Raw content of Bio::Map::CytoMap # $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 <heikki@ebi.ac.uk> # # 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. bioperl-l@bioperl.org - 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: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Heikki Lehvaslaiho Email heikki@ebi.ac.uk =head1 CONTRIBUTORS Jason Stajich jason@bioperl.org Lincoln Stein lstein@cshl.org =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;