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Summary

Bio::MapIO::mapmaker - A Mapmaker Map reader

Package variables

Included modules

Inherit

Bio::MapIO

Synopsis

# do not use this object directly it is accessed through the Bio::MapIO system

    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 object contains code for parsing and processing Mapmaker output
and creating Bio::Map::MapI objects from it.

Methods

Methods description

 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

Methods code

sub next_map {

   my ($self) = @_;
   my ($ready,$map) = (0,new Bio::Map::SimpleMap('-name'  => '',
						 '-units' => 'cM',
						 '-type'  => 'Genetic'));
   my @markers;
   my $runningDistance = 0;
   while( defined($_ = $self->_readline()) ) {
       if ( $ready || /^\s+Markers\s+Distance/ ) { 
	   unless ( $ready ) { $ready = 1; next }
       } else { next }

       last if ( /-{5,}/); # map terminator is ------- 
       s/ +/\t/;
       my ($number,$name,$distance) = split;
       $runningDistance += $distance;
       $runningDistance = '0.0' if $runningDistance == 0;
#       print "$_|$number-$name-$distance---------";
       my $pos = new Bio::Map::LinkagePosition (-order => $number,
						-map => $map,
						-value => $runningDistance
						);
       my $marker = new Bio::Map::Marker(-name=> $name,
					 -position => $pos,
					 );
       $marker->position($pos);
#       use Data::Dumper; print Dumper($marker); exit;
#       print $marker->position->value, "\n";
#       use Data::Dumper; print Dumper($pos);
#	 $map->add_element(new Bio::Map::Marker('-name'=> $name,
#						'-position' => $pos,
#						));   
   }
#   return undef if( ! $ready );
   return $map;

}

sub write_map {

   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

1;

}

General documentation

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Email jason@bioperl.org
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Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _