diff variant_effect_predictor/Bio/Map/MarkerI.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/MarkerI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,256 @@
+# $Id: MarkerI.pm,v 1.9 2002/10/22 07:45:15 lapp Exp $
+#
+# BioPerl module for Bio::Map::MarkerI
+#
+# 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::MarkerI - Interface for basic marker functionality
+
+=head1 SYNOPSIS
+
+Give standard usage here
+
+=head1 DESCRIPTION
+
+Describe the interface here
+
+=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]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Heikki Lehvaslaiho [e-mail]
+Lincoln Stein      [e-mail]
+Jason Stajich      [e-mail]
+Chad Matsalla      [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::MarkerI;
+use vars qw(@ISA);
+use strict;
+use Bio::Map::MappableI;
+
+@ISA = qw(Bio::Map::MappableI);
+
+=head2 name($new_name)
+
+ Title   : name($new_name)
+ Usage   : my $name = $o_usat->name($new_name) _or_
+	   my $name = $o_usat->name()
+ Function: Get/Set the name for this Marker
+ Returns : A scalar representing the current name of this Marker
+ Args    : If provided, the current name of this Marker
+	   will be set to $new_name.
+
+=cut
+
+sub name {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 add_position
+
+ Title   : add_position
+ Usage   : $position->add_position($map,'100')
+ Function: Add a numeric or string position to the PositionI container
+ Returns : none
+ Args    : Map - Reference to Bio::Map::MapI 
+           String or Numeric coding for a position on a map
+
+=cut
+
+sub add_position{
+   my ($self,$map,$value) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 each_position
+
+ Title   : positions
+ Usage   : my @positions = $position->each_position_value('mapname');
+ Function: Retrieve a list of positions coded as strings or ints 
+ Returns : Array of position values 
+ Args    : none
+
+=cut
+
+sub each_position {
+   my ($self,$mapname) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 purge_positions
+
+ Title   : purge_positions
+ Usage   : $position->purge_positions
+ Function: Remove all the position values stored for a Marker
+ Returns : none
+ Args    : [optional] only purge values for a given map
+
+=cut
+
+sub purge_position_values{
+   my ($self, $map) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 known_maps
+
+ Title   : known_maps
+ Usage   : my @maps = $marker->known_maps
+ Function: Returns the list of maps that this position has values for
+ Returns : list of Bio::Map::MapI unique ids
+ Args    : none
+
+=cut
+
+sub known_maps{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 in_map
+
+ Title   : in_map
+ Usage   : if ( $position->in_map($map) ) {}
+ Function: Tests if a position has values in a specific map
+ Returns : boolean
+ Args    : a map unique id OR Bio::Map::MapI
+
+
+=cut
+
+sub in_map{
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 get_position_object
+
+ Title   : get_position_class
+ Usage   : my $pos = $marker->get_position_object();
+ Function: To get an object of the default Position class
+           for this Marker. Subclasses should redefine this method.
+           The Position needs to be L<Bio::Map::PositionI>.
+ Returns : L<Bio::Map::PositionI>
+ Args    : none
+
+=cut
+
+sub get_position_object {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+
+=head2 tuple
+
+ Title   : tuple
+ Usage   : ($me, $you) = $self->_tuple($compare)
+ Function: Utility method to extract numbers and test for missing values.
+           Makes writing subsequent tests easier.
+ Returns : a tuple of values or ranges
+ Args    : Bio::Map::MappableI or Bio::Map::PositionI
+
+=cut
+
+sub tuple {
+   my ($self,@args) = @_;
+   $self->throw_not_implemented();
+}
+
+
+=head2 Bio::Map::MappableI methods
+
+=cut
+
+
+=head2 position
+
+ Title   : position
+ Usage   : my position_string = $position->position('mapname');
+ Function: Get/Set method for single value positions. 
+           Gives a simplified interface when only one map and 
+           one position per marker is used.
+ Returns : a position value
+ Args    : optional:
+           Map - Reference to Bio::Map::MapI 
+           String or Numeric coding for a position on a map
+
+=cut
+
+sub position{
+   my ($self,$map, $value) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 equals
+
+ Title   : equals
+ Usage   : if( $mappable->equals($mapable2)) ...
+ Function: Test if a position is equal to another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI
+
+=head2 less_than
+
+ Title   : less_than
+ Usage   : if( $mappable->less_than($m2) ) ...
+ Function: Tests if a position is less than another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI
+
+=head2 greater_than
+
+ Title   : greater_than
+ Usage   : if( $mappable->greater_than($m2) ) ...
+ Function: Tests if position is greater than another position
+ Returns : boolean
+ Args    : Bio::Map::MappableI
+
+=cut
+
+1;