/ 
bioperl-1.0.2
/ Bio::Map::MarkerI

NAME

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

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the interface here

FEEDBACK

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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 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