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Bio::MapIO.3pm

NAME

Bio::MapIO - A Map Factory object

SYNOPSIS

     use Bio::MapIO;
     my $mapio = Bio::MapIO->new(-format => "mapmaker",
                                -file   => "mapfile.map");
 
     while( my $map = $mapio->next_map ) { 
         # get each map
         foreach my $marker ( $map->each_element ) {
             # loop through the markers associated with the map
         }
     }
 
 

DESCRIPTION

This is the Factory object for reading Maps from a data stream or file.

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 the web:

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

AUTHOR - Jason Stajich

Email jason@bioperl.org

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::MapIO->new();
  Function: Builds a new Bio::MapIO object 
  Returns : Bio::MapIO
  Args    :
 
 

Bio::Factory::MapFactoryI methods

next_map

  Title   : next_tree
  Usage   : my $map = $factory->next_map;
  Function: Get a map from the factory
  Returns : L<Bio::Map::MapI>
  Args    : none
 
 

write_map

  Title   : write_tree
  Usage   : $factory->write_map($map);
  Function: Write a map out through the factory
  Returns : none
  Args    : L<Bio::Map::MapI>
 
 

attach_EventHandler

  Title   : attach_EventHandler
  Usage   : $parser->attatch_EventHandler($handler)
  Function: Adds an event handler to listen for events
  Returns : none
  Args    : L<Bio::Event::EventHandlerI>
 
 

_eventHandler

  Title   : _eventHandler
  Usage   : private
  Function: Get the EventHandler
  Returns : L<Bio::Event::EventHandlerI>
  Args    : none
 
 

_load_format_module

  Title   : _load_format_module
  Usage   : *INTERNAL MapIO stuff*
  Function: Loads up (like use) a module at run time on demand
  Example :
  Returns :
  Args    :
 
 

_guess_format

  Title   : _guess_format
  Usage   : $obj->_guess_format($filename)
  Function:
  Example :
  Returns : guessed format of filename (lower case)
  Args    :