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 / 
bioperl-db-0.1
/ Bio::DB::Map::Map

NAME

Bio::DB::Map::Map - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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/MailList.shtml - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track 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@chg.mc.duke.edu

Describe contact details here

APPENDIX

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

get_markers_for_region

 Title   : get_markers_for_region
 Usage   : my @markers = $map->get_markers_for_region('-start' => $start,
                                                      '-end'   => $end);
 Function: returns a list of markers for this map that fall between
           start and end in this map\'s units.  Omitting 'start' will
           default to the beginning of the map, omitting 'end' will
           default to the end of map.
 Returns : List of Bio::DB::Map::MarkerI objects
 Args    : -start => starting point or region (in units of this map)
           -end   => ending point of region (in units of this map)
           -chrom => chromosome [1,22,X,Y]

get_next_marker

 Title   : get_next_marker
 Usage   : my $marker = $map->get_next_marker(-marker    => $marker,
                                              -direction => 1);
 Function: returns the next marker in the map based on the given marker
           and either a positive or negative direction
 Returns : Bio::DB::Map::MarkerI object or undef 
 Args    : -marker    => $marker Bio::DB::Map::MarkerI object to start with
           -direction => [1,-1]
           -number    => number of markers to retrieve

chrom_length

 Title   : chrom_length
 Usage   : my $len = $map->chrom_length()
 Function: Returns the length of a chromosome in a Map in the map\'s units
 Returns : float
 Args    : none

Get/Set Methods

id

 Title   : id
 Usage   : $obj->id($newval)
 Function: 
 Example : 
 Returns : value of id
 Args    : newvalue (optional)

name

 Title   : name
 Usage   : $obj->name($newval)
 Function: 
 Example : 
 Returns : value of name
 Args    : newvalue (optional)

units

 Title   : units
 Usage   : $obj->units($newval)
 Function: 
 Example : 
 Returns : value of units
 Args    : newvalue (optional)

adaptor

 Title   : adaptor
 Usage   : $obj->adaptor($newval)
 Function: 
 Example : 
 Returns : value of adaptor
 Args    : newvalue (optional)