#
# BioPerl module for Bio::MapIO
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::MapIO - A Map Factory object
=head1 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
}
}
=head1 DESCRIPTION
This is the Factory object for reading Maps from a data stream or file.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::MapIO;
use strict;
use base qw(Bio::Root::Root Bio::Root::IO Bio::Factory::MapFactoryI);
=head2 new
Title : new
Usage : my $obj = Bio::MapIO->new();
Function: Builds a new Bio::MapIO object
Returns : Bio::MapIO
Args :
=cut
sub new {
my($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::MapIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
'mapmaker';
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return unless( $class->_load_format_module($format) );
return "Bio::MapIO::$format"->new(@args);
}
}
=head2 format
Title : format
Usage : $format = $stream->format()
Function: Get the map format
Returns : map format
Args : none
=cut
# format() method inherited from Bio::Root::IO
=head2 Bio::Factory::MapFactoryI methods
=cut
=head2 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
=head2 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>
=cut
=head2 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>
=cut
sub attach_EventHandler{
my ($self,$handler) = @_;
return if( ! $handler );
if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
}
$self->{'_handler'} = $handler;
return;
}
=head2 _eventHandler
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : L<Bio::Event::EventHandlerI>
Args : none
=cut
sub _eventHandler{
my ($self) = @_;
return $self->{'_handler'};
}
sub _initialize {
my($self, @args) = @_;
$self->{'_handler'} = undef;
# initialize the IO part
$self->_initialize_io(@args);
# $self->attach_EventHandler(Bio::MapIO::MapEventBuilder->new());
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL MapIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::MapIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the MapIO system please see the MapIO docs.
This includes ways of checking for formats at compile time, not run time
END
;
}
return $ok;
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'mapmaker' if /\.(map)$/i;
return 'mapxml' if /\.(xml)$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
1;