Bio MapIO
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::MapIO - A Map Factory object
Package variables
No package variables defined.
Inherit
Bio::Factory::MapFactoryI Bio::Root::IO Bio::Root::Root
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.
Methods
newDescriptionCode
attach_EventHandlerDescriptionCode
_eventHandlerDescriptionCode
_initialize
No description
Code
_load_format_moduleDescriptionCode
_guess_formatDescriptionCode
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = Bio::MapIO->new();
 Function: Builds a new Bio::MapIO object 
 Returns : Bio::MapIO
 Args    :
attach_EventHandlercodeprevnextTop
 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::Event::EventHandlerI
_eventHandlercodeprevnextTop
 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::Event::EventHandlerI
 Args    : none
_load_format_modulecodeprevnextTop
 Title   : _load_format_module
 Usage   : *INTERNAL MapIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :
_guess_formatcodeprevnextTop
 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
Methods code
newdescriptionprevnextTop
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::$format"->new(@args);
    }
}
attach_EventHandlerdescriptionprevnextTop
sub attach_EventHandler {
    my ($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'} = $handler;
    return;
}
_eventHandlerdescriptionprevnextTop
sub _eventHandler {
   my ($self) = @_;
   return $self->{'_handler'};
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;
    $self->{'_handler'} = undef;
    
    # initialize the IO part
    $self->_initialize_io(@args);
#    $self->attach_EventHandler(Bio::MapIO::MapEventBuilder->new());
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($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;
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'mapmaker'   if /\.(map)$/i;
   return 'mapxml' if /\.(xml)$/i;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
formatTop
 Title   : format
 Usage   : $format = $stream->format()
 Function: Get the map format
 Returns : map format
 Args    : none
Bio::Factory::MapFactoryI methodsTop
next_mapTop
 Title   : next_tree
 Usage   : my $map = $factory->next_map;
 Function: Get a map from the factory
 Returns : Bio::Map::MapI
 Args    : none
write_mapTop
 Title   : write_tree
 Usage   : $factory->write_map($map);
 Function: Write a map out through the factory
 Returns : none
 Args    : Bio::Map::MapI