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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/LinkageMap.pm	Thu Apr 11 02:01:53 2013 -0400
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+# BioPerl module for Bio::Map::LinkageMap
+#
+# Cared for by Chad Matsalla <[e-mail]>
+#
+# Copyright Chad Matsalla
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Map::LinkageMap - A representation of a genetic linkage map.
+
+=head1 SYNOPSIS
+
+    use Bio::Map::LinkageMap;
+	# create a new map
+    my $map = new Bio::Map::LinkageMap(-name => 'Chads Superterriffic Map',
+                                      -type => 'Linkage',
+                                      -units=> 'cM');
+	# create the location of a marker for that map
+    my $position = new Bio::Map::LinkagePosition( -positions => 1,
+                -distance => "22.3");
+	# create a marker and place it at that position
+    my $marker = new Bio::Map::Marker::Microsatellite(
+			-name => 'SuuuperMarker',
+			-position => $position);
+	# place that marker on that map
+    $map->add_element($marker);
+
+	# done!
+
+=head1 DESCRIPTION
+
+This object describes the basic functionality of a genetic linkage map in
+Bioperl. Each 'position' can have one or more markers that map some number of
+units from the markers at the previous position.
+
+=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 - Chad Matsalla
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+Lincoln Stein       [e-mail]
+Heikki Lehvaslaiho  [e-mail]
+Jason Stajich       [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::LinkageMap;
+use vars qw(@ISA);
+use strict;
+use Bio::Map::SimpleMap;
+
+@ISA = qw(Bio::Map::SimpleMap);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $linkage_map = new Bio::Map::LinkageMap();
+ Function: Builds a new Bio::Map::LinkageMap object
+ Returns : Bio::Map::LinkageMap
+ Args    : -name    => the name of the map (string) [optional]
+	   -type    => the type of this map (string, defaults to Linkage) [optional]
+           -species => species for this map (Bio::Species) [optional]
+           -units   => the map units (string, defaults to cM) [optional]
+           -elements=> elements to initialize with
+                       (arrayref of Bio::Map::MappableI objects) [optional]
+
+          -uid      => Unique ID of this map
+=cut
+
+# new provided by SimpleMap
+
+
+
+=head2 length()
+
+ Title   : length()
+ Usage   : my $length = $map->length();
+ Function: Retrieves the length of the map. In the case of a LinkageMap, the
+	   length is the sum of all marker distances.
+ Returns : An integer representing the length of this LinkageMap. Will return
+	   undef if length is not calculateable
+ Args    : None.
+
+
+=cut
+
+sub length {
+    my ($self) = @_;
+    my $total_distance;
+    foreach (@{$self->{'_elements'}}) {
+	if ($_) {
+	    $total_distance += ($_->position()->each_position_value($self))[0];
+	}
+    }
+    return $total_distance;
+}
+
+=head2 add_element($marker)
+
+ Title   : add_element($marker)
+ Usage   : $map->add_element($marker)
+ Function: Add a Bio::Map::MappableI object to the Map
+ Returns : none
+ Args    : Bio::Map::MappableI object
+ Notes   : It is strongly recommended that you use a
+	   Bio::Map::LinkagePosition as the position in any
+	   Bio::Map::Mappable that you create to place on this
+	   map. Using some other Bio::Map::Position might work but might
+	   be unpredictable.
+           N.B. I've added Bio::Map::OrderedPosition which should achieve
+                similar things from LinkagePosition and will work for
+                RH markers too.
+=cut
+
+#'
+sub _add_element {
+    my ($self,$marker) = @_;
+
+    my $o_position = $marker->position();
+
+    $self->debug( "marker position is ". $marker->position());
+#     print("add_element: \$o_position is $o_position\n");
+#     print("add_element: \$marker is $marker\n");
+
+    my $position;
+    unless ( $o_position->isa('Bio::Map::LinkagePosition') ||
+	     $o_position->isa('Bio::Map::OrderedPosition')
+	     ) {
+	$self->warn("You really should use a Linkage Position for this object. This insures that there is only one position. Trying anyway...");	
+	my @p = ( $o_position->each_position_value($self));
+	$position = shift @p;
+	if( ! defined $position ) {
+	    $self->throw("This marker ($marker) does not have a position in this map ($self)");
+	}
+    } else {
+	$position = $o_position->order;
+    }
+
+    if ($self->{'_elements'}[$position]) {
+	$self->warn("Replacing the marker in position $position because in a linkage map the position is a key.");
+    }	
+    $self->{'_elements'}[$position] = $marker;
+}
+
+=head2 each_element
+
+ Title   : each_element
+ Usage   : my @elements = $map->each_element;
+ Function: Retrieves all the elements in a map
+           _ordered_.
+ Returns : An array containing MappableI objects.
+ Args    : None.
+ Notes   : This is a useless concept in the context of a linkage map but is
+	included if you want a list of all of the marker names on the map.
+
+=cut
+
+sub each_element {
+    my ($self) = @_;
+    return @{$self->{'_elements'}};
+}
+
+=head2 implemented by Bio::Map::SimpleMap
+
+=cut
+
+=head2 name($new_name)
+
+ Title   : name($new_name)
+ Usage   : my $name = $map->name($new_name) _or_
+	   my $length = $map->name()
+ Function: Get/set the name of the map.
+ Returns : The current name of the map.
+ Args    : If provided, the name of the map is set to $new_name.
+
+=head2 species
+
+ Title   : species
+ Usage   : my $species = $map->species;
+ Function: Get/Set Species for a map
+ Returns : Bio::Species object
+ Args    : (optional) Bio::Species
+
+
+=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)
+
+
+=head2 type
+
+ Title   : type
+ Usage   : my $type = $map->type
+ Function: Get/Set Map type
+ Returns : String coding map type
+ Args    : (optional) string
+
+=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
+
+1;