my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);

  @coords = $trmapper->cdna2genomic( 123, 554 );

  @coords = $trmapper->genomic2cdna( 141, 500, -1 );

  @coords = $trmapper->genomic2cds( 141, 500, -1 );

  @coords = $trmapper->pep2genomic( 10, 60 );

  @coords = $trmapper->genomic2pep( 123, 400, 1 );

  my $transcript = shift;

  my $mapper = Bio::EnsEMBL::Mapper->new( 'cdna', 'genomic');

  my $edits_on = $transcript->edits_enabled();
  my @edits;

  if($edits_on) {
    @edits = @{$transcript->get_all_SeqEdits()};
    @edits = sort {$a->start() <=> $b->start()} @edits;
  }

  my $edit_shift = 0;

  my $cdna_start = undef;
  my $cdna_end   = 0;

  foreach my $ex (@{$transcript->get_all_Exons}) {
    my $gen_start = $ex->start();
    my $gen_end   = $ex->end();

    $cdna_start = $cdna_end + 1;
    $cdna_end   = $cdna_start + $ex->length() - 1;

    my $strand = $ex->strand();

    # add deletions and insertions into pairs when SeqEdits turned on
    # ignore mismatches (i.e. treat as matches)
    if($edits_on) {
      while(@edits && $edits[0]->start() + $edit_shift <= $cdna_end) {

        my $edit = shift(@edits);
        my $len_diff = $edit->length_diff();

        if($len_diff) {
          # break pair into two parts, finish first pair just before edit

          my $prev_cdna_end   = $edit->start() + $edit_shift - 1;
          my $prev_cdna_start = $cdna_start;
          my $prev_len        = $prev_cdna_end - $prev_cdna_start + 1;

          my $prev_gen_end;
          my $prev_gen_start;
          if($strand == 1) {
            $prev_gen_start = $gen_start;
            $prev_gen_end   = $gen_start + $prev_len - 1;
          } else {
            $prev_gen_start = $gen_end - $prev_len + 1;
            $prev_gen_end   = $gen_end;
          }

          if($prev_len > 0) { # only create map pair if not boundary case
            $mapper->add_map_coordinates
              ('cdna', $prev_cdna_start, $prev_cdna_end, $strand,
               'genome', $prev_gen_start,$prev_gen_end);
          }

          $cdna_start = $prev_cdna_end  + 1;

          if($strand == 1) {
            $gen_start  = $prev_gen_end + 1;
          } else {
            $gen_end    = $prev_gen_start - 1;
          }

          $cdna_end  += $len_diff;

          if($len_diff > 0) {
            # insert in cdna, shift cdna coords along
            $cdna_start += $len_diff;
          } else {
            # delete in cdna (insert in genomic), shift genomic coords along

            if($strand == 1) {
              $gen_start  -= $len_diff;
            } else {
              $gen_end    += $len_diff;
            }
          }

          $edit_shift += $len_diff;
        }
      }
    }

    my $pair_len = $cdna_end - $cdna_start + 1;

    if($pair_len > 0) {
      $mapper->add_map_coordinates('cdna', $cdna_start, $cdna_end, $strand,
                                   'genome', $gen_start, $gen_end);
    }
  }

  return $mapper;

  my ($self,$start,$end) = @_;

  if( !defined $end ) {
    throw("Must call with start/end");
  }

  my $mapper = $self->{'exon_coord_mapper'};

  return $mapper->map_coordinates( 'cdna', $start, $end, 1, "cdna" );

  my ($self, $start, $end, $strand) = @_;

  unless(defined $start && defined $end && defined $strand) {
    throw("start, end and strand arguments are required\n");
  }

  my $mapper = $self->{'exon_coord_mapper'};

  return $mapper->map_coordinates("genome", $start, $end, $strand,"genomic");

 my ($self, $start, $end, $strand) = @_;

 if(!defined($start) || !defined($end) || !defined($strand)) {
   throw("start, end and strand arguments are required");
 }

 if($start > $end + 1) {
   throw("start arg must be less than or equal to end arg + 1");
 }

 my $cdna_cstart = $self->{'cdna_coding_start'};
 my $cdna_cend   = $self->{'cdna_coding_end'};

 #this is a pseudogene if there is no coding region
 if(!defined($cdna_cstart)) {
   #return a gap of the entire requested region, there is no CDS
   return Bio::EnsEMBL::Mapper::Gap->new($start,$end);
 }

 my @coords = $self->genomic2cdna($start, $end, $strand);

 my @out;

 foreach my $coord (@coords) {
   if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
     push @out, $coord;
   } else {
     my $start = $coord->start;
     my $end   = $coord->end;

     if($coord->strand == -1 || $end < $cdna_cstart || $start > $cdna_cend) {
       #is all gap - does not map to peptide
       push @out, Bio::EnsEMBL::Mapper::Gap->new($start,$end);
     } else {
       #we know area is at least partially overlapping CDS
	
       my $cds_start = $start - $cdna_cstart + 1;
       my $cds_end   = $end   - $cdna_cstart + 1;

       if($start < $cdna_cstart) {
         #start of coordinates are in the 5prime UTR
         push @out, Bio::EnsEMBL::Mapper::Gap->new($start, $cdna_cstart-1);

         #start is now relative to start of CDS
         $cds_start = 1;
       }
	
       my $end_gap = undef;
       if($end > $cdna_cend) {
         #end of coordinates are in the 3prime UTR
         $end_gap = Bio::EnsEMBL::Mapper::Gap->new($cdna_cend + 1, $end);
         #adjust end to relative to CDS start
         $cds_end = $cdna_cend - $cdna_cstart + 1;
       }

       #start and end are now entirely in CDS and relative to CDS start
       $coord->start($cds_start);
       $coord->end($cds_end);

       push @out, $coord;

       if($end_gap) {
         #push out the region which was in the 3prime utr
         push @out, $end_gap;
       }
     }	
   }
 }

 return @out;

 my ($self, $start, $end, $strand) = @_;

 unless(defined $start && defined $end && defined $strand) {
   throw("start, end and strand arguments are required");
 }

 my @coords = $self->genomic2cds($start, $end, $strand);

 my @out;

 my $start_phase = $self->{'start_phase'};

 #take into account possible N padding at beginning of CDS
 my $shift = ($start_phase > 0) ? $start_phase : 0;

 foreach my $coord (@coords) {
   if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
     push @out, $coord;
   } else {

     #start and end are now entirely in CDS and relative to CDS start

     #convert to peptide coordinates
     my $pep_start = int(($coord->start + $shift + 2) / 3);
     my $pep_end   = int(($coord->end   + $shift + 2) / 3);
     $coord->start($pep_start);
     $coord->end($pep_end);

     push @out, $coord;
   }	
 }

 return @out;
}


1;

  my $caller = shift;
  my $transcript = shift;

  my $class = ref($caller) || $caller;

  if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
    throw("Transcript argument is required.");
  }

  # Create a cdna <-> genomic mapper and load it with exon coords
  my $mapper = _load_mapper($transcript);

  my $exons = $transcript->get_all_Exons();
  my $start_phase;
  if(@$exons) {
    $start_phase = $exons->[0]->phase;
  } else {
    $start_phase = -1;
  }

  my $self = bless({'exon_coord_mapper' => $mapper,
                    'start_phase'       => $start_phase,
                    'cdna_coding_start' => $transcript->cdna_coding_start(),
                    'cdna_coding_end'   => $transcript->cdna_coding_end()},
                   $class);

  my ($self,$start,$end) = @_;

  if( !defined $end ) {
    throw("Must call with start/end");
  }

  # move start end into translate cDNA coordinates now.
  # much easier!
  $start = 3* $start-2 + ($self->{'cdna_coding_start'} - 1);
  $end   = 3* $end + ($self->{'cdna_coding_start'} - 1);

  return $self->cdna2genomic( $start, $end );

  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>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.