Bio
MapIO
Summary
Bio::MapIO - A Map Factory object
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::MapIO();
Function: Builds a new Bio::MapIO object
Returns : Bio::MapIO
Args : |
Title : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::Event::EventHandlerI |
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 : |
Methods code
sub new
{ my($caller,@args) = @_;
my $class = ref($caller) || $caller;
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;
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
'mapmaker';
$format = "\L$format";
return undef unless( $class->_load_format_module($format) );
return "Bio::MapIO::$format"->new(@args);
} } | sub attach_EventHandler
{ my ($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'} = $handler;
return;} | sub _eventHandler
{ my ($self) = @_;
return $self->{'_handler'};} | sub _initialize
{ my($self, @args) = @_;
$self->{'_handler'} = undef;
$self->_initialize_io(@args);
} | sub _load_format_module
{ my ($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;} | 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();} | General documentation
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
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://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::Factory::MapFactoryI methods | Top |
Title : next_tree
Usage : my $map = $factory->next_map;
Function: Get a map from the factory
Returns : Bio::Map::MapI
Args : none
Title : write_tree
Usage : $factory->write_map($map);
Function: Write a map out through the factory
Returns : none
Args : Bio::Map::MapI