Bio::Map MappableI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Map::MappableI - An object that can be placed in a map
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Carp
Inherit
Bio::Root::RootI
Synopsis
    # get a Bio::Map::MappableI somehow
    my $position = $element->map_position();
    # these methods will be important for building sorted lists
    if( $position->equals($p2) ) {
	# do something
    } elsif( $position->less_tha($p2) ) {} 
      elsif( $position->greater_than($p2) ) { }
Description
This object handles the generic notion of an element placed on a
(linear) Map. Elements can have multiple positions in a map such as
is the case of Restriction enzyme cut sites on a sequence map. For
exact information about an element's position in a map one must query
the associate PositionI object which is accessible through the
position() method.
Methods
positionDescriptionCode
equalsDescriptionCode
less_thanDescriptionCode
greater_thanDescriptionCode
Methods description
positioncode    nextTop
 Title   : position
 Usage   : my $position = $mappable->position(); 
 Function: Get/Set the Bio::Map::PositionI for a mappable element
 Returns : Bio::Map::PositionI
 Args    : (optional) Bio::Map::PositionI
equalscodeprevnextTop
 Title   : equals
 Usage   : if( $mappable->equals($mapable2)) ...
 Function: Test if a position is equal to another position
 Returns : boolean
 Args    : Bio::Map::MappableI or Bio::Map::PositionI
less_thancodeprevnextTop
 Title   : less_than
 Usage   : if( $mappable->less_than($m2) ) ...
 Function: Tests if a position is less than another position
 Returns : boolean
 Args    : Bio::Map::MappableI or Bio::Map::PositionI
greater_thancodeprevnextTop
 Title   : greater_than
 Usage   : if( $mappable->greater_than($m2) ) ...
 Function: Tests if position is greater than another position
 Returns : boolean
 Args    : Bio::Map::MappableI or Bio::Map::PositionI
Methods code
positiondescriptionprevnextTop
sub position {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
equalsdescriptionprevnextTop
sub equals {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
less_thandescriptionprevnextTop
sub less_than {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
greater_thandescriptionprevnextTop
sub greater_than {
   my ($self,@args) = @_;
   $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
Heikki Lehvaslaiho heikki@ebi.ac.uk
Lincoln Stein lstein@cshl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _