Bio::Map MapI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Map::MapI - Interface for describing Map objects in bioperl
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Carp
Inherit
Bio::Root::RootI
Synopsis
    # get a MapI somehowe
    my $name   = $map->name();     # string
    my $length = $map->length();   # integer
    my $species= $map->species;    # Bio::Species
    my $type   = $map->type();     # genetic/sts/rh/
Description
This object describes the basic functionality of a Map in bioperl.
Maps are anything from Genetic Map to Sequence Map to and Assembly Map
to Restriction Enzyme to FPC.
Methods
speciesDescriptionCode
unitsDescriptionCode
typeDescriptionCode
nameDescriptionCode
lengthDescriptionCode
unique_idDescriptionCode
add_elementDescriptionCode
each_elementDescriptionCode
Methods description
speciescode    nextTop
 Title   : species
 Usage   : my $species = $map->species;
 Function: Get/Set Species for a map
 Returns : Bio::Species object
 Args    : (optional) Bio::Species
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 undef
           in that case
 Returns : integer representing length of map in current units
           will return undef 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   : $map->add_element($marker)
 Function: Add a Bio::Map::MappableI object to the Map
 Returns : none
 Args    : Bio::Map::MappableI object
each_elementcodeprevnextTop
 Title   : each_element
 Usage   : my @elements = $map->each_element;
 Function: Retrieves all the elements in a map
           unordered
 Returns : Array of Map elements (Bio::Map::MarkerI)
 Args    :
Methods code
speciesdescriptionprevnextTop
sub species {
   my ($self) = @_;
   $self->throw_not_implemented();
}
unitsdescriptionprevnextTop
sub units {
   my ($self) = @_;
   $self->throw_not_implemented();
}
typedescriptionprevnextTop
sub type {
   my ($self) = @_;
   $self->throw_not_implemented();
}
namedescriptionprevnextTop
sub name {
   my ($self) = @_;
   $self->throw_not_implemented();
}
lengthdescriptionprevnextTop
sub length {
   my ($self) = @_;
   $self->throw_not_implemented();
}
unique_iddescriptionprevnextTop
sub unique_id {
   my ($self,$id) = @_;
   $self->throw_not_implemented();
}
add_elementdescriptionprevnextTop
sub add_element {
   my ($self) = @_;
   $self->throw_not_implemented();
}
each_elementdescriptionprevnextTop
sub each_element {
   my ($self) = @_;
   $self->throw_not_implemented();
}
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/MailList.shtml  - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _