Bio::Map::SimpleMap.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Map::SimpleMap - A MapI implementation handling the basics of a Map

SYNOPSIS

     use Bio::Map::SimpleMap;
 
     my $map = Bio::Map::SimpleMap->new(-name => 'genethon',
                                       -type => 'Genetic',
                                       -units=> 'cM',
                                       -species => $human);
 
     foreach my $marker ( @markers ) { # get a list of markers somewhere
                 $map->add_element($marker);
     }
 
     foreach my $marker ($map->get_elements) {
         # do something with this Bio::Map::MappableI
     }
 
 

DESCRIPTION

This is the basic implementation of a Bio::Map::MapI. It handles the essential storage of name, species, type, and units.

It knows which map elements (mappables) belong to it, and their position.

Subclasses might need to redefine or hardcode type(), length() and units().

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.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Sendu Bala bix@sendu.me.uk

APPENDIX

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

new

  Title   : new
  Usage   : my $obj = Bio::Map::SimpleMap->new();
  Function: Builds a new Bio::Map::SimpleMap object
  Returns : Bio::Map::SimpleMap
  Args    : -name    => name of map (string)
            -species => species for this map (Bio::Species) [optional]
            -units   => map units (string)
            -uid     => Unique Id [defaults to a unique integer]
 
 

species

  Title   : species
  Usage   : my $species = $map->species;
  Function: Get/Set Species for a map
  Returns : Bio::Taxon object or string
  Args    : (optional) Bio::Taxon or string
 
 

units

  Title   : units
  Usage   : $map->units('cM');
  Function: Get/Set units for a map
  Returns : units for a map
  Args    : units for a map (string)
 
 

type

  Title   : type
  Usage   : my $type = $map->type
  Function: Get/Set Map type
  Returns : String coding map type
  Args    : (optional) string
 
 

name

  Title   : name
  Usage   : my $name = $map->name
  Function: Get/Set Map name
  Returns : Map name
  Args    : (optional) string
 
 

length

  Title   : length
  Usage   : my $length = $map->length();
  Function: Retrieves the length of the map.
            It is possible for the length to be unknown for maps such as
            Restriction Enzyme, will return 0 in that case.
  Returns : integer representing length of map in current units
            will return 0 if length is not calculateable
  Args    : none
 
 

unique_id

  Title   : unique_id
  Usage   : my $id = $map->unique_id;
  Function: Get/Set the unique ID for this map
  Returns : a unique identifier
  Args    : [optional] new identifier to set
 
 

add_element

  Title   : add_element
  Usage   : $map->add_element($element)
  Function: Tell a Bio::Map::MappableI object its default Map is this one; same
            as calling $element->default_map($map).
 
                    *** does not actually add the element to this map! ***
 
  Returns : none
  Args    : Bio::Map::MappableI object
  Status  : Deprecated, will be removed in next version
 
 

get_elements

  Title   : get_elements
  Usage   : my @elements = $map->get_elements;
  Function: Retrieves all the elements on a map (unordered unless all elements
            have just 1 position on the map, in which case sorted)
  Returns : Array of Map elements (L<Bio::Map::MappableI>)
  Args    : none
 
 

each_element

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

purge_element

  Title   : purge_element
  Usage   : $map->purge_element($element)
  Function: Purge an element from the map.
  Returns : none
  Args    : Bio::Map::MappableI object
 
 

annotation

  Title   : annotation
  Usage   : $map->annotation($an_col);
            my $an_col = $map->annotation();
  Function: Get the annotation collection (see Bio::AnnotationCollectionI)
            for this annotatable object.
  Returns : a Bio::AnnotationCollectionI implementing object, or undef
  Args    : none to get, OR
            a Bio::AnnotationCollectionI implementing object to set