Bio::Map::MarkerI - Interface for basic marker functionality
Give standard usage here
Describe the interface here
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Email jason@bioperl.org
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Heikki Lehvaslaiho heikki@ebi.ac.uk Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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
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
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
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
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
Title : get_position_class Usage : my $pos = $marker->get_position_object(); Function: To get an object of the default Position class for this Marker. Subclasses should redefine this method. The Position needs to be L<Bio::Map::PositionI>. Returns : L<Bio::Map::PositionI> Args : none
Title : tuple Usage : ($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
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
Title : equals Usage : if( $mappable->equals($mapable2)) ... Function: Test if a position is equal to another position Returns : boolean Args : Bio::Map::MappableI
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
Title : greater_than Usage : if( $mappable->greater_than($m2) ) ... Function: Tests if position is greater than another position Returns : boolean Args : Bio::Map::MappableI
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.