ProbeAlign documentation.

    use Bio::EnsEMBL::Analysis::Config::Funcgen::ProbeAlign;

This contains the configuration for step 2 of the
process which maps probes to a Genome. This step
is an alignment of probes (dna) against a genome (dna)
using exonerate. So this config looks very similar to that
of any other exonerate-driving config.
The layout of the configuration is a set of hashes,
each one keyed by logic name. There is also a DEFAULT hash,
which is used as the default for all logic names.
There are genomic and transcript based logic names and config
hashes for each discrete format of array.

sub import {

  my ($callpack) = caller(0);	# Name of the calling package
  my $pack = shift;				# Need to move package off @_

  # Get list of variables supplied, or else everything
  my @vars = @_ ? @_ : keys( %Config );
  return unless @vars;
  
  # Predeclare global variables in calling package
  eval "package $callpack; use vars qw("
    . join(' ', map { '$'.$_ } @vars) . ")";
  die $@ if $@;


  foreach (@vars) {
	if ( defined $Config{$_} ) {
	  no strict 'refs';
	  # Exporter does a similar job to the following
	  # statement, but for function names, not
	  # scalar variables:
	  *{"${callpack}::$_"} =\$ Config{ $_ };
	} else {
	  die "Error: Config: $_ not known\n";
	}
  }
}

1;

}