NAME

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

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the interface here

FEEDBACK

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  bioperl-l@bioperl.org              - General discussion
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Reporting Bugs

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://bioperl.org/bioperl-bugs/

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