child navigation not via an Entry object
+ Returns : 
+ Args    : 
+
+=cut
+
+sub residue {
+	my ($self, @args) = @_;
+
+	$self->throw("need to go via Entry object or learn symbolic refs\n");
+}
+
+
+=head2 add_residue()
+
+ Title   : add_residue
+ Usage   : 
+ Function:  will eventually allow parent/child navigation not via an Entry object
+ Returns : 
+ Args    : 
+
+=cut
+
+sub add_residue {
+	my ($self, @args) = @_;
+
+	$self->throw("go via entry->add_residue(chain, residue)\n");
+}
+
+
+
+sub DESTROY {
+	my $self = shift;
+
+	# no specific DESTROY for now
+}
+
+#
+# from here on only private methods
+#
+
+=head2 _remove_chains()
+
+ Title   : _remove_chains
+ Usage   : 
+ Function: Removes the chains attached to a Model. Tells the chains they
+ 	don't belong to this Model any more
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _remove_chains {
+	my ($self) = shift;
+
+	$self->throw("use Entry methods pleae\n");
+}
+
+
+=head2 _remove_entry()
+
+ Title   : _remove_entry
+ Usage   : 
+ Function: Removes the Entry this Model is atttached to.
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _remove_entry {
+	my ($self) = shift;
+
+	$self->throw("use a method based on an Entry object\n");
+}
+
+
+=head2 _create_default_chain()
+
+ Title   : _create_default_chain
+ Usage   : 
+ Function: Creates a default Chain for this Model. Typical situation
+ 	in an X-ray structure where there is only one chain
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _create_default_chain {
+	my ($self) = shift;
+
+	my $chain = Bio::Structure::Chain->new(-id => "default");
+}
+
+
+=head2 _grandparent()
+
+ Title   : _grandparent
+ Usage   : 
+ Function: get/set a symbolic reference to our grandparent
+ Returns : 
+ Args    : 
+
+=cut
+
+sub _grandparent {
+	my($self,$symref) = @_;
+
+	if (ref($symref)) {
+		$self->throw("Thou shall only pass strings in here, no references $symref\n");
+	}
+	if (defined $symref) {
+		$self->{'grandparent'} = $symref;
+	}
+	return $self->{'grandparent'};
+}
+
+1;