Ewan Birney

NAME

Bio::MapIO - A Map Factory object

SYNOPSIS

    use Bio::MapIO;
    my $mapio = new Bio::MapIO(-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/MailList.shtml  - About the mailing lists

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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 = new Bio::MapIO();
 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    :