Bio::Map::MarkerI(3)

NAME
Bio::Map::MarkerI - Interface for basic marker functionality

SYNOPSIS
Give standard usage here

DESCRIPTION
Describe the interface here

FEEDBACK

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AUTHOR - Jason Stajich
Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS
Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com

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

  name($new_name)
 Title   : name($new_name)
 Usage   : my $name = $o_usat->name($new_name) _or_
           my $name = $o_usat->name()
 Function: Get/Set the name for this Marker
 Returns : A scalar representing the current name of this Marker
 Args    : If provided, the current name of this Marker
           will be set to $new_name.

  add_position
 Title   : add_position
 Usage   : $position->add_position($map,'100')
 Function: Add a numeric or string position to the PositionI container
 Returns : none
 Args    : Map - Reference to Bio::Map::MapI
           String or Numeric coding for a position on a map

  each_position
 Title   : positions
 Usage   : my @positions = $position->each_position_value('mapname');
 Function: Retrieve a list of positions coded as strings or ints
 Returns : Array of position values
 Args    : none

  purge_positions
 Title   : purge_positions
 Usage   : $position->purge_positions
 Function: Remove all the position values stored for a Marker
 Returns : none
 Args    : [optional] only purge values for a given map

  known_maps
 Title   : known_maps
 Usage   : my @maps = $marker->known_maps
 Function: Returns the list of maps that this position has values for
 Returns : list of Bio::Map::MapI unique ids
 Args    : none

  in_map
 Title   : in_map
 Usage   : if ( $position->in_map($map) ) {}
 Function: Tests if a position has values in a specific map
 Returns : boolean
 Args    : a map unique id OR Bio::Map::MapI

  get_position_object
 Title   : get_position_class
 Usage   : my $pos = $marker->get_position_object();
 Function: To get an object of the default Position class
           for this Marker. Subclasses should redefine this method.
           The Position needs to be L<Bio::Map::PositionI>.
 Returns : L<Bio::Map::PositionI>
 Args    : none

  tuple
 Title   : tuple
 Usage   : ($me, $you) = $self->_tuple($compare)
 Function: Utility method to extract numbers and test for missing values.
           Makes writing subsequent tests easier.
 Returns : a tuple of values or ranges
 Args    : Bio::Map::MappableI or Bio::Map::PositionI

  Bio::Map::MappableI methods

  position
 Title   : position
 Usage   : my position_string = $position->position('mapname');
 Function: Get/Set method for single value positions.
           Gives a simplified interface when only one map and
           one position per marker is used.
 Returns : a position value
 Args    : optional:
           Map - Reference to Bio::Map::MapI
           String or Numeric coding for a position on a map

  equals
 Title   : equals
 Usage   : if( $mappable->equals($mapable2)) ...
 Function: Test if a position is equal to another position
 Returns : boolean
 Args    : Bio::Map::MappableI

  less_than
 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

  greater_than
 Title   : greater_than
 Usage   : if( $mappable->greater_than($m2) ) ...
 Function: Tests if position is greater than another position
 Returns : boolean
 Args    : Bio::Map::MappableI