Bio::MapIO(3pm) User Contributed Perl Documentation 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:
https://redmine.open-bio.org/projects/bioperl/
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 :
perl v5.14.2 2012-03-02 Bio::MapIO(3pm)