my $self = shift;
	my ($all_transcripts) = @_;
	my $gaps = 0;
	my @sorted_transcripts = sort {$a->start <=> $b->start || $b->end <=> $a->end} @{$all_transcripts};
	my $first_transcript = shift @sorted_transcripts;
	my $pos = $first_transcript->end;
	foreach my $transcript (@sorted_transcripts) {
		next if ($transcript->end < $pos );
		if ($transcript->start < $pos && $transcript->end > $pos ) {
			$pos = $transcript->end;			
			next;
		}
		elsif ($transcript->end > $pos) {
			$gaps++;
			$pos = $transcript->end;
		}
	}
	return $gaps;

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

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  <helpdesk@ensembl.org>.