Bio::Map SimpleMap
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Summary
Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map
Package variables
No package variables defined.
Inherit
Bio::Map::MapI Bio::Root::Root
Synopsis
    use Bio::Map::SimpleMap;
my $map = Bio::Map::SimpleMap->new(-name => 'genethon', -type => 'Genetic', -units=> 'cM', -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); } foreach my $marker ($map->get_elements) { # do something with this Bio::Map::MappableI }
Description
This is the basic implementation of a Bio::Map::MapI. It handles the
essential storage of name, species, type, and units.
It knows which map elements (mappables) belong to it, and their
position.
Subclasses might need to redefine or hardcode type(), length() and
units().
Methods
BEGIN Code
newDescriptionCode
speciesDescriptionCode
unitsDescriptionCode
typeDescriptionCode
nameDescriptionCode
lengthDescriptionCode
unique_idDescriptionCode
add_elementDescriptionCode
get_elementsDescriptionCode
purge_elementDescriptionCode
annotationDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Map::SimpleMap->new();
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)
-uid => Unique Id [defaults to a unique integer]
speciescodeprevnextTop
 Title   : species
Usage : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Taxon object or string
Args : (optional) Bio::Taxon or string
unitscodeprevnextTop
 Title   : units
Usage : $map->units('cM');
Function: Get/Set units for a map
Returns : units for a map
Args : units for a map (string)
typecodeprevnextTop
 Title   : type
Usage : my $type = $map->type
Function: Get/Set Map type
Returns : String coding map type
Args : (optional) string
namecodeprevnextTop
 Title   : name
Usage : my $name = $map->name
Function: Get/Set Map name
Returns : Map name
Args : (optional) string
lengthcodeprevnextTop
 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 0 in that case.
Returns : integer representing length of map in current units
will return 0 if length is not calculateable
Args : none
unique_idcodeprevnextTop
 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
add_elementcodeprevnextTop
 Title   : add_element
Usage : $map->add_element($element)
Function: Tell a Bio::Map::MappableI object its default Map is this one; same
as calling $element->default_map($map).
*** does not actually add the element to this map! *** Returns : none Args : Bio::Map::MappableI object Status : Deprecated, will be removed in next version
get_elementscodeprevnextTop
 Title   : get_elements
Usage : my @elements = $map->get_elements;
Function: Retrieves all the elements on a map (unordered unless all elements
have just 1 position on the map, in which case sorted)
Returns : Array of Map elements (Bio::Map::MappableI)
Args : none
purge_elementcodeprevnextTop
 Title   : purge_element
Usage : $map->purge_element($element)
Function: Purge an element from the map.
Returns : none
Args : Bio::Map::MappableI object
annotationcodeprevnextTop
 Title   : annotation
Usage : $map->annotation($an_col);
my $an_col = $map->annotation();
Function: Get the annotation collection (see Bio::AnnotationCollectionI)
for this annotatable object.
Returns : a Bio::AnnotationCollectionI implementing object, or undef
Args : none to get, OR
a Bio::AnnotationCollectionI implementing object to set
Methods code
BEGINTop
BEGIN {
 $MAPCOUNT = 1;
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

  $self->{'_name'}     = '';
  $self->{'_species'}  = '';
  $self->{'_units'}    = '';
  $self->{'_type'}    = '';
  $self->{'_uid'} = $MAPCOUNT++;
  my ($name, $type,$species, $units,$uid) = $self->_rearrange([qw(NAME TYPE
					      SPECIES UNITS
					      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);
    
  return $self;
}
speciesdescriptionprevnextTop
sub species {
   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_species'} = $value;
   }
   return $self->{'_species'};
}
unitsdescriptionprevnextTop
sub units {
   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_units'} = $value;
   }
   return $self->{'_units'};
}
typedescriptionprevnextTop
sub type {
   my ($self,$value) = @_;
   # this may be hardcoded/overriden by subclasses
if( defined $value ) { $self->{'_type'} = $value; } return $self->{'_type'};
}
namedescriptionprevnextTop
sub name {
   my ($self,$value) = @_;
   if( defined $value ) {
       $self->{'_name'} = $value;
   }
   return $self->{'_name'};
}
lengthdescriptionprevnextTop
sub length {
	my $self = shift;
    
	my $len = 0;
    foreach my $element ($self->get_elements) {
        foreach my $pos ($element->get_positions($self)) {
            if ($pos->value) {
                $len = $pos->end if $pos->end > $len;
            }
        }
	}
    
	return $len;
}
unique_iddescriptionprevnextTop
sub unique_id {
   my ($self,$id) = @_;
   if( defined $id ) {
       $self->{'_uid'} = $id;
   }
   return $self->{'_uid'};
}
add_elementdescriptionprevnextTop
sub add_element {
    my ($self, $element) = @_;
    return unless $element;
	
    $self->throw("This is not a Bio::Map::MappableI object but a [$element]")
	unless $element->isa('Bio::Map::MappableI');
	
    $element->default_map($self);
}
get_elementsdescriptionprevnextTop
sub get_elements {
	my $self = shift;
	
    my @elements = $self->SUPER::get_elements;
    
	# for backward compatability with MapIO tests, and for 'niceness', when
# there is only 1 position per element we will return the elements in
# order, as long as the positions have values set
my $only_1 = 1; foreach my $element (@elements) { my @positions = $element->get_positions($self); if (@positions > 1 || (@positions == 1 && ! $positions[0]->value)) { $only_1 = 0; } } if ($only_1) { @elements = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [${[$_->get_positions($self)]}[0]->sortable, $_] } @elements; } return @elements;
}
purge_elementdescriptionprevnextTop
sub purge_element {
    my ($self, $element) = @_;
    $self->throw("Must supply an argument") unless $element;
    $self->throw("This is [$element], not an object") unless ref($element);
    $self->throw("This is [$element], not a Bio::Map::MappableI object") unless $element->isa('Bio::Map::MappableI');
	
	$self->purge_positions($element);
}
annotationdescriptionprevnextTop
sub annotation {
    my $self = shift;
    if (@_) { $self->{_annotation} = shift }
    return $self->{_annotation} || return;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Lincoln Stein lstein@cshl.org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
each_elementTop
 Title   : each_element
Function: Synonym of the get_elements() method.
Status : deprecated, will be removed in the next version