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://github.com/bioperl/bioperl-live/issues
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 :
Title : format
Usage : $format = $stream->format()
Function: Get the map format
Returns : map format
Args : none
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
Title : _load_format_module
Usage : *INTERNAL MapIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :