Bio::Map
MarkerI
Summary
Bio::Map::MarkerI - Interface for basic marker functionality
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Give standard usage here
Description
Describe the interface here
Methods
Methods description
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 : 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 = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position needs to be Bio::Map::PositionI.
Returns : Bio::Map::PositionI
Args : none |
Title : tuple
Usage : ($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 = $position->position('mapname');
Function: Get/Set method for single value positions.
Gives a simplified interface when only one map and
one position per marker is used.
Returns : a position value
Args : optional:
Map - Reference to Bio::Map::MapI
String or Numeric coding for a position on a map |
Methods code
sub name
{ my ($self) = @_;
$self->throw_not_implemented();} | sub add_position
{ my ($self,$map,$value) = @_;
$self->throw_not_implemented(); } | sub each_position
{ my ($self,$mapname) = @_;
$self->throw_not_implemented(); } | sub purge_position_values
{ my ($self, $map) = @_;
$self->throw_not_implemented(); } | sub known_maps
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub in_map
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub get_position_object
{ my ($self) = @_;
$self->throw_not_implemented();} | sub tuple
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub position
{ my ($self,$map, $value) = @_;
$self->throw_not_implemented(); } | General documentation
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
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 | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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
| Bio::Map::MappableI methods | Top |
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