=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=cut

=head1 NAME

Bio::EnsEMBL::Transcript - object representing an Ensembl transcript

=head1 SYNOPSIS

Creation:

  my $tran = new Bio::EnsEMBL::Transcript();
  my $tran = new Bio::EnsEMBL::Transcript( -EXONS => \@exons );

Manipulation:

  # Returns an array of Exon objects
  my @exons = @{ $tran->get_all_Exons() };

  # Returns the peptide translation of the exons as a Bio::Seq
  if ( $tran->translation() ) {
    my $pep = $tran->translate();
  } else {
    print "Transcript ", $tran->stable_id(), " is non-coding\n";
  }

=head1 DESCRIPTION

A representation of a transcript within the Ensembl system.  A transcript
consists of a set of Exons and (possibly) a Translation which defines the
coding and non-coding regions of the exons.

=cut

package Bio::EnsEMBL::Transcript;

use strict;

use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::UTR;
use Bio::EnsEMBL::Intron;
use Bio::EnsEMBL::ExonTranscript;
use Bio::EnsEMBL::CDS;
use Bio::EnsEMBL::MANE;
use Bio::EnsEMBL::TranscriptMapper;
use Bio::EnsEMBL::SeqEdit;
use Bio::EnsEMBL::Biotype;
use Bio::EnsEMBL::Utils::Argument qw( rearrange );
use Bio::EnsEMBL::Utils::Exception qw(warning throw );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );

use parent qw(Bio::EnsEMBL::Feature);

use constant SEQUENCE_ONTOLOGY => {
  acc  => 'SO:0000673',
  term => 'transcript',
};

=head2 new

  Arg [-EXONS] :
        reference to list of Bio::EnsEMBL::Exon objects - exons which make up 
        this transcript
  Arg [-STABLE_ID] :
        string - the stable identifier of this transcript
  Arg [-VERSION] :
        int - the version of the stable identifier of this transcript
  Arg [-EXTERNAL_NAME] :
        string - the external database name associated with this transcript
  Arg [-EXTERNAL_DB] :
        string - the name of the database the external name is from
  Arg [-EXTERNAL_STATUS]:
        string - the status of the external identifier
  Arg [-DISPLAY_XREF]:
        Bio::EnsEMBL::DBEntry - The external database entry that is used
        to label this transcript when it is displayed.
  Arg [-CREATED_DATE]:
        string - the date the transcript was created
  Arg [-MODIFIED_DATE]:
        string - the date the transcript was last modified
  Arg [-DESCRIPTION]:
        string - the transcripts description
  Arg [-BIOTYPE]: 
        string - the biotype e.g. "protein_coding"
  Arg [-IS_CURRENT]:
        Boolean - specifies if this is the current version of the transcript
  Arg [-SOURCE]:
        string - the transcript source, e.g. "ensembl"

  Example    : $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons);
  Description: Constructor. Instantiates a Transcript object.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : throw on bad arguments
  Caller     : general
  Status     : Stable

=cut

sub new {
  my $proto = shift;

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

  my $self = $class->SUPER::new(@_);

  my (
    $exons,            $stable_id,    $version,
    $external_name,    $external_db,  $external_status,
    $display_xref,     $created_date, $modified_date,
    $description,      $biotype,      $confidence,
    $external_db_name, $is_current,
    $source
  );

    (
      $exons,            $stable_id,    $version,
      $external_name,    $external_db,  $external_status,
      $display_xref,     $created_date, $modified_date,
      $description,      $biotype,      $confidence,
      $external_db_name, $is_current,
      $source
      )
      = rearrange( [
        'EXONS',            'STABLE_ID',
        'VERSION',          'EXTERNAL_NAME',
        'EXTERNAL_DB',      'EXTERNAL_STATUS',
        'DISPLAY_XREF',     'CREATED_DATE',
        'MODIFIED_DATE',    'DESCRIPTION',
        'BIOTYPE',          'CONFIDENCE',
        'EXTERNAL_DB_NAME',
        'IS_CURRENT',       'SOURCE'
      ],
      @_
      );

  if ($exons) {
    $self->{'_trans_exon_array'} = $exons;
    $self->recalculate_coordinates();
  }

  $self->stable_id($stable_id);
  $self->{'created_date'}  = $created_date;
  $self->{'modified_date'} = $modified_date;
  $self->external_name($external_name) if ( defined $external_name );
  $self->external_db($external_db)     if ( defined $external_db );
  $self->external_status($external_status)
    if ( defined $external_status );
  $self->display_xref($display_xref) if ( defined $display_xref );
  $self->edits_enabled(1);

  $self->description($description);

  $self->{'biotype'} = $biotype;

  $self->source($source);

  # Default version
  if ( !defined($version) ) { $version = 1 }
  $self->{'version'} = $version;

  # default is_current
  $is_current = 1 unless ( defined($is_current) );
  $self->{'is_current'} = $is_current;

  return $self;
} ## end sub new

=head2 get_all_DBLinks

  Arg [1]    : String database name (optional)
               SQL wildcard characters (_ and %) can be used to
               specify patterns.

  Arg [2]    : (optional) String, external database type, can be one of
               ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
               SQL wildcard characters (_ and %) can be used to
               specify patterns.

  Example    : my @dblinks = @{ $transcript->get_all_DBLinks() };
               @dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };}
               @dblinks = @{ $transcript->get_all_DBLinks('%', 'ENSEMBL') };

  Description: Retrieves *all* related DBEntries for this
               transcript.  This includes all DBEntries that are
               associated with the corresponding translation.

               If you only want to retrieve the DBEntries associated
               with the transcript (and not the translation) then
               you should use the get_all_DBEntries() call instead.

               Note: Each entry may be listed more than once.  No
               uniqueness checks are done.  Also if you put in an
               incorrect external database name no checks are done
               to see if this exists, you will just get an empty
               list.

  Return type: Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_DBLinks {
  my ( $self, $db_name_exp, $ex_db_type ) = @_;

  my @links =
    @{ $self->get_all_DBEntries( $db_name_exp, $ex_db_type ) };

  # Add all of the transcript and translation xrefs to the return list.
  my $translation = $self->translation();
  if ( defined($translation) ) {
    push( @links,
          @{$translation->get_all_DBEntries( $db_name_exp, $ex_db_type ) }
    );
  }

  @links = sort { _compare_xrefs() } @links;

  return \@links;
}

=head2 get_all_xrefs

  Arg [1]    : String database name (optional)
               SQL wildcard characters (_ and %) can be used to
               specify patterns.

  Example    : @xrefs = @{ $transcript->get_all_xrefs() };
               @xrefs = @{ $transcript->get_all_xrefs('Uniprot%') };

  Description: Retrieves *all* related xrefs for this transcript.
               This includes all xrefs that are associated with the
               corresponding translation of this transcript.

               If you want to retrieve the xrefs associated with
               only the transcript (and not the translation) then
               you should use the get_all_object_xrefs() method
               instead.

               Note: Each entry may be listed more than once.  No
               uniqueness checks are done.  Also if you put in an
               incorrect external database name no checks are done
               to see if this exists, you will just get an empty
               list.

                NB: This method is an alias for the
                    get_all_DBLinks() method.

  Return type: Listref of Bio::EnsEMBL::DBEntry objects

  Status     : Stable

=cut

sub get_all_xrefs {
  my $self = shift;
  return $self->get_all_DBLinks(@_);
}

=head2 get_all_DBEntries

  Arg [1]    : (optional) String, external database name,
               SQL wildcard characters (_ and %) can be used to
               specify patterns.

  Arg [2]    : (optional) String, external database type, can be one of
               ('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
               SQL wildcard characters (_ and %) can be used to
               specify patterns.

  Example    : my @dbentries = @{ $transcript->get_all_DBEntries() };
               @dbentries = @{ $transcript->get_all_DBEntries('Uniprot%') };}
               @dbentries = @{ $transcript->get_all_DBEntries('%', 'ENSEMBL') };}

  Description: Retrieves DBEntries (xrefs) for this transcript.
               This does *not* include the corresponding
               translations DBEntries (see get_all_DBLinks()).

               This method will attempt to lazy-load DBEntries
               from a database if an adaptor is available and no
               DBEntries are present on the transcript (i.e. they
               have not already been added or loaded).

  Returntype : Listref of Bio::EnsEMBL::DBEntry objects
  Exceptions : none
  Caller     : get_all_DBLinks, TranscriptAdaptor::store
  Status     : Stable

=cut

sub get_all_DBEntries {
  my ( $self, $ex_db_exp, $ex_db_type ) = @_;

  my $cache_name = 'dbentries';

  if ( defined($ex_db_exp) ) {
    $cache_name .= $ex_db_exp;
  }

  if ( defined($ex_db_type) ) {
    $cache_name .= $ex_db_type;
  }

  # if not cached, retrieve all of the xrefs for this transcript
  if ( !defined( $self->{$cache_name} ) && defined( $self->adaptor() ) )
  {
    $self->{$cache_name} =
      $self->adaptor()->db()->get_DBEntryAdaptor()
      ->fetch_all_by_Transcript( $self, $ex_db_exp, $ex_db_type );
  }

  $self->{$cache_name} ||= [];

  return $self->{$cache_name};
} ## end sub get_all_DBEntries

=head2 get_all_object_xrefs

  Arg [1]    : (optional) String, external database name

  Arg [2]    : (optional) String, external_db type

  Example    : @oxrefs = @{ $transcript->get_all_object_xrefs() };

  Description: Retrieves xrefs for this transcript.  This does
               *not* include xrefs that are associated with the
               corresponding translations of this transcript (see
               get_all_xrefs()).

               This method will attempt to lazy-load xrefs from a
               database if an adaptor is available and no xrefs are
               present on the transcript (i.e. they have not already
               been added or loaded).

                NB: This method is an alias for the
                    get_all_DBentries() method.

  Return type: Listref of Bio::EnsEMBL::DBEntry objects

  Status     : Stable

=cut

sub get_all_object_xrefs {
  my $self = shift;
  return $self->get_all_DBEntries(@_);
}

=head2 add_DBEntry

  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
               The dbEntry to be added
  Example    : my $dbe = Bio::EnsEMBL::DBEntery->new(...);
               $transcript->add_DBEntry($dbe);
  Description: Associates a DBEntry with this transcript. Note that adding
               DBEntries will prevent future lazy-loading of DBEntries for this
               gene (see get_all_DBEntries).
  Returntype : none
  Exceptions : thrown on incorrect argument type
  Caller     : general
  Status     : Stable

=cut

sub add_DBEntry {
  my $self = shift;
  my $dbe = shift;

  unless($dbe && ref($dbe) && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
    throw('Expected DBEntry argument');
  }

  $self->{'dbentries'} ||= [];
  push @{$self->{'dbentries'}}, $dbe;
}


=head2 get_all_supporting_features

  Example    : my @evidence = @{ $transcript->get_all_supporting_features };
  Description: Retrieves any supporting features added manually by 
               calls to add_supporting_features.
  Returntype : Listref of Bio::EnsEMBL::FeaturePair objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_supporting_features {
  my $self = shift;

  if( !exists  $self->{_supporting_evidence} )  {
    if($self->adaptor) {
      my $tsfa = $self->adaptor->db->get_TranscriptSupportingFeatureAdaptor();
      $self->{_supporting_evidence} = $tsfa->fetch_all_by_Transcript($self);
    }
  }
  
  return $self->{_supporting_evidence} || [];
}


=head2 add_supporting_features

  Arg [1-N]  : Bio::EnsEMBL::FeaturePair $feature
               The supporting features to add
  Example    : $transcript->add_supporting_features(@features);
  Description: Adds a list of supporting features to this Transcript.
               The added features can be retieved by
               get_all_supporting_features().
  Returntype : none
  Exceptions : throw if any of the features are not FeaturePairs
               throw if any of the features are not in the same coordinate
               system as the Transcript
  Caller     : general
  Status     : Stable
 
=cut
 
sub add_supporting_features {
  my ($self, @features) = @_;

  return unless @features;
 
  $self->{_supporting_evidence} ||= [];
  
  # check whether this feature object has been added already
  FEATURE: foreach my $feature (@features) {

    if (!defined($feature) || ref($feature) eq "ARRAY") {
      throw("Element in transcript supporting features array is undefined or is an ARRAY for " . $self->dbID);
    }
    if (!$feature || !$feature->isa("Bio::EnsEMBL::FeaturePair")) {
      print "feature = " . $feature . "\n";
      throw("Supporting feat [$feature] not a " .
            "Bio::EnsEMBL::FeaturePair");
    } 
    
    if ((defined $self->slice() && defined $feature->slice())&&
      ( $self->slice()->name() ne $feature->slice()->name())){
      throw("Supporting feat not in same coord system as transcript\n" .
            "transcript is attached to [".$self->slice()->name()."]\n" .
            "feat is attached to [".$feature->slice()->name()."]");
    }

    foreach my $added_feature ( @{ $self->{_supporting_evidence} } ){
      # compare objects
      if ( $feature == $added_feature ){
  #this feature has already been added
  next FEATURE;
      }
    }
    
    #no duplicate was found, add the feature
    push(@{$self->{_supporting_evidence}}, $feature);
  }
}


=head2 flush_supporting_features

  Example     : $transcript->flush_supporting_features;
  Description : Removes all supporting evidence from the transcript.
  Return type : (Empty) listref
  Exceptions  : none
  Caller      : general
  Status      : Stable

=cut

sub flush_supporting_features {
  my $self = shift;
  $self->{'_supporting_evidence'} = [];
}


=head2 external_db

  Arg [1]    : (optional) String - name of external db to set
  Example    : $transcript->external_db('HGNC');
  Description: Getter/setter for attribute external_db. The db is the one that 
               belongs to the external_name.  
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub external_db {
  my ( $self, $ext_dbname ) = @_;

  if(defined $ext_dbname) { 
    return ( $self->{'external_db'} = $ext_dbname );
  }

  if( exists $self->{'external_db'} ) {
    return $self->{'external_db'};
  }

  my $display_xref = $self->display_xref();

  if( defined $display_xref ) {
    return $display_xref->dbname()
  } else {
    return undef;
  }
}


=head2 external_status

  Arg [1]    : (optional) String - status of the external db
  Example    : $transcript->external_status('KNOWNXREF');
  Description: Getter/setter for attribute external_status. The status of
               the external db of the one that belongs to the external_name.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub external_status { 
  my ( $self, $ext_status ) = @_;

  if(defined $ext_status) {
    return ( $self->{'external_status'} = $ext_status );
  }

  if( exists $self->{'external_status'} ) {
    return $self->{'external_status'};
  }

  my $display_xref = $self->display_xref();

  if( defined $display_xref ) {
    return $display_xref->status()
  } else {
    return undef;
  }
}


=head2 external_name

  Arg [1]    : (optional) String - the external name to set
  Example    : $transcript->external_name('BRCA2-001');
  Description: Getter/setter for attribute external_name.
  Returntype : String or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub external_name {
  my ($self, $ext_name) = @_;

  if(defined $ext_name) { 
    return ( $self->{'external_name'} = $ext_name );
  }

  if( exists $self->{'external_name'} ) {
    return $self->{'external_name'};
  }

  my $display_xref = $self->display_xref();

  if( defined $display_xref ) {
    return $display_xref->display_id()
  } else {
    return undef;
  }
}

=head2 source

  Arg [1]    : (optional) String - the source to set
  Example    : $transcript->source('ensembl');
  Description: Getter/setter for attribute source
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub source {
  my $self = shift;
  $self->{'source'} = shift if( @_ );
  return ( $self->{'source'} || "ensembl" );
}

=head2 display_xref

  Arg [1]    : (optional) Bio::EnsEMBL::DBEntry - the display xref to set
  Example    : $transcript->display_xref($db_entry);
  Description: Getter/setter for display_xref for this transcript.
  Returntype : Bio::EnsEMBL::DBEntry
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub display_xref {
  my $self = shift;
  $self->{'display_xref'} = shift if(@_);
  return $self->{'display_xref'};
}

=head2 is_canonical

  Args [1]      : (optional) Boolean is_canonical

  Example       : if ($transcript->is_canonical()) { ... }

  Description : Returns true (non-zero) if the transcript is the
                canonical transcript of its gene, false (0) if not. If the code
                returns an undefined it is because its state is not currently
                known. Internally the code will consult the database for this
                value if it is unknown and the transcript has a dbID and an
                attached adaptor

  Return type   : Boolean

  Status        : Stable

=cut

sub is_canonical {
  my ( $self, $value ) = @_;
  
  #Shortcut call
  return $self->{is_canonical} if defined $self->{is_canonical};
  
  if ( defined($value) ) {
    $self->{is_canonical} = ( $value ? 1 : 0 );
  }
  else {
    if(! defined $self->{is_canonical} && $self->dbID() && $self->adaptor()) {
      $self->{is_canonical} = $self->adaptor()->is_Transcript_canonical($self);
    }
  }

  return $self->{is_canonical};
}

=head2 translation

  Args       : None
  Example    : if ( $transcript->translation() ) {
                 print( $transcript->translation()->stable_id(), "\n" );
               } else {
                 print("Pseudogene\n");
               }
  Description: Getter/setter for the Translation object which
               defines the CDS (and as a result the peptide encoded
               by) this transcript.  This function will return
               undef if this transcript is a pseudogene, i.e. a
               non-translating transcript such as an ncRNA.  This
               is the accepted method of determining whether a
               transcript is a pseudogene or not.
  Returntype : Bio::EnsEMBL::Translation
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub translation {
  my ( $self, $translation ) = @_;

  if ( defined($translation) ) {
    assert_ref( $translation, 'Bio::EnsEMBL::Translation' );

    $self->{'translation'} = $translation;
    $translation->transcript($self);

    $self->{'cdna_coding_start'} = undef;
    $self->{'cdna_coding_end'}   = undef;

    $self->{'coding_region_start'} = undef;
    $self->{'coding_region_end'}   = undef;

    $self->{'transcript_mapper'} = undef;

  } elsif ( @_ > 1 ) {
    if ( defined( $self->{'translation'} ) ) {
      # Removing existing translation

      $self->{'translation'}->transcript(undef);
      delete( $self->{'translation'} );

      $self->{'cdna_coding_start'} = undef;
      $self->{'cdna_coding_end'}   = undef;

      $self->{'coding_region_start'} = undef;
      $self->{'coding_region_end'}   = undef;

      $self->{'transcript_mapper'} = undef;
    }
  } elsif (   !exists( $self->{'translation'} )
            && defined( $self->adaptor() ) )
  {
    $self->{'translation'} =
      $self->adaptor()->db()->get_TranslationAdaptor()
      ->fetch_by_Transcript($self);
  }

  return $self->{'translation'};
} ## end sub translation

=head2 get_all_alternative_translations

  Args       : None
  Example    :

    my @alt_translations =
      @{ $transcript->get_all_alternative_translations() };

  Description:  Fetches all alternative translations defined for this
                transcript.  The canonical translation is not returned.

  Returntype : Arrayref to Bio::EnsEMBL::Translation
  Exceptions : None
  Caller     : General
  Status     : Stable

=cut

sub get_all_alternative_translations {
  my ($self) = @_;

  if (   !exists( $self->{'alternative_translations'} )
       && defined( $self->adaptor() ) )
  {
    my $pa = $self->adaptor()->db()->get_TranslationAdaptor();
    my @translations =
      @{ $pa->fetch_all_alternative_by_Transcript($self) };

    $self->{'alternative_translations'} = \@translations;
  }

  return $self->{'alternative_translations'};
}

=head2 add_alternative_translation

  Args       : Bio::EnsEMBL::Translation $translation
  Example    :

    $transcript->add_alternative_translation($translation);

  Description: Adds an alternative translation to this transcript.
  Returntype : None
  Exceptions : None
  Caller     : General
  Status     : Stable

=cut

sub add_alternative_translation {
  my ( $self, $translation ) = @_;

  if ( !(    defined($translation)
          && ref($translation)
          && $translation->isa('Bio::EnsEMBL::Translation') ) )
  {
    throw("Bio::EnsEMBL::Translation argument expected.");
  }

  # Load the existsing alternative translations from the database if
  # they haven't already been loaded.
  $self->get_all_alternative_translations();

  push( @{ $self->{'alternative_translations'} }, $translation );
}

=head2 spliced_seq

  Args       : soft_mask (opt)
               if specified, will return a sequence where UTR regions are lowercased
  Description: Retrieves all Exon sequences and concats them together.
               No phase padding magic is done, even if phases do not align.
  Returntype : Text
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub spliced_seq {
  my ( $self, $soft_mask ) = @_;

  my $seq_string = "";
  for my $ex ( @{$self->get_all_Exons()} ) {
    my $seq = $ex->seq();
    if(!$seq) {
      warning("Could not obtain seq for exon.  Transcript sequence may not " .
              "be correct.");
      $seq_string .= 'N' x $ex->length();
    } else {
      my $exon_seq = $seq->seq();
      if ($soft_mask) {
        my $padstr;
        if (!defined ($ex->coding_region_start($self))) {
          $exon_seq = lc($exon_seq);
        }

        if ($ex->coding_region_start($self) > $ex->start()) {
          my $forward_length = $ex->coding_region_start($self) - $ex->start();
          my $reverse_length = $ex->end() - $ex->coding_region_start($self);
          if ($ex->strand == 1) {
            $exon_seq = lc (substr($exon_seq, 0, $forward_length)) . substr($exon_seq, $forward_length); 
          } else {
            $exon_seq = substr($exon_seq, 0, $reverse_length+1) . lc(substr($exon_seq, $reverse_length+1));
          }
        }

        if ($ex->coding_region_end($self) < $ex->end()) {
          my $forward_length = $ex->coding_region_end($self) - $ex->start();
          my $reverse_length = $ex->end() - $ex->coding_region_end($self);
          if ($ex->strand == 1) {
            $exon_seq = substr($exon_seq, 0, $forward_length+1) . lc(substr($exon_seq, $forward_length+1));
          } else {
            $exon_seq = lc(substr($exon_seq, 0, $reverse_length)) . substr($exon_seq, $reverse_length);
          }
        }
      }
      $seq_string .= $exon_seq;
    }
  }

  # apply post transcriptional edits
  if($self->edits_enabled()) {
    my @seqeds = @{$self->get_all_SeqEdits()};

    # sort edits in reverse order to remove complication of
    # adjusting downstream edits
    @seqeds = sort {$b->start() <=> $a->start()} @seqeds;

    foreach my $se (@seqeds) {
      $se->apply_edit(\$seq_string);
    }
  }

  return $seq_string;
}


=head2 translateable_seq

  Args       : none
  Example    : print $transcript->translateable_seq(), "\n";
  Description: Returns a sequence string which is the the translateable part
               of the transcripts sequence.  This is formed by splicing all
               Exon sequences together and apply all defined RNA edits.
               Then the coding part of the sequence is extracted and returned.
               The code will not support monkey exons any more. If you want to
               have non phase matching exons, defined appropriate _rna_edit
               attributes!

               An empty string is returned if this transcript is a pseudogene
               (i.e. is non-translateable).
  Returntype : Text
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub translateable_seq {
  my ( $self ) = @_;

  if ( !$self->translation() ) {
    return '';
  }

  my $mrna = $self->spliced_seq();

  my $start = $self->cdna_coding_start();
  my $end   = $self->cdna_coding_end();

  $mrna = substr( $mrna, $start - 1, $end - $start + 1 );

  my $start_phase = $self->translation->start_Exon->phase();
  if( $start_phase > 0 ) {
    $mrna = "N"x$start_phase . $mrna;
  }
  if( ! $start || ! $end ) {
    return "";
  }

  return $mrna;
}


=head2 cdna_coding_start

  Arg [1]    : (optional) $value
  Example    : $relative_coding_start = $transcript->cdna_coding_start;
  Description: Retrieves the position of the coding start of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs).

               This will return undef if this is a pseudogene (i.e. a
               transcript with no translation).
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

=cut

sub cdna_coding_start {
  my $self = shift;

  if( @_ ) {
    $self->{'cdna_coding_start'} = shift;
  }

  if(!defined $self->{'cdna_coding_start'} && defined $self->translation){
    # calc coding start relative from the start of translation (in cdna coords)
    my $start = 0;

    my @exons = @{$self->get_all_Exons};
    my $exon;

    while($exon = shift @exons) {
      if($exon == $self->translation->start_Exon) {
        #add the utr portion of the start exon
        $start += $self->translation->start;
        last;
      } else {
        #add the entire length of this non-coding exon
        $start += $exon->length;
      }
    }

    # adjust cdna coords if sequence edits are enabled
    if($self->edits_enabled()) {
      my @seqeds = @{$self->get_all_SeqEdits()};
      if (scalar @seqeds) {
        my $transl_start = $self->get_all_Attributes('_transl_start');
        if (@{$transl_start}) {
          $start = $transl_start->[0]->value;
        } else {
          # sort in reverse order to avoid adjustment of downstream edits
          @seqeds = sort {$b->start() <=> $a->start()} @seqeds;

          foreach my $se (@seqeds) {
            # use less than start so that start of CDS can be extended
            if($se->start() < $start) {
              $start += $se->length_diff();
            }
          }
        }
      }
    }

    $self->{'cdna_coding_start'} = $start;
  }

  return $self->{'cdna_coding_start'};
}


=head2 cdna_coding_end

  Arg [1]    : (optional) $value
  Example    : $cdna_coding_end = $transcript->cdna_coding_end;
  Description: Retrieves the end of the coding region of this transcript in
               cdna coordinates (relative to the five prime end of the
               transcript, excluding introns, including utrs).

               This will return undef if this transcript is a pseudogene
               (i.e. a transcript with no translation and therefor no CDS).
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub cdna_coding_end {
  my $self = shift;

  if( @_ ) {
    $self->{'cdna_coding_end'} = shift;
  }

  if(!defined $self->{'cdna_coding_end'} && defined $self->translation) {
    my @exons = @{$self->get_all_Exons};

    my $end = 0;
    while(my $exon = shift @exons) {
      if($exon == $self->translation->end_Exon) {
        # add coding portion of the final coding exon
        $end += $self->translation->end;
        last;
      } else {
        # add entire exon
        $end += $exon->length;
      }
    }

    # adjust cdna coords if sequence edits are enabled
    if($self->edits_enabled()) {
      my @seqeds = @{$self->get_all_SeqEdits()};
      if (scalar @seqeds) {
        my $transl_end = $self->get_all_Attributes('_transl_end');
        if (@{$transl_end}) {
          $end = $transl_end->[0]->value;
        } else {
          # sort in reverse order to avoid adjustment of downstream edits
          @seqeds = sort {$b->start() <=> $a->start()} @seqeds;

          foreach my $se (@seqeds) {
            # use less than or equal to end+1 so end of the CDS can be extended
            if($se->start() <= $end + 1) {
              $end += $se->length_diff();
            }
          }
        }
      }
    }

    $self->{'cdna_coding_end'} = $end;
  }

  return $self->{'cdna_coding_end'};
}


=head2 coding_region_start

  Arg [1]    : (optional) $value
  Example    : $coding_region_start = $transcript->coding_region_start
  Description: Retrieves the start of the coding region of this transcript
               in genomic coordinates (i.e. in either slice or contig coords).
               By convention, the coding_region_start is always lower than
               the value returned by the coding_end method.
               The value returned by this function is NOT the biological
               coding start since on the reverse strand the biological coding
               start would be the higher genomic value.

               This function will return undef if this is a pseudogene
               (a non-translated transcript).
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub coding_region_start {
  my ($self, $value) = @_;

  if( defined $value ) {
    $self->{'coding_region_start'} = $value;
  } elsif(!defined $self->{'coding_region_start'} &&
    defined $self->translation) {
    #calculate the coding start from the translation
    my $start;
    my $strand = $self->translation()->start_Exon->strand();
    if( $strand == 1 ) {
      $start = $self->translation()->start_Exon->start();
      $start += ( $self->translation()->start() - 1 );
    } else {
      $start = $self->translation()->end_Exon->end();
      $start -= ( $self->translation()->end() - 1 );
    }
    $self->{'coding_region_start'} = $start;
  }

  return $self->{'coding_region_start'};
}


=head2 coding_region_end

  Arg [1]    : (optional) $value
  Example    : $coding_region_end = $transcript->coding_region_end
  Description: Retrieves the end of the coding region of this transcript
               in genomic coordinates (i.e. in either slice or contig coords).
               By convention, the coding_region_end is always higher than the
               value returned by the coding_region_start method.
               The value returned by this function is NOT the biological
               coding end since on the reverse strand the biological coding
               end would be the lower genomic value.

               This function will return undef if this is a pseudogene
               (a non-translated transcript).
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub coding_region_end {
  my ($self, $value ) = @_;

  my $strand;
  my $end;

  if( defined $value ) {
    $self->{'coding_region_end'} = $value;
  } elsif( ! defined $self->{'coding_region_end'}
     && defined $self->translation() ) {
    $strand = $self->translation()->start_Exon->strand();
    if( $strand == 1 ) {
      $end = $self->translation()->end_Exon->start();
      $end += ( $self->translation()->end() - 1 );
    } else {
      $end = $self->translation()->start_Exon->end();
      $end -= ( $self->translation()->start() - 1 );
    }
    $self->{'coding_region_end'} = $end;
  }

  return $self->{'coding_region_end'};
}


=head2 edits_enabled

  Arg [1]    : (optional) boolean $newval
  Example    : $transcript->edits_enabled(1);
  Description: Enables/Disables the application of SeqEdits to this transcript.
               Edits are enabled by default, and affect the cdna/mrna
               sequences coordinates and the resultant translation.
  Returntype : boolean - the current value of the edits
  Exceptions : none
  Caller     : general, cdna_coding_start, cdna_coding_end, length
  Status     : Stable

=cut

sub edits_enabled {
  my ( $self, $boolean ) = @_;

  if ( defined($boolean) ) {
    $self->{'edits_enabled'} = $boolean;

    # flush cached values that will be different with/without edits
    $self->{'cdna_coding_start'} = undef;
    $self->{'cdna_coding_end'}   = undef;
    $self->{'transcript_mapper'} = undef;
  }

  return $self->{'edits_enabled'};
}


=head2 get_all_SeqEdits

  Arg [1]    : none
  Example    : my @seqeds = @{$transcript->get_all_SeqEdits()};
  Description: Retrieves all post transcriptional sequence modifications for
               this transcript.
  Returntype : Bio::EnsEMBL::SeqEdit
  Exceptions : none
  Caller     : spliced_seq()
  Status     : Stable

=cut

sub get_all_SeqEdits {
  my $self = shift;

  my @seqeds;

  my $attribs = $self->get_all_Attributes('_rna_edit');

  # convert attributes to SeqEdit objects
  foreach my $a (@$attribs) {
    push @seqeds, Bio::EnsEMBL::SeqEdit->new(-ATTRIB => $a);
  }

  return \@seqeds;
}


=head2 get_all_Attributes

  Arg [1]    : optional string $attrib_code
               The code of the attribute type to retrieve values for.
  Example    : ($rna_edits) = @{$transcript->get_all_Attributes('_rna_edit')};
               @transc_attributes    = @{$transcript->get_all_Attributes()};
  Description: Gets a list of Attributes of this transcript.
               Optionally just get Attrubutes for given code.
  Returntype : listref Bio::EnsEMBL::Attribute
  Exceptions : warning if transcript does not have attached adaptor and 
               attempts lazy load.
  Caller     : general
  Status     : Stable

=cut

sub get_all_Attributes {
  my $self = shift;
  my $attrib_code = shift;

  if( ! exists $self->{'attributes' } ) {
    if(!$self->adaptor() ) {
      return [];
    }

    my $attribute_adaptor = $self->adaptor->db->get_AttributeAdaptor();
    $self->{'attributes'} = $attribute_adaptor->fetch_all_by_Transcript($self);
  }

  if( defined $attrib_code) {
    my @results = grep { uc($_->code()) eq uc($attrib_code) }
      @{$self->{'attributes'}};
    return \@results;
  } else {
    return $self->{'attributes'};
  }
}


=head2 add_Attributes

  Arg [1...] : Bio::EnsEMBL::Attribute $attribute
               You can have more Attributes as arguments, all will be added.
  Example    : $transcript->add_Attributes($rna_edit_attribute);
  Description: Adds an Attribute to the Transcript. Usefull to do _rna_edits.
               If you add an attribute before you retrieve any from database, 
               lazy load will be disabled.
  Returntype : none
  Exceptions : throw on incorrect arguments
  Caller     : general
  Status     : Stable

=cut

sub add_Attributes {
  my ( $self, @attribs ) = @_;

  if ( !exists( $self->{'attributes'} ) ) {
    $self->{'attributes'} = [];
  }

  my $seq_change = 0;
  foreach my $attrib (@attribs) {
    assert_ref( $attrib, 'Bio::EnsEMBL::Attribute' );

    push( @{ $self->{'attributes'} }, $attrib );

    if ( $attrib->code() eq "_rna_edit" ) {
      $seq_change = 1;
    }
  }

  if ($seq_change) {
    my $translation = $self->translation();
    if ( defined($translation) ) {
      delete( $translation->{'seq'} );
    }
  }

  # flush cdna coord cache b/c we may have added a SeqEdit
  delete( $self->{'cdna_coding_start'} );
  delete( $self->{'cdna_coding_end'} );
  delete( $self->{'transcript_mapper'} );
} ## end sub add_Attributes


=head2 add_Exon

 Title   : add_Exon
 Example : $trans->add_Exon($exon)
 Returns : None
 Args [1]: Bio::EnsEMBL::Exon object to add
 Args [2]: rank
 Exceptions: throws if not a valid Bio::EnsEMBL::Exon
           : or exon clashes with another one
 Status  : Stable

=cut

sub add_Exon {
  my ( $self, $exon, $rank ) = @_;

  assert_ref( $exon, 'Bio::EnsEMBL::Exon' );

  $self->{'_trans_exon_array'} ||= [];

  if ( defined($rank) ) {
    $self->{'_trans_exon_array'}->[ $rank - 1 ] = $exon;
    return;
  }

  my $was_added = 0;

  my $ea = $self->{'_trans_exon_array'};

  if ( @{$ea} ) {
    if ( $exon->strand() == 1 ) {

      my $exon_start = $exon->start();

      if ( $exon_start > $ea->[-1]->end() ) {
        push( @{$ea}, $exon );
        $was_added = 1;
      } else {
        # Insert it at correct place

        my $i = 0;
        foreach my $e ( @{$ea} ) {
          if ( $exon_start < $e->start() ) {
            if ( $exon->end() >= $e->start() ) {
              # Overlap
              last;
            }
            if ( $i and $exon_start <= $ea->[$i-1]->end() ) {
              # Overlap
              last;
            }
            splice( @{$ea}, $i, 0, $exon );
            $was_added = 1;
            last;
          }
          ++$i;
        }

      }

    } else {

      my $exon_end = $exon->end();

      if ( $exon_end < $ea->[-1]->start() ) {
        push( @{$ea}, $exon );
        $was_added = 1;
      } else {
        # Insert it at correct place

        my $i = 0;
        foreach my $e ( @{$ea} ) {
          if ( $exon_end > $e->end() ) {
            if ( $exon->start() <= $e->end() ) {
              # Overlap
              last;
            }
            if ( $i and $exon_end >= $ea->[$i-1]->start() ) {
              # Overlap
              last;
            }
            splice( @{$ea}, $i, 0, $exon );
            $was_added = 1;
            last;
          }
          ++$i;
        }

      }

    } ## end else [ if ( $exon->strand() ==...)]
  } else {
    push( @{$ea}, $exon );
    $was_added = 1;
  }

  # sanity check:
  if ( !$was_added ) {
    # The exon was not added because it was overloapping with an
    # existing exon.
    my $all_str = '';

    foreach my $e ( @{$ea} ) {
      $all_str .= '  '
        . $e->start() . '-'
        . $e->end() . ' ('
        . $e->strand() . ') '
        . ( $e->stable_id() || '' ) . "\n";
    }

    my $cur_str = '  '
      . $exon->start() . '-'
      . $exon->end() . ' ('
      . $exon->strand() . ') '
      . ( $exon->stable_id() || '' ) . "\n";

    throw(   "Exon overlaps with other exon in same transcript.\n"
           . "Transcript Exons:\n$all_str\n"
           . "This Exon:\n$cur_str" );
  }

  # recalculate start, end, slice, strand
  $self->recalculate_coordinates();
} ## end sub add_Exon


=head2 get_all_Exons

  Arg [1]    : Boolean
               Only return constitutive exons if true (non-zero)

  Example    : my @exons = @{ $transcript->get_all_Exons() };
               my @exons = @{ $transcript->get_all_Exons( -constitutive => 1 ) };

  Description: Returns an listref of the exons in this transcript
               in order, i.e. the first exon in the listref is the
               5prime most exon in the transcript.  Only returns
               constitutive exons if the CONSTITUTIVE argument is
               true.

  Returntype : listref to Bio::EnsEMBL::Exon objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_Exons {
  my ( $self, @args ) = @_;

  my $constitutive;
  if (@args) {
    $constitutive = rearrange( ['CONSTITUTIVE'], @args );
  }

  if (!defined( $self->{'_trans_exon_array'} )
    && defined( $self->adaptor() ) )
  {
    $self->{'_trans_exon_array'} =
      $self->adaptor()->db()->get_ExonAdaptor()
      ->fetch_all_by_Transcript($self);
  }

  my @result;
  if ( defined($constitutive) && $constitutive != 0 ) {
    foreach my $exon ( @{ $self->{'_trans_exon_array'} } ) {
      if ( $exon->is_constitutive() ) {
        push( @result, $exon );
      }
    }
  } else {
    @result = @{ $self->{'_trans_exon_array'} };
  }

  return \@result;
} ## end sub get_all_Exons


=head2 get_all_ExonTranscripts

  Example    : my @exon_transcripts = @{ $transcript->get_all_ExonTranscripts() };

  Description: Returns an listref of the exons in this transcript
               in order, i.e. the first exon in the listref is the
               5prime most exon in the transcript.

  Returntype : listref to Bio::EnsEMBL::ExonTranscript objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_ExonTranscripts {
  my ( $self, @args ) = @_;

  if (!defined( $self->{'_trans_exon_array'} )
    && defined( $self->adaptor() ) )
  {
    $self->{'_trans_exon_array'} =
      $self->adaptor()->db()->get_ExonAdaptor()
      ->fetch_all_by_Transcript($self);
  }

  my @result;
  my $i = 0;
  foreach my $exon ( @{ $self->{'_trans_exon_array'} } ) {
    $i++;
    my $exon_transcript = Bio::EnsEMBL::ExonTranscript->new(
      -EXON => $exon,
      -RANK => $i,
      -TRANSCRIPT => $self
    );
    push (@result, $exon_transcript) ;
  }

  return \@result;
} ## end sub get_all_ExonTranscripts

=head2 get_all_constitutive_Exons

  Arg        :  None

  Example   :  my @exons = @{ $transcript->get_all_constitutive_Exons() };

  Description:  Returns an listref of the constitutive exons in this
                transcript in order, i.e. the first exon in the
                listref is the 5prime most exon in the transcript.

  Returntype : listref to Bio::EnsEMBL::Exon objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_constitutive_Exons {
  my ($self) = @_;
  return $self->get_all_Exons( '-constitutive' => 1 );
}

=head2 get_all_IntronSupportingEvidence

  Example     : $ise->get_all_IntronSupportingEvidence();
  Description : Fetches all ISE instances linked to this Transript
  Returntype  : ArrayRef[Bio::EnsEMBL::IntronSupportEvidence] retrieved from 
                the DB or from those added via C<add_IntronSupportingEvidence>
  Exceptions  : None

=cut

sub get_all_IntronSupportingEvidence {
  my ($self) = @_;
  if(! defined $self->{_ise_array} && defined $self->adaptor()) {
    my $isea = $self->adaptor()->db()->get_IntronSupportingEvidenceAdaptor();
    $self->{_ise_array} = $isea->fetch_all_by_Transcript($self);
  }
  return $self->{_ise_array} || [];
}


=head2 add_IntronSupportingEvidence

  Arg [1]     : Bio::EnsEMBL::IntronSupportEvidence Object to add
  Example     : $ise->add_IntronSupportingEvidence($ise);
  Description : Adds the IntronSupportEvidence instance to this Transcript. The
                code checks to see if it is a unique ISE instance
  Returntype  : Boolean; true means it was added. False means it was not 
                as this ISE was already attached
  Exceptions  : None

=cut

sub add_IntronSupportingEvidence {
  my ($self, $ise) = @_;
  assert_ref($ise, 'Bio::EnsEMBL::IntronSupportingEvidence', 'IntronSupportingEvidence');
  my $unique = 1;
  foreach my $other_ise (@{$self->{_ise_array}}) {
    if($ise->equals($other_ise)) {
      $unique = 0;
      last;
    }
  }
  if($unique) {
    push(@{$self->{_ise_array}}, $ise);
    return 1;
  }
  return 0;
}

=head2 get_all_Introns

  Arg [1]    : none
  Example    : my @introns = @{$transcript->get_all_Introns()};
  Description: Returns an listref of the introns in this transcript in order.
               i.e. the first intron in the listref is the 5prime most exon in 
               the transcript.
  Returntype : listref to Bio::EnsEMBL::Intron objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_Introns {
   my ($self) = @_;
   if( ! defined $self->{'_trans_exon_array'} && defined $self->adaptor() ) {
     $self->{'_trans_exon_array'} = $self->adaptor()->db()->
       get_ExonAdaptor()->fetch_all_by_Transcript( $self );
   }

   my @introns=();
   my @exons = @{$self->{'_trans_exon_array'}};
   for(my $i=0; $i < scalar(@exons)-1; $i++){
     my $intron = new Bio::EnsEMBL::Intron($exons[$i],$exons[$i+1]);
     push(@introns, $intron)
   }
   return \@introns;
}

=head2 get_all_CDS_Introns

  Arg [1]    : none
  Example    : my @introns = @{$transcript->get_all_CDS_Introns()};
  Description: Returns an listref of the introns between coding exons in this transcript in order.
  Returntype : listref to Bio::EnsEMBL::Intron objects
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub get_all_CDS_Introns {
   my ($self) = @_;
   # return an empty list if there is no translation
   my $translation = $self->translation or return [];
   if( ! defined $self->{'_trans_exon_array'} && defined $self->adaptor() ) {
     $self->{'_trans_exon_array'} = $self->adaptor()->db()->
       get_ExonAdaptor()->fetch_all_by_Transcript( $self );
   }

   my @introns=();
   my @exons = @{$self->{'_trans_exon_array'}};
   for(my $i=0; $i < scalar(@exons)-1; $i++){
     if (!$exons[$i]->is_coding($self)) { next; }
     my $intron = new Bio::EnsEMBL::Intron($exons[$i],$exons[$i+1]);
     push(@introns, $intron)
   }
   return \@introns;
}


=head2 length

  Args       : none
  Example    : my $t_length = $transcript->length
  Description: Returns the sum of the length of all the exons in the transcript.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub length {
  my( $self ) = @_;

  my $length = 0;
  foreach my $ex (@{$self->get_all_Exons}) {
    $length += $ex->length;
  }

  # adjust the length if post transcriptional edits are enabled
  if($self->edits_enabled()) {
    foreach my $se (@{$self->get_all_SeqEdits()}) {
      $length += $se->length_diff();
    }
  }

  return $length;
}


=head2 flush_Exons

  Arg [1]    : none
  Example    : $transcript->flush_Exons();
  Description: Removes all Exons from this transcript and flushes related
               internal caches.
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub flush_Exons {
  my ($self) = @_;

  $self->{'transcript_mapper'}   = undef;
  $self->{'coding_region_start'} = undef;
  $self->{'coding_region_end'}   = undef;
  $self->{'cdna_coding_start'}   = undef;
  $self->{'cdna_coding_end'}     = undef;
  $self->{'start'}               = undef;
  $self->{'end'}                 = undef;
  $self->{'strand'}              = undef;

  $self->{'_trans_exon_array'} = [];
}

=head2 flush_IntronSupportingEvidence

  Example    : $transcript->flush_IntronSupportingEvidence();
  Description: Removes all IntronSupportingEvidence from this transcript
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub flush_IntronSupportingEvidence {
  my ($self) = @_;
  $self->{_ise_array} = [];
  return;
}

=head2 five_prime_utr

  Arg [1]    : none
  Example    : my $five_prime  = $transcrpt->five_prime_utr
                 or warn "No five prime UTR";
  Description: Obtains a Bio::Seq object of the five prime UTR of this
               transcript.  If this transcript is a pseudogene
               (i.e. non-translating) or has no five prime UTR undef is
               returned instead.
  Returntype : Bio::Seq or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub five_prime_utr {
  my $self = shift;

  my $cdna_coding_start  = $self->cdna_coding_start();

  return undef if(!$cdna_coding_start);

  my $seq = substr($self->spliced_seq, 0, $cdna_coding_start - 1);

  return undef if(!$seq);

  return
    Bio::Seq->new( -id       => $self->display_id,
                   -moltype  => 'dna',
                   -alphabet => 'dna',
                   -seq      => $seq );
}


=head2 three_prime_utr

  Arg [1]    : none
  Example    : my $three_prime  = $transcrpt->three_prime_utr
                 or warn "No three prime UTR";
  Description: Obtains a Bio::Seq object of the three prime UTR of this
               transcript.  If this transcript is a pseudogene
               (i.e. non-translating) or has no three prime UTR,
               undef is returned instead.
  Returntype : Bio::Seq or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub three_prime_utr {
  my $self = shift;

  my $cdna_coding_end = $self->cdna_coding_end();

  return undef if(!$cdna_coding_end);

  my $seq = substr($self->spliced_seq, $cdna_coding_end);

  return undef if(!$seq);

  return
    Bio::Seq->new( -id       => $self->display_id,
                   -moltype  => 'dna',
                   -alphabet => 'dna',
                   -seq      => $seq );
}

=head2 five_prime_utr_Feature

  Example    : my $five_prime  = $transcrpt->five_prime_utr_Feature
                 or warn "No five prime UTR";
  Description: Returns the genomic coordinates of the start and end of the
               5' UTR of this transcript. Note that if you want the sequence
               of the 5' UTR use C<five_prime_utr> as this will return the
               sequence from the spliced transcript. 
  Returntype : Bio::EnsEMBL::Feature or undef if there is no UTR
  Exceptions : none

=cut

sub five_prime_utr_Feature {
  my ($self) = @_;
  my $start = $self->seq_region_end();
  my $end = 0;
  my $features = $self->get_all_five_prime_UTRs();
  if (scalar(@$features) == 0) { return; }
  foreach my $feature (@$features) {
    if ($feature->start() < $start) {
      $start = $feature->start();
    }
    if ($feature->end() > $end) {
      $end = $feature->end();
    }
  }
  my $feature = Bio::EnsEMBL::Feature->new(
    -START => $start,
    -END => $end,
    -STRAND => $self->strand(),
    -SLICE => $self->slice(),
    -TYPE => 'five_prime_UTR',
    -TRANSCRIPT => $self
  );
  return $feature;
}



=head2 three_prime_utr_Feature

  Example    : my $five_prime  = $transcrpt->three_prime_utr_Feature
                 or warn "No three prime UTR";
  Description: Returns the genomic coordinates of the start and end of the
               3' UTR of this transcript. Note that if you want the sequence
               of the 3' UTR use C<three_prime_utr> as this will return the
               sequence from the spliced transcript. 
  Returntype : Bio::EnsEMBL::Feature or undef if there is no UTR
  Exceptions : none

=cut

sub three_prime_utr_Feature {
  my ($self) = @_;
  my $start = $self->seq_region_end();
  my $end = 0;
  my $features = $self->get_all_three_prime_UTRs();
  if (scalar(@$features) == 0) { return; }
  foreach my $feature (@$features) {
    if ($feature->start() < $start) {
      $start = $feature->start();
    }
    if ($feature->end() > $end) {
      $end = $feature->end();
    }
  }
  my $feature = Bio::EnsEMBL::Feature->new(
    -START => $start,
    -END => $end,
    -STRAND => $self->strand(),
    -SLICE => $self->slice(),
    -TYPE => 'three_prime_UTR',
    -TRANSCRIPT => $self
  );
  return $feature;
}


=head2 get_all_five_prime_UTRs

  Example    : my $five_primes  = $transcript->get_all_five_prime_UTRs
  Description: Returns a list of features forming the 5' UTR of this transcript.
  Returntype : listref of Bio::EnsEMBL::UTR
  Exceptions : none

=cut

sub get_all_five_prime_UTRs {
  my ($self) = @_;
  my $translation = $self->translation();
  return [] if ! $translation;

  my @utrs;

  my $cdna_coding_start = $self->cdna_coding_start();

  # if it is greater than 1 then it must have UTR
  if($cdna_coding_start > 1) {
    my @projections = $self->cdna2genomic(1, ($cdna_coding_start-1));
    foreach my $projection (@projections) {
      next if $projection->isa('Bio::EnsEMBL::Mapper::Gap');
      my $utr = Bio::EnsEMBL::UTR->new(
        -START  => $projection->start - $self->slice->start + 1,
        -END    => $projection->end - $self->slice->start + 1,
        -SEQ_REGION_START => $projection->start,
        -SEQ_REGION_END   => $projection->end,
        -STRAND => $projection->strand,
        -SLICE  => $self->slice,
        -TRANSCRIPT => $self,
        -TYPE   => 'five_prime_utr'
      );
      push(@utrs, $utr);
    }
  }

  return \@utrs;
}


=head2 get_all_three_prime_UTRs

  Example    : my $three_primes  = $transcript->get_all_three_prime_UTRs
  Description: Returns a list of features forming the 3' UTR of this transcript.
  Returntype : listref of Bio::EnsEMBL::UTR
  Exceptions : none

=cut

sub get_all_three_prime_UTRs {
  my ($self) = @_;
  my $translation = $self->translation();
  return [] if ! $translation;

  my @utrs;

  my $cdna_coding_end = $self->cdna_coding_end();
  if($cdna_coding_end < $self->length()) {
    my @projections = $self->cdna2genomic(($cdna_coding_end+1), $self->length());
    foreach my $projection (@projections) {
      next if $projection->isa('Bio::EnsEMBL::Mapper::Gap');
      my $utr = Bio::EnsEMBL::UTR->new(
        -START  => $projection->start - $self->slice->start + 1,
        -END    => $projection->end - $self->slice->start + 1,
        -SEQ_REGION_START => $projection->start,
        -SEQ_REGION_END   => $projection->end,
        -STRAND => $projection->strand,
        -SLICE  => $self->slice,
        -TRANSCRIPT => $self,
        -TYPE   => 'three_prime_utr'
      );
      push(@utrs, $utr);
    }
  }

  return \@utrs;
}

=head2 get_all_CDS

  Example    : my $cds  = $transcript->get_all_CDS
  Description: Returns a list of features forming the coding regions of the transcript
  Returntype : listref of Bio::EnsEMBL::CDS
  Exceptions : none

=cut

sub get_all_CDS {
  my ($self) = @_;
  my $translation = $self->translation();
  return [] if ! $translation;

  my @cds;
  my $translation_id = $translation->stable_id();

  foreach my $exon (@{ $self->get_all_translateable_Exons}) {
    my $phase = $exon->phase();
    $phase = 0 if $phase < 0;
    $phase =~ tr/12/21/;

    my $cds = Bio::EnsEMBL::CDS->new(
        -START           => $exon->start,
        -END             => $exon->end,
        -STRAND          => $exon->strand,
        -SEQ_REGION_START => $exon->seq_region_start,
        -SEQ_REGION_END   => $exon->seq_region_end,
        -TRANSLATION_ID  => $translation_id,
        -SLICE           => $self->slice,
        -TRANSCRIPT      => $self,
        -PHASE           => $phase 
    );
    push(@cds, $cds);
  }

  return \@cds;
}



=head2 get_all_translateable_Exons

  Args       : none
  Description: Returns a list of exons that translate with the
               start and end exons truncated to the CDS regions.
               This function does not take into account any SeqEdits
               (post transcriptional RNA modifictions) when constructing the
               the 'translateable' exons, and it does not update the phase
               information of the created 'translateable' exons.

               If this transcript is a pseudogene (i.e. non-translateable)
               a reference to an empty list is returned.

  Returntype : listref Bio::EnsEMBL::Exon
  Exceptions : throw if translation has invalid information
  Caller     : Genebuild
  Status     : Stable

=cut


sub get_all_translateable_Exons {
  my ( $self ) = @_;

  #return an empty list if there is no translation (i.e. pseudogene)
  my $translation = $self->translation or return [];
  my $start_exon      = $translation->start_Exon;
  my $end_exon        = $translation->end_Exon;
  my $t_start         = $translation->start;
  my $t_end           = $translation->end;

  my( @translateable );

  foreach my $ex (@{$self->get_all_Exons}) {

    if ($ex ne $start_exon and ! @translateable) {
      next;   # Not yet in translated region
    }

    my $length  = $ex->length;

    my $adjust_start = 0;
    my $adjust_end = 0;
    # Adjust to translation start if this is the start exon
    if ($ex == $start_exon ) {
      if ($t_start < 1 or $t_start > $length) {
        warning("WARN: Translation start '$t_start' is outside exon " . $ex->display_id . " length=$length");
  return [];
      }
      $adjust_start = $t_start - 1;
    }

    # Adjust to translation end if this is the end exon
    if ($ex == $end_exon) {
#      if ($t_end < 1 or $t_end > $length) {
#        throw("Translation end '$t_end' is outside exon $ex length=$length");
#      }
      $adjust_end = $t_end - $length;
    }

    # Make a truncated exon if the translation start or
    # end causes the coordinates to be altered.
    if ($adjust_end || $adjust_start) {
      my $newex = $ex->adjust_start_end( $adjust_start, $adjust_end );

      push( @translateable, $newex );
    } else {
      push(@translateable, $ex);
    }

    # Exit the loop when we've found the last exon
    last if $ex eq $end_exon;
  }
  return \@translateable;
}


=head2 translate

  Arg [1]    : Boolean, emulate the behavior of old bioperl versions where
               an incomplete final codon of 2 characters is padded and guessed
  Example    : none
  Description: Return the peptide (plus eventual stop codon) for
               this transcript.  Does N-padding of non-phase
               matching exons.  It uses translateable_seq
               internally.  Returns undef if this Transcript does
               not have a translation (i.e. pseudogene).
  Returntype : Bio::Seq or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub translate {
  my ($self, $complete_codon) = @_;

  if ( !defined( $self->translation() ) ) { return undef }

  my $mrna = $self->translateable_seq();

  # Alternative codon tables (such as the mitochondrial codon table)
  # can be specified for a sequence region via the seq_region_attrib
  # table.  A list of codon tables and their codes is at:
  # http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

  my $codon_table_id;
  my ( $complete5, $complete3 );
  if ( defined( $self->slice() ) ) {
    my $attrib;

    ($attrib) = @{ $self->slice()->get_all_Attributes('codon_table') };
    if ( defined($attrib) ) {
      $codon_table_id = $attrib->value();
    }

    ($attrib) = @{ $self->slice()->get_all_Attributes('complete5') };
    if ( defined($attrib) ) {
      $complete5 = $attrib->value();
    }

    ($attrib) = @{ $self->slice()->get_all_Attributes('complete3') };
    if ( defined($attrib) ) {
      $complete3 = $attrib->value();
    }
  }
  $codon_table_id ||= 1;    # default vertebrate codon table

  # Remove final stop codon from the mrna if it is present.  Produced
  # peptides will not have '*' at end.  If terminal stop codon is
  # desired call translatable_seq directly and produce a translation
  # from it.

  if ( CORE::length($mrna) % 3 == 0 ) {
    my $codon_table =
      Bio::Tools::CodonTable->new( -id => $codon_table_id );

    if ( $codon_table->is_ter_codon( substr( $mrna, -3, 3 ) ) ) {
      substr( $mrna, -3, 3, '' );
    }
  } elsif ( CORE::length($mrna) % 3 == 2 ) {
      # If we have a partial codon of 2 bp we need to decide if we
      # trim it or not to fix some bad behaviour in older bioperl
      # versions
      if ( $complete_codon ) {
	  # If we want to do the bad behavior of bioperl 1.6.1 and older
	  # where we guess the last codon if inomplete, pad an N
	  # to the mrna sequence
	  $mrna .= 'N';
      } else {
	  # Otherwise trim those last two bp off so the behavior is
	  # consistent across bioperl versions
	  substr( $mrna, -2, 2, '' );
      }
  }

  if ( CORE::length($mrna) < 1 ) { return undef }

  my $display_id = $self->translation->display_id()
    || scalar( $self->translation() );

  my $peptide = Bio::Seq->new( -seq      => $mrna,
                               -moltype  => 'dna',
                               -alphabet => 'dna',
                               -id       => $display_id );

  my $translation =
    $peptide->translate( undef, undef, undef, $codon_table_id, undef,
                         undef, $complete5, $complete3 );

  if ( $self->edits_enabled() ) {
    $self->translation()->modify_translation($translation);
  }

  return $translation;
} ## end sub translate


=head2 seq

  Description: Returns a Bio::Seq object which consists of just
             : the sequence of the exons concatenated together,
             : without messing about with padding with N\'s from
             : Exon phases like B<dna_seq> does.
  Args       : none
  Example    : none
  Returntype : Bio::Seq
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub seq {
  my ($self) = @_;

  return
    Bio::Seq->new( -id       => $self->display_id,
                   -moltype  => 'dna',
                   -alphabet => 'dna',
                   -seq      => $self->spliced_seq );
}


=head2 pep2genomic

  Description: See Bio::EnsEMBL::TranscriptMapper::pep2genomic

=cut

sub pep2genomic {
  my $self = shift;
  return $self->get_TranscriptMapper()->pep2genomic(@_);
}


=head2 genomic2pep

  Description: See Bio::EnsEMBL::TranscriptMapper::genomic2pep

=cut

sub genomic2pep {
  my $self = shift;
  return $self->get_TranscriptMapper()->genomic2pep(@_);
}


=head2 cdna2genomic

  Description: See Bio::EnsEMBL::TranscriptMapper::cdna2genomic

=cut

sub cdna2genomic {
  my $self = shift;
  return $self->get_TranscriptMapper()->cdna2genomic(@_);
}


=head2 genomic2cdna

  Description: See Bio::EnsEMBL::TranscriptMapper::genomic2cdna

=cut

sub genomic2cdna {
  my $self = shift;
  return $self->get_TranscriptMapper->genomic2cdna(@_);
}


=head2 get_TranscriptMapper

  Args       : none
  Example    : my $trans_mapper = $transcript->get_TranscriptMapper();
  Description: Gets a TranscriptMapper object which can be used to perform
               a variety of coordinate conversions relating this transcript,
               genomic sequence and peptide resulting from this transcripts
               translation.
  Returntype : Bio::EnsEMBL::TranscriptMapper
  Exceptions : none
  Caller     : cdna2genomic, pep2genomic, genomic2cdna, cdna2genomic
  Status     : Stable

=cut

sub get_TranscriptMapper {
  my ( $self ) = @_;
  return $self->{'transcript_mapper'} ||=
    Bio::EnsEMBL::TranscriptMapper->new($self);
}


=head2 start_Exon

 Title       : start_Exon
 Usage       : $start_exon = $transcript->start_Exon;
 Returntype  : Bio::EnsEMBL::Exon
 Description : The first exon in the transcript.
 Args        : NONE
 Status      : Stable

=cut

sub start_Exon {
  my $self = shift;
  return $self->get_all_Exons()->[0];
}


=head2 end_Exon

 Title       : end_exon
 Usage       : $end_exon = $transcript->end_Exon;
 Description : The last exon in the transcript.
 Returntype  : Bio::EnsEMBL::Exon
 Args        : NONE
 Status      : Stable

=cut

sub end_Exon {
   my $self = shift;
   return $self->get_all_Exons()->[-1];
}


=head2 description

 Title   : description
 Usage   : $obj->description($newval)
 Function: 
 Returns : String
 Args    : newvalue (optional)
 Status  : Stable

=cut

sub description {
  my $self = shift;
  $self->{'description'} = shift if( @_ );
  return $self->{'description'};
}


=head2 version

 Title   : version
 Usage   : $obj->version()
 Function: 
 Returns : String
 Args    : 
 Status  : Stable

=cut

sub version {
  my $self = shift;
  $self->{'version'} = shift if( @_ );
  return $self->{'version'};
}

=head2 stable_id

 Title   : stable_id
 Usage   : $obj->stable_id
 Function: 
 Returns : String
 Args    : 
 Status  : Stable

=cut

sub stable_id {
  my $self = shift;
  $self->{'stable_id'} = shift if( @_ );
  return $self->{'stable_id'};
}

=head2 stable_id_version

  Arg [1]    : (optional) String - the stable ID with version to set
  Example    : $transcript->stable_id("ENST0000000001.3");
  Description: Getter/setter for stable id with version for this transcript.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub stable_id_version {
    my $self = shift;
    if(my $stable_id = shift) {
	# See if there's an embedded period, assume that's a
	# version, might not work for some species but you
	# should use ->stable_id() and version() if you're worried
	# about ambiguity
	my $vindex = rindex($stable_id, '.');
	# Set the stable_id and version pair depending on if
	# we found a version delimiter in the stable_id
	($self->{stable_id}, $self->{version}) = ($vindex > 0 ?
						  (substr($stable_id,0,$vindex), substr($stable_id,$vindex+1)) :
						  $stable_id, undef);
    }
    return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');
}

=head2 is_current

  Arg [1]    : Boolean $is_current
  Example    : $transcript->is_current(1)
  Description: Getter/setter for is_current state of this transcript.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub is_current {
  my $self = shift;
  $self->{'is_current'} = shift if (@_);
  return $self->{'is_current'};
}


=head2 created_date

  Arg [1]    : (optional) string to be used for the created date
  Example    : none
  Description: get/set for attribute created date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub created_date {
  my $self = shift;
  $self->{'created_date'} = shift if ( @_ );
  return $self->{'created_date'};
}


=head2 modified_date

  Arg [1]    : (optional) string to be used for the modified date
  Example    : none
  Description: get/set for attribute modified date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub modified_date {
  my $self = shift;
  $self->{'modified_date'} = shift if ( @_ );
  return $self->{'modified_date'};
}


=head2 swap_exons

  Arg [1]    : Bio::EnsEMBL::Exon $old_Exon
               An exon that should be replaced
  Arg [2]    : Bio::EnsEMBL::Exon $new_Exon
               The replacement Exon
  Example    : none
  Description: exchange an exon in the current Exon list with a given one.
               Usually done before storing of Gene, so the Exons can
               be shared between Transcripts.
  Returntype : none
  Exceptions : none
  Caller     : GeneAdaptor->store()
  Status     : Stable

=cut

sub swap_exons {
  my ( $self, $old_exon, $new_exon, $skip_exon_sf) = @_;
  
  my $arref = $self->{'_trans_exon_array'};
  for(my $i = 0; $i < @$arref; $i++) {
    if($arref->[$i] == $old_exon ) {
      $new_exon->add_supporting_features(@{$old_exon->get_all_supporting_features}) unless $skip_exon_sf;
      $arref->[$i] = $new_exon;
      last;
    }
  }

  if( defined $self->{'translation'} ) {
     if( $self->translation()->start_Exon() == $old_exon ) {
      $self->translation()->start_Exon( $new_exon );
    }
    if( $self->translation()->end_Exon() == $old_exon ) {
      $self->translation()->end_Exon( $new_exon );
    }
  }
}

=head2 exon_rank

  Arg [1]    : Bio::EnsEMBL::Exon $Exon
               Query exon
  Example    : $rank = $transcript->exon_rank($exon);
  Description: Returns the rank of an exon relative to the transcript
  Returntype : none
  Exceptions : Throws if the exon does not belong to the transcript
  Caller     : General
  Status     : Stable

=cut

sub exon_rank {
  my ( $self, $exon ) = @_;

  if (!defined( $self->{'_trans_exon_array'} )
    && defined( $self->adaptor() ) )
  {
    $self->{'_trans_exon_array'} =
      $self->adaptor()->db()->get_ExonAdaptor()
      ->fetch_all_by_Transcript($self);
  }

  my $arref = $self->{'_trans_exon_array'};
  my $rank;

  if (!defined $arref) {
    throw "Transcript does not have any exons";
  }
  for(my $i = 0; $i < @$arref; $i++) {
    if($arref->[$i]->stable_id() eq $exon->stable_id()) {
      $rank = $i+1;
      last;
    }
  }

 if (!defined $rank) {
   throw "Exon does not belong to transcript";
  }

  return $rank;
}


=head2 equals

  Arg [1]       : Bio::EnsEMBL::Transcript transcript
  Example       : if ($transcriptA->equals($transcriptB)) { ... }
  Description   : Compares two transcripts for equality.
                  The test for eqality goes through the following list
                  and terminates at the first true match:

                  1. If Bio::EnsEMBL::Feature::equals() returns false,
                     then the transcripts are *not* equal.
                  2. If the biotypes differ, then the transcripts are
                     *not* equal.
                  3. If both transcripts have stable IDs: if these are
                     the same, the transcripts are equal, otherwise not.
                  4. If both transcripts have the same number of exons
                     and if these are (when compared pair-wise sorted by
                     start-position and length) the same, then they are
                     equal, otherwise not.

  Return type   : Boolean (0, 1)

  Exceptions    : Thrown if a non-transcript is passed as the argument.

=cut

sub equals {
  my ( $self, $transcript ) = @_;

  if ( !defined($transcript) ) { return 0 }
  if ( $self eq $transcript ) { return 1 }

  assert_ref( $transcript, 'Bio::EnsEMBL::Transcript' );

  my $feature_equals = $self->SUPER::equals($transcript);
  if ( defined($feature_equals) && $feature_equals == 0 ) {
    return 0;
  }

  if ( $self->get_Biotype->name ne $transcript->get_Biotype->name ) {
    return 0;
  }

  if ( defined( $self->stable_id() ) &&
       defined( $transcript->stable_id() ) )
  {
    if ( $self->stable_id() eq $transcript->stable_id() ) {
      return 1;
    }
    else {
      return 0;
    }
  }

  my @self_exons = sort {
    $a->start() <=> $b->start() ||
      $a->length() <=> $b->length()
  } @{ $self->get_all_Exons() };
  my @transcript_exons = sort {
    $a->start() <=> $b->start() ||
      $a->length() <=> $b->length()
  } @{ $transcript->get_all_Exons() };

  if ( scalar(@self_exons) != scalar(@transcript_exons) ) {
    return 0;
  }

  while (@self_exons) {
    my $self_exon       = shift(@self_exons);
    my $transcript_exon = shift(@transcript_exons);

    if ( !$self_exon->equals($transcript_exon) ) {
      return 0;
    }
  }

  return 1;
} ## end sub equals

=head2 transform

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    : $transcript = $transcript->transform('contig');
               $transcript = $transcript->transform('chromosome', 'NCBI33');
  Description: Moves this Transcript to the given coordinate system.
               If this Transcript has Exons attached, they move as well.
               A new Transcript is returned. If the transcript cannot be
               transformed to the destination coordinate system undef is
               returned instead.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : wrong parameters
  Caller     : general
  Status     : Medium Risk
             : deprecation needs to be removed at some time

=cut


sub transform {
  my $self = shift;

  my $new_transcript = $self->SUPER::transform(@_);
  if ( !defined($new_transcript) ) {
    my @segments = @{ $self->project(@_) };
    # if it projects, maybe the exons transform well?
    # lazy load them here
    if ( !@segments ) {
      return undef;
    }
    $self->get_all_Exons();
  }


  if( exists $self->{'_trans_exon_array'} ) {
    my @new_exons;
    my ( $low_start, $hi_end, $slice );
    # we want to check whether the transform preserved 5prime 3prime
    # ordering. This assumes 5->3 order. No complaints on transsplicing.

    my ( $last_new_start, $last_old_strand, 
   $last_new_strand, $start_exon, $end_exon,
  $last_seq_region_name );
    my $first = 1;
    my $ignore_order = 0;
    my $order_broken = 0;

    for my $old_exon ( @{$self->{'_trans_exon_array'}} ) {      
      my $new_exon = $old_exon->transform( @_ );
      return undef if( !defined $new_exon );
      if( ! defined $new_transcript ) {
  if( !$first ) {
    if( $old_exon->strand() != $last_old_strand ) {
      # transsplicing, ignore ordering
      $ignore_order = 1;  
    }

    if( $new_exon->slice()->seq_region_name() ne 
        $last_seq_region_name ) {
      return undef;
    }

    if( $last_new_strand == 1 and 
        $new_exon->start() < $last_new_start ) {
      $order_broken = 1;
    }

    if( $last_new_strand == -1 and
        $new_exon->start() > $last_new_start ) {
      $order_broken = 1;
    }

    #additional check that if exons were on same strand previously, they should be again
    if(($last_old_strand == $old_exon->strand()) and !($last_new_strand == $new_exon->strand())){
      return undef;
    }

    if( $new_exon->start() < $low_start ) {
      $low_start = $new_exon->start();
    }
    if( $new_exon->end() > $hi_end ) {
      $hi_end = $new_exon->end();
    }
  } else {
    $first = 0;
    $low_start = $new_exon->start();
    $hi_end = $new_exon->end();
  }

  $last_seq_region_name = $new_exon->slice()->seq_region_name();
  $last_old_strand = $old_exon->strand();
  $last_new_start = $new_exon->start();
  $last_new_strand = $new_exon->strand();
      }

      if( defined $self->{'translation'} ) {
        if( $self->translation()->start_Exon() == $old_exon ) {
          $start_exon = $new_exon;
        }
        if( $self->translation()->end_Exon() == $old_exon ) {
          $end_exon = $new_exon;
        }
      }
      push( @new_exons, $new_exon );
    }

    if( $order_broken && !$ignore_order ) {
      warning( "Order of exons broken in transform of ".$self->dbID() ); 
      return undef;
    }

    if( !defined $new_transcript ) {
      %$new_transcript = %$self;
      bless $new_transcript, ref( $self );
      $new_transcript->start( $low_start );
      $new_transcript->end( $hi_end );
      $new_transcript->slice( $new_exons[0]->slice() );
      $new_transcript->strand( $new_exons[0]->strand() );
    }

    $new_transcript->{'_trans_exon_array'} = \@new_exons;

    # should be ok to do inside exon array loop
    # translations only exist together with the exons ...

    if( defined $self->{'translation'} ) {
      my $new_translation;
      %$new_translation = %{$self->{'translation'}};;
      bless $new_translation, ref( $self->{'translation'} );
      $new_transcript->{'translation'} = $new_translation;
      $new_translation->start_Exon( $start_exon );
      $new_translation->end_Exon( $end_exon );
    }
  }

  if( exists $self->{'_supporting_evidence'} ) {
    my @new_features;
    for my $old_feature ( @{$self->{'_supporting_evidence'}} ) {
      my $new_feature = $old_feature->transform( @_ );
      if (defined $new_feature) { 
        push @new_features, $new_feature;
      }
    }
    $new_transcript->{'_supporting_evidence'} = \@new_features;
  }
  
  if(exists $self->{_ise_array}) {
    my @new_features;
    foreach my $old_feature ( @{$self->{_ise_array}} ) {
      my $new_feature = $old_feature->transform(@_);
      push( @new_features, $new_feature );
    }
    $new_transcript->{_ise_array} = \@new_features;
  }

  if(exists $self->{attributes}) {
    $new_transcript->{attributes} = [@{$self->{attributes}}];
  }

  # flush cached internal values that depend on the exon coords
  $new_transcript->{'transcript_mapper'}   = undef;
  $new_transcript->{'coding_region_start'} = undef;
  $new_transcript->{'coding_region_end'}   = undef;
  $new_transcript->{'cdna_coding_start'}   = undef;
  $new_transcript->{'cdna_coding_end'}     = undef;

  return $new_transcript;
}


=head2 transfer

  Arg  1     : Bio::EnsEMBL::Slice $destination_slice
  Example    : $transcript = $transcript->transfer($slice);
  Description: Moves this transcript to the given slice.
               If this Transcripts has Exons attached, they move as well.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut


sub transfer {
  my $self = shift;

  my $new_transcript = $self->SUPER::transfer( @_ );
  return undef unless $new_transcript;

  if( defined $self->{'translation'} ) {
    my $new_translation;
    %$new_translation = %{$self->{'translation'}};;
    bless $new_translation, ref( $self->{'translation'} );
    $new_transcript->{'translation'} = $new_translation;
  }

  if( exists $self->{'_trans_exon_array'} ) {
    my @new_exons;
    for my $old_exon ( @{$self->{'_trans_exon_array'}} ) {
      my $new_exon = $old_exon->transfer( @_ );
      if( defined $new_transcript->{'translation'} ) {
        if( $new_transcript->translation()->start_Exon() == $old_exon ) {
          $new_transcript->translation()->start_Exon( $new_exon );
        }
        if( $new_transcript->translation()->end_Exon() == $old_exon ) {
          $new_transcript->translation()->end_Exon( $new_exon );
        }
      }
      push( @new_exons, $new_exon );
    }

    $new_transcript->{'_trans_exon_array'} = \@new_exons;
  }

  if( exists $self->{'_supporting_evidence'} ) {
    my @new_features;
    for my $old_feature ( @{$self->{'_supporting_evidence'}} ) {
      my $new_feature = $old_feature->transfer( @_ );
      push( @new_features, $new_feature );
    }
    $new_transcript->{'_supporting_evidence'} = \@new_features;
  }
  
  if(exists $self->{_ise_array}) {
    my @new_features;
    foreach my $old_feature ( @{$self->{_ise_array}} ) {
      my $new_feature = $old_feature->transfer(@_);
      push( @new_features, $new_feature );
    }
    $new_transcript->{_ise_array} = \@new_features;
  }

  if(exists $self->{attributes}) {
    $new_transcript->{attributes} = [@{$self->{attributes}}];
  }

  # flush cached internal values that depend on the exon coords
  $new_transcript->{'transcript_mapper'}   = undef;
  $new_transcript->{'coding_region_start'} = undef;
  $new_transcript->{'coding_region_end'}   = undef;
  $new_transcript->{'cdna_coding_start'}   = undef;
  $new_transcript->{'cdna_coding_end'}     = undef;

  return $new_transcript;
}


=head recalculate_coordinates

  Args       : none
  Example    : none
  Description: called when exon coordinate change happened to recalculate the
               coords of the transcript.  This method should be called if one
               of the exons has been changed.
  Returntype : none
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut

sub recalculate_coordinates {
  my ($self) = @_;

  my $exons = $self->get_all_Exons();

  if ( !$exons || !@{$exons} ) { return }

  my ( $slice, $start, $end, $strand );

  my $e_index;
  for ( $e_index = 0; $e_index < @{$exons}; $e_index++ ) {
    my $e = $exons->[$e_index];

    # Skip missing or unmapped exons!
    if ( defined($e) && defined( $e->start() ) ) {
      $slice  = $e->slice();
      $strand = $e->strand();
      $start  = $e->start();
      $end    = $e->end();

      last;
    }
  }

  my $transsplicing = 0;

  # Start loop after first exon with coordinates
  for ( ; $e_index < @{$exons}; $e_index++ ) {
    my $e = $exons->[$e_index];

    # Skip missing or unmapped exons!
    if ( !defined($e) || !defined( $e->start() ) ) { next }

    if ( $e->start() < $start ) {
      $start = $e->start();
    }

    if ( $e->end() > $end ) {
      $end = $e->end();
    }

    if (    defined($slice)
         && $e->slice()
         && $e->slice()->name() ne $slice->name() )
    {
      throw(   "Exons with different slices "
             . "are not allowed on one Transcript" );
    }

    if ( $e->strand() != $strand ) {
      $transsplicing = 1;
    }
  } ## end for ( ; $e_index < @{$exons...})
  if ($transsplicing) {
    warning("Transcript contained trans splicing event");
  }

  $self->start($start);
  $self->end($end);
  $self->strand($strand);
  $self->slice($slice);

  # flush cached internal values that depend on the exon coords
  $self->{'transcript_mapper'}   = undef;
  $self->{'coding_region_start'} = undef;
  $self->{'coding_region_end'}   = undef;
  $self->{'cdna_coding_start'}   = undef;
  $self->{'cdna_coding_end'}     = undef;
} ## end sub recalculate_coordinates


=head2 display_id

  Arg [1]    : none
  Example    : print $transcript->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier. For transcripts this is (depending on
               availability and in this order) the stable Id, the dbID or an
               empty string.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : Stable

=cut

sub display_id {
  my $self = shift;
  return $self->{'stable_id'} || $self->dbID || '';
}


=head2 get_all_DASFactories

  Arg [1]   : none
  Function  : Retrieves a listref of registered DAS objects
  Returntype: [ DAS_objects ]
  Exceptions:
  Caller    :
  Example   : $dasref = $prot->get_all_DASFactories
  Status    : Stable

=cut

sub get_all_DASFactories {
   my $self = shift;
   return [ $self->adaptor()->db()->_each_DASFeatureFactory ];
}


=head2 get_all_DAS_Features

  Arg [1]    : none
  Example    : $features = $prot->get_all_DAS_Features;
  Description: Retrieves a hash reference to a hash of DAS feature
               sets, keyed by the DNS, NOTE the values of this hash
               are an anonymous array containing:
                (1) a pointer to an array of features;
                (2) a pointer to the DAS stylesheet
  Returntype : hashref of Bio::SeqFeatures
  Exceptions : ?
  Caller     : webcode
  Status    : Stable


=cut

sub get_all_DAS_Features {
  my ($self,@args) = @_;

  my $db = $self->adaptor->db;
  my $GeneAdaptor = $db->get_GeneAdaptor;
  my $Gene = $GeneAdaptor->fetch_by_transcript_stable_id($self->stable_id); 
  my $slice = $Gene->feature_Slice;
  return $self->SUPER::get_all_DAS_Features($slice);
}


=head2 get_all_RNAProducts

  Arg [1]    : optional string $type_code type of rnaproducts to retrieve
  Example    : @transc_mirnas = @{$transcript->get_all_RNAProducts('miRNA')};
               @transc_rnaproducts = @{$transcript->get_all_RNAProducts()};
  Description: Gets a list of RNAProducts of this transcript.
               Optionally just get RNAProducts for given type code.
  Returntype : listref Bio::EnsEMBL::RNAProduct
  Exceptions : none
  Caller     : general
  Status     : In Development

=cut

sub get_all_RNAProducts {
  my ($self, $type_code) = @_;

  if (!exists $self->{'rnaproducts'}) {
    if (!$self->adaptor()) {
      return [];
    }

    my $rnaproduct_adaptor = $self->adaptor->db->get_RNAProductAdaptor();
    $self->{'rnaproducts'} = $rnaproduct_adaptor->fetch_all_by_Transcript($self);
  }

  if (defined $type_code) {
    my @results = grep { $_->type_code() eq $type_code } @{$self->{'rnaproducts'}};
    return \@results;
  } else {
    return $self->{'rnaproducts'};
  }
}



=head2 _compare_xrefs

  Description: compare xrefs based on priority (descending), then
               name (ascending), then display_label (ascending)

=cut

sub _compare_xrefs {
  # compare on priority first (descending)
  if ( $a->priority() != $b->priority() ) {
    return $b->priority() <=> $a->priority();
  } else {
    # equal priorities, compare on external_db name
    if ( $a->dbname() ne $b->dbname() ) {
      return $a->dbname() cmp $b->dbname();
    } else {
      # equal priorities and names, compare on display_label
      return $a->display_id() cmp $b->display_id();
    }
  }
}


=head2 load

  Arg [1]       : Boolean $load_xrefs
                  Load (or don't load) xrefs.  Default is to load xrefs.
  Example       : $transcript->load();
  Description   : The Ensembl API makes extensive use of
                  lazy-loading.  Under some circumstances (e.g.,
                  when copying genes between databases), all data of
                  an object needs to be fully loaded.  This method
                  loads the parts of the object that are usually
                  lazy-loaded.  It will also call the equivalent
                  method on any translation and on all exons of the
                  transcript.
  Returntype    : None

=cut

sub load {
  my ( $self, $load_xrefs ) = @_;

  if ( !defined($load_xrefs) ) { $load_xrefs = 1 }

  my $translation = $self->translation();
  if ( defined($translation) ) {
    $translation->load($load_xrefs);

    my $alt_translations = $self->get_all_alternative_translations();

    if ( defined($alt_translations) ) {
      foreach my $alt_translation ( @{$alt_translations} ) {
        $alt_translation->load($load_xrefs);
      }
    }
  }

  foreach my $exon ( @{ $self->get_all_Exons() } ) {
    $exon->load();
  }

  $self->stable_id();
  $self->analysis();
  $self->get_all_Attributes();
  $self->get_all_supporting_features();
  $self->get_all_IntronSupportingEvidence();

  if ($load_xrefs) {
    $self->get_all_DBEntries();
  }

} ## end sub load

=head2 summary_as_hash

  Example       : $transcript_summary = $transcript->summary_as_hash();
  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this Transcript.
  Returns       : hashref of descriptive strings
  Status        : Intended for internal use
=cut

sub summary_as_hash {
  my $self = shift;
  my $summary_ref = $self->SUPER::summary_as_hash;
  $summary_ref->{'description'} = $self->description;
  $summary_ref->{'Name'} = $self->external_name if $self->external_name;
  $summary_ref->{'biotype'} = $self->get_Biotype->name;
  $summary_ref->{'logic_name'} = $self->analysis->logic_name() if defined $self->analysis();
  my $parent_gene = $self->get_Gene();
  $summary_ref->{'Parent'} = $parent_gene->stable_id;
  $summary_ref->{'source'} = $self->source();
  $summary_ref->{'transcript_id'} = $summary_ref->{'id'};

  ## Specific attributes for merged species
  ## No data will be stored if these fields are not available
  my $havana_transcript = $self->havana_transcript();
  $summary_ref->{'havana_transcript'} = $havana_transcript->display_id() if defined $havana_transcript;
  $summary_ref->{'havana_version'} = $havana_transcript->version() if defined $havana_transcript;
  $summary_ref->{'ccdsid'} = $self->ccds->display_id() if $self->ccds();
  $summary_ref->{'transcript_support_level'} = $self->tsl() if $self->tsl();
  $summary_ref->{'tag'} = 'basic' if $self->gencode_basic();

  ## Stable identifier of the parent transcript this transcript was projected from
  my $proj_parent_attributes = $self->get_all_Attributes("proj_parent_t");
  if (@{$proj_parent_attributes}) {
    $summary_ref->{'projection_parent_transcript'} = $proj_parent_attributes->[0]->value;
  }
  return $summary_ref;
}

=head2 gencode_basic

  Example       : $gencode_basic = $transcript->tag();
  Description   : Returns true if gencode_basic is set
  Returns       : boolean
=cut

sub gencode_basic {
  my $self = shift;
  my @attributes = @{ $self->get_all_Attributes('gencode_basic') };
  my $basic = 0;
  $basic = 1 if scalar(@attributes) > 0;
  return $basic;
}

=head2 tsl

  Example       : $tsl = $transcript->tsl();
  Description   : Returns the corresponding transcript support level
  Returns       : string
=cut

sub tsl {
  my $self = shift;
  my @attributes = @{ $self->get_all_Attributes('TSL') };
  my $tsl;
  $tsl = $attributes[0]->value if scalar(@attributes) > 0;
  if (defined $tsl) { $tsl =~ s/tsl//; }
  return $tsl;
}

=head2 appris

  Example       : $appris = $transcript->appris();
  Description   : Returns the corresponding APPRIS tag
  Returns       : string

=cut

sub appris {
  my $self = shift;
  my @attributes = @{ $self->get_all_Attributes('appris') };
  my $appris;
  $appris = $attributes[0]->value if scalar(@attributes) > 0;

  return $appris;
}

=head2 havana_transcript

  Example       : $havana_transcript = $transcript->havana_transcript();
  Description   : Locates the corresponding havana transcript
  Returns       : Bio::EnsEMBL::DBEntry
=cut

sub havana_transcript {
  my $self = shift;
  my @otts = @{ $self->get_all_DBEntries('Vega_transcript') };
  my $ott;
  foreach my $xref (@otts) {
    if ($xref->display_id() =~ /OTT/) {
      $ott = $xref;
      last;
    }
  }
  return $ott;
}

=head2 ccds

  Example       : $ccds = $transcript->ccds();
  Description   : Locates the corresponding ccds xref
  Returns       : Bio::EnsEMBL::DBEntry
=cut

sub ccds {
  my $self = shift;
  my @ccds = @{ $self->get_all_DBEntries('CCDS') };
  my $ccds;
  $ccds = $ccds[0] if scalar(@ccds) > 0;
  return $ccds;
}



=head2 get_Gene
  
  Example     : $gene = $transcript->get_Gene;
  Description : Locates the parent Gene using a transcript dbID
  Returns     : Bio::EnsEMBL::Gene

=cut

sub get_Gene {
  my $self = shift;
  my $gene_adaptor = $self->adaptor->db->get_GeneAdaptor();
  my $parent_gene = $gene_adaptor->fetch_by_transcript_id($self->dbID);
  return $parent_gene;
}

=head2 get_Biotype

  Example    : my $biotype = $transcript->get_Biotype;
  Description: Returns the Biotype object of this transcript.
               When no biotype exists, defaults to 'protein_coding'.
               When used to set to a biotype that does not exist in
               the biotype table, a biotype object is created with
               the provided argument as name and object_type transcript.
  Returntype : Bio::EnsEMBL::Biotype
  Exceptions : none

=cut

sub get_Biotype {
  my ( $self ) = @_;

  # have a biotype object, return it
  if ( ref $self->{'biotype'} eq 'Bio::EnsEMBL::Biotype' ) {
    return $self->{'biotype'};
  }

  # biotype is first set as a string retrieved from the transcript table
  # there is no biotype object in the transcript object, retrieve it using the biotype string
  # if no string, default to protein_coding. this is legacy behaviour and should probably be revisited
  my $biotype_name = $self->{'biotype'} // 'protein_coding';

  return $self->set_Biotype( $biotype_name );
}

=head2 set_Biotype

  Arg [1]    : Arg [1] : String - the biotype name to set
  Example    : my $biotype = $transcript->set_Biotype('protin_coding');
  Description: Sets the Biotype of this transcript to the provided biotype name.
               Returns the Biotype object of this transcript.
               When no biotype exists, defaults to 'protein_coding' name.
               When setting a biotype that does not exist in
               the biotype table, a biotype object is created with
               the provided argument as name and object_type transcript.
  Returntype : Bio::EnsEMBL::Biotype
  Exceptions : If no argument provided

=cut

sub set_Biotype {
  my ( $self, $name ) = @_;

  throw('No argument provided') unless defined $name;

  # retrieve biotype object from the biotype adaptor
  if( defined $self->adaptor() ) {
    my $ba = $self->adaptor()->db()->get_BiotypeAdaptor();
    $self->{'biotype'} = $ba->fetch_by_name_object_type( $name, 'transcript' );
  }
  # if $self->adaptor is unavailable, create a new biotype object containing name and object_type only
  else {
    $self->{'biotype'} = Bio::EnsEMBL::Biotype->new(
            -NAME          => $name,
            -OBJECT_TYPE   => 'transcript',
    )
  }

  return $self->{'biotype'} ;
}

=head2 biotype
  Arg [1]    : (optional) String - the biotype to set
  Example    : $transcript->biotype("protein_coding");
  Description: Getter/setter for the attribute biotype name.
               Recommended to use instead for a getter:
                 $biotype = $transcript->get_Biotype;
               and for a setter:
                 $biotype = $transcript->set_Biotype("protein_coding");
               The String biotype name can then be retrieved by
               calling name on the Biotype object:
                 $biotype_name = $biotype->name;
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
=cut

sub biotype {
  my ( $self, $biotype_name) = @_;

  # Setter? set_Biotype()
  if (defined $biotype_name) {
    return $self->set_Biotype($biotype_name)->name;
  }

  # Getter? get_Biotype()
  return $self->get_Biotype->name;
}

=head2 mane_transcript
  Example    : $mane = $transcript->mane_transcript();
  Description: Retrieve the corresponding MANE transcript
  Returntype : Bio::EnsEMBL::MANE
  Exceptions : none
  Caller     : general
  Status     : Stable
=cut

sub mane_transcript {
  my ($self) = @_;
  if ($self->is_mane) {

    my $mane = Bio::EnsEMBL::MANE->new(
        -SEQ_REGION_START => $self->seq_region_start,
        -SEQ_REGION_END   => $self->seq_region_end,
        -START            => $self->start,
        -END              => $self->end,
        -STABLE_ID        => $self->stable_id,
        -SLICE            => $self->slice,
        -TRANSCRIPT       => $self
    );
    return $mane;
  }
  return undef;
}

=head2 is_mane
  Example    : $boolean = $transcript->is_mane();
  Description: Check if a transcript is part of MANE
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable
=cut

sub is_mane {
  my ($self) = @_;
  my $is_mane = 0;
  foreach my $attribute (@{ $self->get_all_Attributes() } ) {
    if ($attribute->code=~ /MANE/) {
      $is_mane = 1;
    }
  }
  return $is_mane;
}

1;
