diff variant_effect_predictor/Bio/Map/MapI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/MapI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,203 @@
+# $Id: MapI.pm,v 1.6 2002/10/22 07:45:15 lapp Exp $
+#
+# BioPerl module for Bio::Map::MapI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Map::MapI - Interface for describing Map objects in bioperl 
+
+=head1 SYNOPSIS
+
+    # get a MapI somehowe
+    my $name   = $map->name();     # string
+    my $length = $map->length();   # integer
+    my $species= $map->species;    # Bio::Species
+    my $type   = $map->type();     # genetic/sts/rh/
+
+=head1 DESCRIPTION
+
+This object describes the basic functionality of a Map in bioperl.
+Maps are anything from Genetic Map to Sequence Map to and Assembly Map
+to Restriction Enzyme to FPC.
+
+=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
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]            - General discussion
+http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+Lincoln Stein, [e-mail]
+Heikki Lehvaslaiho, [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::Map::MapI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+use Carp;
+
+@ISA = qw(Bio::Root::RootI);
+
+=head2 species
+
+ Title   : species
+ Usage   : my $species = $map->species;
+ Function: Get/Set Species for a map
+ Returns : L<Bio::Species> object
+ Args    : (optional) Bio::Species
+
+=cut
+
+sub species{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 units
+
+ Title   : units
+ Usage   : $map->units('cM');
+ Function: Get/Set units for a map
+ Returns : units for a map
+ Args    : units for a map (string)
+
+=cut
+
+sub units{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 type
+
+ Title   : type
+ Usage   : my $type = $map->type
+ Function: Get/Set Map type
+ Returns : String coding map type
+ Args    : (optional) string
+
+=cut
+
+sub type {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 name
+
+ Title   : name
+ Usage   : my $name = $map->name
+ Function: Get/Set Map name
+ Returns : Map name
+ Args    : (optional) string
+
+=cut
+
+sub name {
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 length
+
+ Title   : length
+ Usage   : my $length = $map->length();
+ Function: Retrieves the length of the map, 
+           It is possible for the length to be unknown
+           for maps such as Restriction Enzyme, will return undef
+           in that case
+ Returns : integer representing length of map in current units
+           will return undef if length is not calculateable
+ Args    : none
+
+=cut
+
+sub length{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 unique_id
+
+ Title   : unique_id
+ Usage   : my $id = $map->unique_id;
+ Function: Get/Set the unique ID for this map
+ Returns : a unique identifier
+ Args    : [optional] new identifier to set 
+
+=cut
+
+sub unique_id{
+   my ($self,$id) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 add_element
+
+ Title   : add_element
+ Usage   : $map->add_element($marker)
+ Function: Add a Bio::Map::MappableI object to the Map
+ Returns : none
+ Args    : Bio::Map::MappableI object
+
+=cut
+
+sub add_element{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 each_element
+
+ Title   : each_element
+ Usage   : my @elements = $map->each_element;
+ Function: Retrieves all the elements in a map
+           unordered
+ Returns : Array of Map elements (L<Bio::Map::MarkerI>)
+ Args    :
+
+
+=cut
+
+sub each_element{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+1;