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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Map/CytoMap.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,230 @@
+# $Id: CytoMap.pm,v 1.2 2002/10/22 07:45:15 lapp Exp $
+#
+# BioPerl module for Bio::Map::CytoMap
+#
+# Cared for by Heikki Lehvaslaiho <[e-mail]>
+#
+# Copyright Heikki Lehvaslaiho
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Map::CytoMap - A Bio::MapI compliant map implementation handling cytogenic bands 
+
+=head1 SYNOPSIS
+
+    use Bio::Map::CytoMap;
+    my $map = new Bio::Map::CytoMap(-name => 'human1',
+				      -species => $human);
+    foreach my $marker ( @markers ) { # get a list of markers somewhere
+	$map->add_element($marker);
+    }
+
+=head1 DESCRIPTION
+
+This is the simple implementation of cytogenetic maps based on
+L<Bio::Map::MapI>.  It handles the essential storage of name, species,
+type, and units as well as in memory representation of the elements of
+a map.
+
+For CytoMaps type is hard coded to be 'cytogeneticmap' and
+units are set to '' but can be set to something else.
+
+=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 - Heikki Lehvaslaiho
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+Jason Stajich      [e-mail]
+Lincoln Stein      [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::CytoMap;
+use vars qw(@ISA $MAPCOUNT);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::Root::Root;
+use Bio::Map::SimpleMap;
+
+@ISA = qw(Bio::Root::Root Bio::Map::SimpleMap);
+BEGIN { $MAPCOUNT = 1; }
+
+=head2 Modified methods 
+
+All methods present in L<Bio::Map::SimpleMap> are implemted by this
+class. Most of the methods are inherited from SimpleMap. The following
+methods have been modified to refelect the needs of cytogenetic maps.
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Map::CytoMap();
+ Function: Builds a new Bio::Map::CytoMap object
+ Returns : Bio::Map::CytoMap
+ Args    : -name    => name of map (string)
+           -species => species for this map (Bio::Species) [optional]
+           -elements=> elements to initialize with
+                       (arrayref of Bio::Map::MappableI objects) [optional]
+
+           -uid     => Unique Id
+=cut
+
+sub new {
+    my($class,@args) = @_;
+
+    my $self = $class->SUPER::new(@args);
+
+    $self->{'_elements'} = [];
+    $self->{'_name'}     = '';
+    $self->{'_species'}  = '';
+    $self->{'_units'}    = '';
+    $self->{'_type'}    = 'cyto';
+    $self->{'_uid'} = $MAPCOUNT++;
+    my ($name, $type,$species, $units,
+	$elements,$uid) = $self->_rearrange([qw(NAME TYPE
+						SPECIES UNITS
+						ELEMENTS UID)], @args);
+    defined $name     && $self->name($name);
+    defined $species  && $self->species($species);
+    defined $units    && $self->units($units);
+    defined $type     && $self->type($type);
+    defined $uid      && $self->unique_id($uid);
+
+    if( $elements && ref($elements) =~ /array/ ) {
+	foreach my $item ( @$elements ) {
+	    $self->add_element($item);
+	}
+    }
+    return $self;
+}
+
+=head2 type
+
+ Title   : type
+ Usage   : my $type = $map->type
+ Function: Get hard-coded  Map type
+ Returns : String coding map type
+ Args    : 
+
+=cut
+
+sub type {
+   my ($self) = @_;
+   return $self->{'_type'};
+}
+
+
+=head2 length
+
+ Title   : length
+ Usage   : my $length = $map->length();
+ Function: Retrieves the length of the map,
+ Returns : undef since length is not calculatable for 
+           cytogenetic maps
+ Args    : none
+
+=cut
+
+sub length{
+   my ($self,@args) = @_;
+   return undef;
+}
+
+=head2 Methods inherited from L<Bio::Map::SimpleMap>
+
+=cut
+
+=head2 species
+
+ Title   : species
+ Usage   : my $species = $map->species;
+ Function: Get/Set Species for a map
+ Returns : Bio::Species object or string
+ Args    : (optional) Bio::Species or string
+
+=cut
+
+=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
+
+=head2 name
+
+ Title   : name
+ Usage   : my $name = $map->name
+ Function: Get/Set Map name
+ Returns : Map name
+ Args    : (optional) string
+
+=cut
+
+=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
+
+=head2 each_element
+
+ Title   : each_element
+ Usage   : my @elements = $map->each_element;
+ Function: Retrieves all the elements in a map
+           unordered
+ Returns : Array of Bio::Map::MappableI objects
+ Args    : none
+
+
+=cut
+
+=head2 New methods
+
+=cut
+
+
+1;