Bio::Map::MappableI(3pm)

NAME

Bio::Map::MappableI - An object that can be placed in a map

SYNOPSIS

    # do not use this module directly
    # See Bio::Map::Mappable for an example of
    # implementation.

DESCRIPTION

This object handles the generic notion of an element placed on a (linear) Map. A Mappable can have multiple positions in multiple maps, such as is the case of Restriction enzyme cut sites on sequence maps. For exact information about a mappable's position in a map one must query the associate PositionI objects which are accessible through the get_positions() method.

FEEDBACK

Mailing Lists

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email [email protected]

CONTRIBUTORS

Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein [email protected] Sendu Bala [email protected]

APPENDIX

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

EntityI methods

 These are fundamental to coordination of Mappables and other entities, so are
 implemented at the interface level

get_position_handler

 Title   : get_position_handler
 Usage   : my $position_handler = $entity->get_position_handler();
 Function: Gets a PositionHandlerI that $entity is registered with.
 Returns : Bio::Map::PositionHandlerI object
 Args    : none

PositionHandlerI-related methods

 These are fundamental to coordination of Mappables and other entities, so are
 implemented at the interface level

add_position

 Title   : add_position
 Usage   : $mappable->add_position($position);
 Function: Add a position to this mappable (defining where on which map it is).
 Returns : n/a
 Args    : L<Bio::Map::PositionI> object

get_positions

 Title   : get_positions
 Usage   : my @positions = $mappable->get_positions();
 Function: Get all the Positions of this Mappable (sorted).
 Returns : Array of L<Bio::Map::PositionI> objects
 Args    : none for all, OR
           L<Bio::Map::MapI> object for positions on the given map, AND/OR some
           other true value to avoid sorting

each_position

 Title   : each_position
 Function: Synonym of the get_positions() method.
 Status  : deprecated, will be removed in next version

purge_positions

 Title   : purge_positions
 Usage   : $mappable->purge_positions();
 Function: Remove positions from this mappable.
 Returns : n/a
 Args    : none to remove all positions, OR
           L<Bio::Map::PositionI> object to remove just that Position, OR
                   L<Bio::Map::MapI> object to remove only those positions on the given
                   map

known_maps

 Title   : known_maps
 Usage   : my @maps = $marker->known_maps()
 Function: Returns the maps that this mappable is found on
 Returns : Array of L<Bio::Map::MapI> objects
 Args    : none

MappableI-specific methods

name

 Title   : name
 Usage   : my $name = $marker->name();
           $marker->name($new_name);
 Function: Get/Set the name for this Mappable.
 Returns : A scalar representing the current name of this Mappable
 Args    : none to get
           string to set

id

 Title   : id
 Usage   : my $id = $marker->id();
           $marker->id($new_id);
 Function: Get/Set the id for this Mappable.
 Returns : A scalar representing the current id of this Mappable
 Args    : none to get
           string to set

in_map

 Title   : in_map
 Usage   : if ($marker->in_map($map)) {...}
 Function: Tests if this mappable is found on a specific map
 Returns : boolean
 Args    : L<Bio::Map::MapI>

RangeI-related Methods

They throw an error if start and end are not defined in the Positions of the Mappables supplied.

equals

 Title   : equals
 Usage   : if ($mappable->equals($other_mappable)) {...}
           my @equal_positions = $mappable->equals($other_mappable);
 Function: Finds the positions in this mappable that are equal to any
           comparison positions.
 Returns : array of L<Bio::Map::PositionI> objects
 Args    : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
                    this one to (mandatory)
           arg #2 = optionally, the key => value pairs below
                   -map => Bio::Map::MapI           : optionally a Map to only consider
                                                      positions on the given map
                   -relative => Bio::Map::RelativeI : optionally a Relative to ask if
                                                                                          the Positions equal in terms of
                                                                                          their relative position to the
                                                                                          thing described by that Relative

overlaps

 Title   : overlaps
 Usage   : if ($mappable->overlaps($other_mappable)) {...}
           my @overlapping_positions = $mappable->overlaps($other_mappable);
 Function: Finds the positions in this mappable that overlap with any
           comparison positions.
 Returns : array of L<Bio::Map::PositionI> objects
 Args    : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
                    this one to (mandatory)
           arg #2 = optionally, the key => value pairs below
                   -map => Bio::Map::MapI           : optionally a Map to only consider
                                                      positions on the given map
                   -relative => Bio::Map::RelativeI : optionally a Relative to ask if
                                              the Positions overlap in terms of
                                              their relative position to the
                                              thing described by that Relative

contains

 Title   : contains
 Usage   : if ($mappable->contains($other_mappable)) {...}
           my @container_positions = $mappable->contains($other_mappable);
 Function: Finds the positions in this mappable that contain any comparison
           positions.
 Returns : array of L<Bio::Map::PositionI> objects
 Args    : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
                    this one to (mandatory)
           arg #2 = optionally, the key => value pairs below
                   -map => Bio::Map::MapI           : optionally a Map to only consider
                                                      positions on the given map
                   -relative => Bio::Map::RelativeI : optionally a Relative to ask if
                                              the Positions contains in terms of
                                              their relative position to the
                                              thing described by that Relative

intersection

 Title   : intersection
 Usage   : my $position = $mappable->intersection($other_mappable);
           my $position = Bio::Map::Mappable->intersection(\@mappables);
 Function: Make the position that is at the intersection of all positions of all
           supplied mappables.
 Returns : L<Bio::Map::PositionI> object or undef (if not all positions overlap)
 Args    : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to  compare
                    this one to, or an array ref of such objects (mandatory)
           arg #2 = optionally, the key => value pairs below
                   -map => Bio::Map::MapI           : optionally a Map to only consider
                                                      positions on the given map
                   -relative => Bio::Map::RelativeI : optionally a Relative to to ask
                                                                                          how the Positions intersect in
                                                                                          terms of their relative position
                                                                                          to the thing described by that
                                                                                          Relative

union

 Title   : union
 Usage   : my $position = $mappable->union($other_mappable);
           my $position = Bio::Map::Mappable->union(@mappables);
 Function: Make the minimal position that contains all of the positions of all
           supplied mappables.
 Returns : L<Bio::Map::PositionI> object or undef (if not all positions overlap)
 Args    : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to  compare
                    this one to, or an array ref of such objects (mandatory)
           arg #2 = optionally, the key => value pairs below
                   -map => Bio::Map::MapI           : optionally a Map to only consider
                                                      positions on the given map
                   -relative => Bio::Map::RelativeI : optionally a Relative to to ask
                                                                                          if the union of the Positions in
                                                                                          terms of their relative position
                                                                                          to the thing described by that
                                                                                          Relative