Inheritance diagram for Bio::EnsEMBL::Transcript:

Class Summary

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";
  }

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.

Definition at line 39 of file Transcript.pm.

Available Methods
protected	_compare_xrefs ()
protected	_deprecated_transform ()
protected	_translation_id ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public void	add_alternative_translation ()
public void	add_Attributes ()
public void	add_DBEntry ()
public void	add_Exon ()
public	add_sub_SeqFeature ()
public void	add_supporting_features ()
public Bio::EnsEMBL::Analysis	analysis ()
public String	biotype ()
public	cdna2genomic ()
public Int	cdna_coding_end ()
public Int	cdna_coding_start ()
public Int	coding_region_end ()
public Int	coding_region_start ()
public	confidence ()
public	contig ()
public String	coord_system_name ()
public	created ()
public String	created_date ()
public Int	dbID ()
public String	description ()
public String	display_id ()
public Bio::EnsEMBL::DBEntry	display_xref ()
public Boolean	edits_enabled ()
public Int	end ()
public Bio::EnsEMBL::Exon	end_Exon ()
public Boolean	equals ()
public String	external_db ()
public String	external_name ()
public String	external_status ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public Bio::Seq	five_prime_utr ()
public void	flush_Exons ()
public	flush_sub_SeqFeature ()
public	flush_supporting_features ()
public	genomic2cdna ()
public	genomic2pep ()
public Reference	get_all_alt_locations ()
public Arrayref	get_all_alternative_translations ()
public Listref	get_all_Attributes ()
public	get_all_cdna_SNPs ()
public Listref	get_all_constitutive_Exons ()
public Hashref	get_all_DAS_Features ()
public	get_all_DASFactories ()
public Listref	get_all_DBEntries ()
public Listref	get_all_DBLinks ()
public Listref	get_all_Exons ()
public Listref	get_all_Introns ()
public Listref	get_all_object_xrefs ()
public	get_all_peptide_variations ()
public Bio::EnsEMBL::SeqEdit	get_all_SeqEdits ()
public	get_all_SNPs ()
public Listref	get_all_supporting_features ()
public Listref	get_all_translateable_Exons ()
public Listref	get_all_xrefs ()
public Bio::EnsEMBL::Gene	get_Gene ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::TranscriptMapper	get_TranscriptMapper ()
public	id ()
public Boolean	is_canonical ()
public Int	is_current ()
public Boolean	is_known ()
public Boolean	is_stored ()
public Int	length ()
public void	load ()
public	modified ()
public String	modified_date ()
public void	move ()
public Bio::EnsEMBL::Transcript	new ()
public Bio::EnsEMBL::Feature	new_fast ()
public Boolean	overlaps ()
public	pep2genomic ()
public List	project ()
public List	project_to_slice ()
public	recalculate_coordinates ()
public Bio::Seq	seq ()
public Int	seq_region_end ()
public Unsigned	seq_region_length ()
public String	seq_region_name ()
public Int	seq_region_start ()
public Boolean	seq_region_strand ()
public String	seqname ()
public Bio::EnsEMBL::Slice	slice ()
public	sort ()
public String	species ()
public Text	spliced_seq ()
public String	stable_id ()
public Int	start ()
public Bio::EnsEMBL::Exon	start_Exon ()
public String	status ()
public Int	strand ()
public	sub_SeqFeature ()
public Hashref	summary_as_hash ()
public void	swap_exons ()
public	temporary_id ()
public Bio::Seq	three_prime_utr ()
public Bio::EnsEMBL::Transcript	transfer ()
public Bio::EnsEMBL::Transcript	transform ()
public Bio::Seq	translate ()
public Text	translateable_seq ()
public Bio::EnsEMBL::Translation	translation ()
public	type ()
public String	version ()

Method Documentation

protected Bio::EnsEMBL::Transcript::_compare_xrefs ( )

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

Code:

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protected Bio::EnsEMBL::Feature::_deprecated_transform ( ) [inherited]

Undocumented method

Code:

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protected Bio::EnsEMBL::Transcript::_translation_id ( )

Undocumented method

Code:

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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable

Code:

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public void Bio::EnsEMBL::Transcript::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

Code:

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public void Bio::EnsEMBL::Transcript::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

Code:

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public void Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public void Bio::EnsEMBL::Transcript::add_Exon ( )

 Title   : add_Exon
 Usage   : $trans->add_Exon($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

Code:

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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

public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( ) [inherited]

Undocumented method

Code:

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public void Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Analysis Bio::EnsEMBL::Feature::analysis ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::Analysis $analysis
  Example    : $feature->analysis(new Bio::EnsEMBL::Analysis(...))
  Description: Getter/Setter for the analysis that is associated with 
               this feature.  The analysis describes how this feature 
               was derived.
  Returntype : Bio::EnsEMBL::Analysis
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DensityFeature.

public String Bio::EnsEMBL::Transcript::biotype ( )

  Arg [1]    : string $biotype
  Example    : none
  Description: get/set for attribute biotype
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript::cdna2genomic ( )

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

Code:

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public Int Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Int Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Int Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Int Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Transcript::confidence ( )

  Description:
Deprecated:
. Use status() instead.

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public Bio::EnsEMBL::Feature::contig ( ) [inherited]

Undocumented method

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public String Bio::EnsEMBL::Feature::coord_system_name ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->coord_system_name()
  Description: Gets the name of the coord_system which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript::created ( )

Description:

Deprecated:

this attribute is not part of transcript anymore

Code:

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public String Bio::EnsEMBL::Transcript::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

Code:

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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]

  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable

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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Transcript::description ( )

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

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public String Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::Transcript::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

Code:

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public Boolean Bio::EnsEMBL::Transcript::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

Code:

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public Int Bio::EnsEMBL::Feature::end ( ) [inherited]

  Arg [1]    : (optional) int $end
  Example    : $end = $feat->end();
  Description: Getter/Setter for the end of this feature relative to the
               start of the slice that it is on.  Note that negative values,
               of values exceeding the length of the slice are permitted.  End
               must be greater than or equal to start regardless of the strand.
               Coordinate values start at 1 and are inclusive.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Transcript::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

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public Boolean Bio::EnsEMBL::Transcript::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.

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public String Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public String Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public String Bio::EnsEMBL::Transcript::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

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::feature_Slice ( ) [inherited]

  Args       : none
  Example    : $slice = $feature->feature_Slice()
  Description: This is a convenience method to return a slice that covers the
               Area of this feature. The feature start will be at 1 on it, and
               it will have the length of this feature.
  Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
               Slice.
  Exceptions : warning if Feature does not have attached slice.
  Caller     : web drawing code
  Status     : Stable

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public Bio::Seq Bio::EnsEMBL::Transcript::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

Code:

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public void Bio::EnsEMBL::Transcript::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

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public Bio::EnsEMBL::Feature::flush_sub_SeqFeature ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Transcript::genomic2cdna ( )

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

Code:

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public Bio::EnsEMBL::Transcript::genomic2pep ( )

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

Code:

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public Reference Bio::EnsEMBL::Feature::get_all_alt_locations ( ) [inherited]

  Arg [1]    : none
  Example    : @features = @{$feature->get_all_alt_locations()};
               foreach $f (@features) {
                 print $f->slice->seq_region_name,' ',$f->start, $f->end,"\\n";
               }

  Description: Retrieves shallow copies of this feature in its alternate
               locations.  A feature can be considered to have multiple
               locations when it sits on a alternative structural haplotype
               or when it is on a pseudo autosomal region.  Most features will
               just return a reference to an empty list though.
               The features returned by this method will be on a slice which
               covers the entire alternate region.

               Currently this method does not take into account alternate
               locations on the alternate locations (e.g. a reference
               sequence may have multiple alternate haplotypes.  Asking
               for alternate locations of a feature on one of the alternate
               haplotypes will give you back the reference location, but not
               locations on the other alternate haplotypes).

  Returntype : reference to list of features of the same type of this feature.
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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sub get_all_alt_locations {
  my $self = shift;
  my $return_all = shift || 0;

  my $slice = $self->{'slice'} or return [];
  my $sa = $slice->adaptor() or return [];

  # get slice of entire region
  $slice = $sa->fetch_by_seq_region_id($slice->get_seq_region_id);

  my $axfa = $sa->db->get_AssemblyExceptionFeatureAdaptor();
  my $axfs = $axfa->fetch_all_by_Slice($slice);

  my (@haps, @alt);

  foreach my $axf (@$axfs) {
    if(uc($axf->type()) eq 'HAP') {
      push @haps, $axf;
    } elsif(uc($axf->type()) =~ 'PAR') {
      push @alt, $axf;
    } elsif( $axf->type() eq "PATCH_FIX"){
      push @haps, $axf;
    } elsif( $axf->type() eq "PATCH_FIX REF"){
      push @haps, $axf  if $return_all > 0 ;
    } elsif( $axf->type() eq "HAP REF" ) {
      push @haps, $axf if $return_all > 0 ;
      # do nothing when you are on REF
    } elsif( $axf->type() eq "PATCH_NOVEL"){
      push @haps, $axf;
    }elsif( $axf->type() eq "PATCH_NOVEL REF"){
      push @haps, $axf  if $return_all > 0 ;
    } else {
      warning("Unknown exception feature type ". $axf->type()."- ignoring.");
    }
  }

  # regions surrounding hap are those of interest, not hap itself
  # convert hap alt. exc. features to regions around haps instead
  foreach my $h (@haps) {
    my $haslice = $h->alternate_slice();
    my $hacs    = $haslice->coord_system();

    if($h->start() > 1 && $haslice->start() > 1) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        1,
                                        $haslice->start()-1,
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => 1,
         -end    => $h->start()-1,
         -alternate_slice => $aslice);
    }

    if($h->end() < $slice->seq_region_length() &&
       $haslice->end < $haslice->seq_region_length()) {
      my $aslice = $sa->fetch_by_region($hacs->name(),
                                        $haslice->seq_region_name(),
                                        $haslice->end()+1,
                                        $haslice->seq_region_length(),
                                        $haslice->strand(),
                                        $hacs->version());

      push @alt, Bio::EnsEMBL::AssemblyExceptionFeature->new
        (-start  => $h->end() + 1,
         -end    => $slice->seq_region_length(),
         -alternate_slice => $aslice);
    }
  }


  # check if exception regions contain our feature

  my @features;

  foreach my $axf (@alt) {
    # ignore other region if feature is not entirely on it
    next if($self->seq_region_start() < $axf->start() ||
            $self->seq_region_end()   > $axf->end());

    # quick shallow copy of the feature
    my $f;
    %$f = %$self;
    bless $f, ref($self);

    my $aslice = $axf->alternate_slice();

    # position feature on entire slice of other region
    $f->{'start'}  = $f->seq_region_start() - $axf->start() + $aslice->start();
    $f->{'end'}    = $f->seq_region_end()   - $axf->start() + $aslice->start();
    $f->{'strand'} *= $aslice->strand();

    $f->{'slice'} = $sa->fetch_by_seq_region_id($aslice->get_seq_region_id());

    push @features, $f;
  }

  return \@features;
}

public Arrayref Bio::EnsEMBL::Transcript::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

Code:

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public Listref Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Transcript::get_all_cdna_SNPs ( )

  Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_cdna_SNPs

  Status  : At Risk
          : Will be replaced with modules from the ensembl-variation package

Code:

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public Listref Bio::EnsEMBL::Transcript::get_all_constitutive_Exons ( )

  Arg        :  None

  Examples   :  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

Code:

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public Hashref Bio::EnsEMBL::Transcript::get_all_DAS_Features ( )

  Arg [1]    : none
  Example    : $features = $prot->get_all_DAS_Features;
  Description: Retreives 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

Code:

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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Transcript::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

Code:

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public Listref Bio::EnsEMBL::Transcript::get_all_DBEntries ( )

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

  Arg [2]    : (optional) String, external database type

  Example    : my @dbentries = @{ $transcript->get_all_DBEntries() };

  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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Listref Bio::EnsEMBL::Transcript::get_all_DBLinks ( )

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

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

  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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Listref Bio::EnsEMBL::Transcript::get_all_Exons ( )

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

  Examples  :   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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Listref Bio::EnsEMBL::Transcript::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

Code:

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public Listref Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Transcript::get_all_peptide_variations ( )

  Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_peptide_variations
  Status  : At Risk
          : Will be replaced with modules from the ensembl-variation package

Code:

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public Bio::EnsEMBL::SeqEdit Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Transcript::get_all_SNPs ( )

  Description: See Bio::EnsEMBL::Utils::TranscriptSNPs::get_all_SNPs

  Status  : At Risk
          : Will be replaced with modules from the ensembl-variation package

Code:

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public Listref Bio::EnsEMBL::Transcript::get_all_supporting_features ( )

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

Code:

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public Listref Bio::EnsEMBL::Transcript::get_all_translateable_Exons ( )

  Args       : none
  Example    : 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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Listref Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Transcript::get_Gene ( )

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

Code:

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public Bio::EnsEMBL::Gene Bio::EnsEMBL::Feature::get_nearest_Gene ( ) [inherited]

  Description: Get all the nearest  gene to the feature
  Returntype : Bio::EnsEMBL::Gene
  Caller     : general
  Status     : UnStable

Code:

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public List Bio::EnsEMBL::Feature::get_overlapping_Genes ( ) [inherited]

  Description: Get all the genes that overlap this feature.
  Returntype : list ref of Bio::EnsEMBL::Gene
  Caller     : general
  Status     : UnStable

Code:

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public Bio::EnsEMBL::TranscriptMapper Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Feature::id ( ) [inherited]

Undocumented method

Code:

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public Boolean Bio::EnsEMBL::Transcript::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

Code:

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public Int Bio::EnsEMBL::Transcript::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

Code:

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public Boolean Bio::EnsEMBL::Transcript::is_known ( )

  Example    : print "Transcript ".$transcript->stable_id." is KNOWN\\n" if
                  $transcript->is_known;
  Description: Returns TRUE if this gene has a status of 'KNOWN'
  Returntype : TRUE if known, FALSE otherwise
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public void Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Transcript::modified ( )

Description:

Deprecated:

this attribute is not part of transcript anymore

Code:

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public String Bio::EnsEMBL::Transcript::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

Code:

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public void Bio::EnsEMBL::Feature::move ( ) [inherited]

  Arg [1]    : int start
  Arg [2]    : int end
  Arg [3]    : (optional) int strand
  Example    : None
  Description: Sets the start, end and strand in one call rather than in 
               3 seperate calls to the start(), end() and strand() methods.
               This is for convenience and for speed when this needs to be
               done within a tight loop.
  Returntype : none
  Exceptions : Thrown is invalid arguments are provided
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, and Bio::EnsEMBL::Map::QtlFeature.

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::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 transcipts description
  Arg [-BIOTYPE]: 
        string - the biotype e.g. "protein_coding"
  Arg [-STATUS]:
        string - the transcripts status i.e. "KNOWN","NOVEL"
  Arg [-IS_CURRENT]:
        Boolean - specifies if this is the current version of the transcript
  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

Code:

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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, $status,       $is_current
  );

  # Catch for old style constructor calling:
  if ( ( @_ > 0 ) && ref( $_[0] ) ) {
    $exons = [@_];
    deprecate( "Transcript constructor should use named arguments.\n"
        . "Use Bio::EnsEMBL::Transcript->new(-EXONS => \@exons);\n"
        . "instead of Bio::EnsEMBL::Transcript->new(\@exons);" );
  } else {
    (
      $exons,            $stable_id,    $version,
      $external_name,    $external_db,  $external_status,
      $display_xref,     $created_date, $modified_date,
      $description,      $biotype,      $confidence,
      $external_db_name, $status,       $is_current
      )
      = rearrange( [
        'EXONS',            'STABLE_ID',
        'VERSION',          'EXTERNAL_NAME',
        'EXTERNAL_DB',      'EXTERNAL_STATUS',
        'DISPLAY_XREF',     'CREATED_DATE',
        'MODIFIED_DATE',    'DESCRIPTION',
        'BIOTYPE',          'CONFIDENCE',
        'EXTERNAL_DB_NAME', 'STATUS',
        'IS_CURRENT'
      ],
      @_
      );
  }

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

  $self->stable_id($stable_id);
  $self->version($version);
  $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);
  $self->status($confidence);    # old style name
  $self->status($status);        # new style name
  $self->biotype($biotype);

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

  return $self;
} ## end sub new

Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Feature Bio::EnsEMBL::Feature::new_fast ( ) [inherited]

  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Feature
  Caller     : general, subclass constructors
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::AssemblyExceptionFeature, Bio::EnsEMBL::BaseAlignFeature, Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::DnaPepAlignFeature, Bio::EnsEMBL::MiscFeature, Bio::EnsEMBL::RepeatFeature, and Bio::EnsEMBL::SimpleFeature.

public Boolean Bio::EnsEMBL::Feature::overlaps ( ) [inherited]

  Arg [1]    : Bio::EnsEMBL::Feature $f
               The other feature you want to check overlap with this feature
               for.
  Description: This method does a range comparison of this features start and
               end and compares it with another features start and end. It will
               return true if these ranges overlap and the features are on the
               same seq_region.
  Returntype : TRUE if features overlap, FALSE if they don't
  Exceptions : warning if features are on different seq_regions
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Transcript::pep2genomic ( )

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

Code:

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public List Bio::EnsEMBL::Feature::project ( ) [inherited]

  Arg [1]    : string $name
               The name of the coordinate system to project this feature onto
  Arg [2]    : string $version (optional)
               The version of the coordinate system (such as 'NCBI34') to
               project this feature onto
  Example    :
    my $clone_projection = $feature->project('clone');

    foreach my $seg (@$clone_projection) {
      my $clone = $seg->to_Slice();
      print "Features current coords ", $seg->from_start, '-',
        $seg->from_end, " project onto clone coords " .
        $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
        $clone->strand, "\\n";
    }
  Description: Returns the results of 'projecting' this feature onto another
               coordinate system.  This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.

               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]

               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.

               If the feature projects entirely into a gap then a reference to
               an empty list is returned.

  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : Stable

Code:

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public List Bio::EnsEMBL::Feature::project_to_slice ( ) [inherited]

  Arg [1]    : slice to project to

  Example    :
    my $clone_projection = $feature->project_to_slice($slice);

    foreach my $seg (@$clone_projection) {
      my $clone = $seg->to_Slice();
      print "Features current coords ", $seg->from_start, '-',
        $seg->from_end, " project onto clone coords " .
        $clone->seq_region_name, ':', $clone->start, '-', $clone->end,
        $clone->strand, "\\n";
    }
  Description: Returns the results of 'projecting' this feature onto another
               slcie . This is useful to see where a feature
               would lie in a coordinate system in which it
               crosses a boundary.

               This method returns a reference to a list of
               Bio::EnsEMBL::ProjectionSegment objects.
               ProjectionSegments are blessed arrays and can also be used as
               triplets [from_start,from_end,to_Slice]. The from_start and
               from_end are the coordinates relative to the feature start.
               For example, if a feature is current 100-200bp on a slice
               then the triplets returned might be:
               [1,50,$slice1],
               [51,101,$slice2]

               The to_Slice is a slice spanning the region on the requested
               coordinate system that this feature projected to.

               If the feature projects entirely into a gap then a reference to
               an empty list is returned.

  Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
               which can also be used as [$start,$end,$slice] triplets
  Exceptions : slice does not have an adaptor
  Caller     : general
  Status     : At Risk

Code:

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public Bio::EnsEMBL::Transcript::recalculate_coordinates ( )

Undocumented method

Code:

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public Bio::Seq Bio::EnsEMBL::Transcript::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 dna_seq does.
  Args       : none
  Example    : none
  Returntype : Bio::Seq
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public Int Bio::EnsEMBL::Feature::seq_region_end ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->seq_region_end();
  Description: Convenience method which returns the absolute end of this
               feature on the seq_region, as opposed to the relative (slice)
               position.

               Returns undef if this feature is not on a slice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Unsigned Bio::EnsEMBL::Feature::seq_region_length ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->seq_region_length();
  Description: Returns the length of the seq_region which this feature is on 
               Returns undef if this Feature is not on a slice.
  Returntype : unsigned int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Feature::seq_region_name ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->seq_region_name();
  Description: Gets the name of the seq_region which this feature is on.
               Returns undef if this Feature is not on a slice.
  Returntype : string or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Int Bio::EnsEMBL::Feature::seq_region_start ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->seq_region_start();
  Description: Convenience method which returns the absolute start of this
               feature on the seq_region, as opposed to the relative (slice) 
               position.

               Returns undef if this feature is not on a slice.
  Returntype : int or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Boolean Bio::EnsEMBL::Feature::seq_region_strand ( ) [inherited]

  Arg [1]    : none
  Example    : print $feature->seq_region_strand();
  Description: Returns the strand of the seq_region which this feature is on 
               (i.e. feature_strand * slice_strand)
               Returns undef if this Feature is not on a slice.
  Returntype : 1,0,-1 or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public String Bio::EnsEMBL::Feature::seqname ( ) [inherited]

  Arg [1]    : (optional) $seqname
  Example    : $seqname = $feat->seqname();
  Description: Getter/Setter for the name of the sequence that this feature
               is on. Normally you can get away with not setting this value
               and it will default to the name of the slice on which this
               feature is on.  It is useful to set this value on features which
               do not ordinarily sit on features such as ProteinFeatures which
               sit on peptides.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Feature::slice ( ) [inherited]

  Arg [1]    : (optional) Bio::EnsEMBL::Slice $slice
  Example    : $seqname = $feature->slice()->name();
  Description: Getter/Setter for the Slice that is associated with this 
               feature.  The slice represents the underlying sequence that this
               feature is on.  Note that this method call is analagous to the
               old SeqFeature methods contig(), entire_seq(), attach_seq(),
               etc.
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : thrown if an invalid argument is passed
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Exon, and Bio::EnsEMBL::Map::DitagFeature.

public Bio::EnsEMBL::Transcript::sort ( )

Description:

Deprecated:: . This method is no longer needed. Exons are sorted automatically when added to the transcript.

Code:

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public String Bio::EnsEMBL::Feature::species ( ) [inherited]

  Example			: $feature->species();
  Description	: Shortcut to the feature's DBAdaptor and returns its species name 
  Returntype 	: String the species name
  Exceptions 	: Thrown if there is no attached adaptor
  Caller      : Webcode

Code:

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Reimplemented in Bio::EnsEMBL::FeaturePair.

public Text Bio::EnsEMBL::Transcript::spliced_seq ( )

  Args       : none
  Example    : none
  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

Code:

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public String Bio::EnsEMBL::Transcript::stable_id ( )

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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Int Bio::EnsEMBL::Feature::start ( ) [inherited]

  Arg [1]    : (optional) int $start
               The start of this feature relative to the start of the slice
               that it is on.
  Example    : $start = $feat->start()
  Description: Getter/Setter for the start of this feature relative to the 
               start of the slice it is on.  Note that negative values, or
               values exceeding the length of the slice are permitted.
               Start must be less than or equal to the end regardless of the 
               strand. Coordinate values start at 1 and are inclusive.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::Exon, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::SplicingEventFeature, and Bio::EnsEMBL::SplicingTranscriptPair.

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Transcript::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

Code:

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public String Bio::EnsEMBL::Transcript::status ( )

  Arg [1]    : string $status
  Example    : none
  Description: get/set for attribute status
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Medium Risk

Code:

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public Int Bio::EnsEMBL::Feature::strand ( ) [inherited]

  Arg [1]    : (optional) int $strand
  Example    : $feat->strand(-1);
  Description: Getter/Setter for the strand of this feature relative to the
               slice it is on.  0 is an unknown or non-applicable strand.  
               -1 is the reverse (negative) strand and 1 is the forward 
               (positive) strand.  No other values are permitted.
  Returntype : int
  Exceptions : thrown if an invalid strand argument is passed
  Caller     : general
  Status     : Stable

Code:

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Reimplemented in Bio::EnsEMBL::DensityFeature, Bio::EnsEMBL::Exon, Bio::EnsEMBL::KaryotypeBand, Bio::EnsEMBL::Map::DitagFeature, Bio::EnsEMBL::Map::QtlFeature, and Bio::EnsEMBL::ProteinFeature.

public Bio::EnsEMBL::Feature::sub_SeqFeature ( ) [inherited]

Undocumented method

Code:

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public Hashref Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

public void Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Transcript::temporary_id ( )

Function:

Deprecated:: : Use dbID or stable_id or something else instead

Code:

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public Bio::Seq Bio::EnsEMBL::Transcript::three_prime_utr ( )

  Arg [1]    : none
  Example    : my $three_prime  = $transcrpt->three_prime_utr
                 or warn "No five 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

Code:

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public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::Transcript::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

Code:

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sub transform {
  my $self = shift;

  # catch for old style transform calls
  if( ref $_[0] eq 'HASH') {
    deprecate("Calling transform with a hashref is deprecate.\n" .
              'Use $trans->transfer($slice) or ' .
              '$trans->transform("coordsysname") instead.');
    my (undef, $new_ex) = each(%{$_[0]});
    return $self->transfer($new_ex->slice);
  }

  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;
  }


  # 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;
}

Reimplemented from Bio::EnsEMBL::Feature.

Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::Seq Bio::EnsEMBL::Transcript::translate ( )

  Args       : none
  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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Text Bio::EnsEMBL::Transcript::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

Code:

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public Bio::EnsEMBL::Translation Bio::EnsEMBL::Transcript::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

Code:

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Reimplemented in Bio::EnsEMBL::PredictionTranscript.

public Bio::EnsEMBL::Transcript::type ( )

  Description:
Deprecated:
. Use biotype() instead.

Code:

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public String Bio::EnsEMBL::Transcript::version ( )

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

Code:

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The documentation for this class was generated from the following file:

Bio/EnsEMBL/Transcript.pm

Class Summary

Synopsis

Description

Available Methods

Method Documentation