Summary

Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map

Package variables

Included modules

Inherit

Bio::Map::MapI Bio::Root::Root

Synopsis

    use Bio::Map::SimpleMap;
    my $map = new Bio::Map::SimpleMap(-name => 'genethon',
				      -type => 'Genetic',
				      -units=> 'cM',
				      -species => $human);
    foreach my $marker ( @markers ) { # get a list of markers somewhere
	$map->add_element($marker);
    }

Description

This is the basic implementation of a 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.
Subclasses might need to redefine or hardcode type(), length() and
units().

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Map::SimpleMap();
 Function: Builds a new Bio::Map::SimpleMap object
 Returns : Bio::Map::SimpleMap
 Args    : -name    => name of map (string)
           -species => species for this map (Bio::Species) [optional]
           -units   => map units (string)
           -elements=> elements to initialize with
                       (arrayref of Bio::Map::MappableI objects) [optional]

           -uid     => Unique Id

 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

 Title   : units
 Usage   : $map->units('cM');
 Function: Get/Set units for a map
 Returns : units for a map
 Args    : units for a map (string)

 Title   : type
 Usage   : my $type = $map->type
 Function: Get/Set Map type
 Returns : String coding map type
 Args    : (optional) string

 Title   : name
 Usage   : my $name = $map->name
 Function: Get/Set Map name
 Returns : Map name
 Args    : (optional) string

 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

 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

 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

 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

Methods code

BEGIN {

 $MAPCOUNT = 1;

}

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  $self->{'_elements'} = [];
  $self->{'_name'}     = '';
  $self->{'_species'}  = '';
  $self->{'_units'}    = '';
  $self->{'_type'}    = '';
  $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;

}

sub species {

   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_species'} = $value;
   }
   return $self->{'_species'};

}

sub units {

   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_units'} = $value;
   }
   return $self->{'_units'};

}

sub type {

   my ($self,$value) = @_;
   # this may be hardcoded/overriden by subclasses

   if( defined $value ) {
       $self->{'_type'} = $value;
   }
   return $self->{'_type'};

}

sub name {

   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_name'} = $value;
   }
   return $self->{'_name'};

}

sub length {

   my ($self) = @_;
   my ($len ) = 0;

   foreach my $marker ($self->each_element) {
       $len = $marker->position->numeric if  $marker->position->numeric > $len;
   }
   return $len;

}

sub unique_id {

   my ($self,$id) = @_;
   if( defined $id ) {
       $self->{'_uid'} = $id;
   }
   return $self->{'_uid'};

}

sub add_element {

    my ($self,$mapelement) = @_;
    return unless ( defined $mapelement);

    $self->throw("This is not a Bio::Map::MarkerI object but a [$self]")
	unless $mapelement->isa('Bio::Map::MarkerI');

    $mapelement->map($self);	# tell the marker its default map

    push @{$self->{'_elements'}}, $mapelement;

}

sub each_element {

   my ($self) = @_;
   return @{$self->{'_elements'}};

}

General documentation

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

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/

Email jason@bioperl.org

Heikki Lehvaslaiho heikki@ebi.ac.uk
Lincoln Stein lstein@cshl.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _