Bio::EnsEMBL::PredictionTranscript Class Reference

Inheritance diagram for Bio::EnsEMBL::PredictionTranscript:

List of all members.

---

Class Summary

Synopsis

Description

Container for single transcript ab initio gene prediction such as
GenScan or SNAP. Is directly storable/retrievable in Ensembl using
PredictionTranscriptAdaptor.

Creation:

  my $tran = new Bio::EnsEMBL::PredictionTranscript();
  $tran->add_Exon($pred_exon);

  my $tran =
    new Bio::EnsEMBL::PredictionTranscript( -EXONS => @pred_exons );

Manipulation:

  # Returns an array of PredictionExon objects
  my @pred_exons = @{ $tran->get_all_Exons };

  # Returns the peptide translation as string
  my $pep = $tran->translate()->seq();

  # Get the exon cdna sequence.
  my $cdna = $trans->spliced_seq();

Definition at line 38 of file PredictionTranscript.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	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 String	display_label ()
public Bio::EnsEMBL::DBEntry	display_xref ()
public Boolean	edits_enabled ()
public Int	end ()
public Bio::EnsEMBL::Exon	end_Exon ()
public Boolean	equals ()
public	external_db ()
public	external_name ()
public	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 EMPTY	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	get_all_DBEntries ()
public	get_all_DBLinks ()
public A	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	get_cdna ()
public	get_exon_count ()
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	is_known ()
public Boolean	is_stored ()
public Int	length ()
public void	load ()
public	modified ()
public String	modified_date ()
public void	move ()
public Bio::EnsEMBL::PredictionTranscript	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	set_exon_count ()
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::PredictionTranscript	transfer ()
public Bio::EnsEMBL::PredictionTranscript	transform ()
public A	translate ()
public Text	translateable_seq ()
public Int	translation ()
public	type ()
public String	version ()

---

Method Documentation

protected Bio::EnsEMBL::Transcript::_compare_xrefs

(

)

[inherited]

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

Code:

protected Bio::EnsEMBL::Feature::_deprecated_transform

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Transcript::_translation_id

(

)

[inherited]

Undocumented method

Code:

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:

public void Bio::EnsEMBL::Transcript::add_alternative_translation

(

)

[inherited]

  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:

public void Bio::EnsEMBL::Transcript::add_Attributes

(

)

[inherited]

  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:

public Bio::EnsEMBL::PredictionTranscript::add_DBEntry

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public void Bio::EnsEMBL::Transcript::add_Exon

(

)

[inherited]

 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:

public Bio::EnsEMBL::Feature::add_sub_SeqFeature

(

)

[inherited]

Undocumented method

Code:

public void Bio::EnsEMBL::Transcript::add_supporting_features

(

)

[inherited]

  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:

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:

Reimplemented in Bio::EnsEMBL::DensityFeature.

public String Bio::EnsEMBL::Transcript::biotype

(

)

[inherited]

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

Code:

public Bio::EnsEMBL::Transcript::cdna2genomic

(

)

[inherited]

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

Code:

public Int Bio::EnsEMBL::PredictionTranscript::cdna_coding_end

(

)

  Arg [1]    : none
  Example    : $relative_coding_start = $transcript->cdna_coding_end();
  Description: Retrieves the position of the coding end of this transcript
               in cdna coordinates (relative to the start of the 5prime end of
               the transcript, excluding introns, including utrs). This is
               always te length of the cdna for prediction transcripts because
               they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Int Bio::EnsEMBL::PredictionTranscript::cdna_coding_start

(

)

  Arg [1]    : none
  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 is
               always 1 for prediction transcripts because they have no UTRs.
  Returntype : int
  Exceptions : none
  Caller     : five_prime_utr, get_all_snps, general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Int Bio::EnsEMBL::PredictionTranscript::coding_region_end

(

)

  Arg [1]    : none
  Example    : $coding_region_end = $transcript->coding_region_end
  Description: Retrieves the start of the coding region of this prediction
               transcript. For prediction transcripts this is always the same
               as the end since no UTRs are stored.
               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 start since on the reverse strand the biological coding
               end would be the lower genomic value.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Int Bio::EnsEMBL::PredictionTranscript::coding_region_start

(

)

  Arg [1]    : none
  Example    : $coding_region_start = $pt->coding_region_start
  Description: Retrieves the start of the coding region of this transcript in
               slice coordinates.  For prediction transcripts this
               is always the start of the transcript (i.e. there is no UTR).
               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.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Transcript::confidence

(

)

[inherited]

  Description:

Deprecated:
. Use status() instead.

Code:

public Bio::EnsEMBL::Feature::contig

(

)

[inherited]

Undocumented method

Code:

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:

public Bio::EnsEMBL::Transcript::created

(

)

[inherited]

 Description:

Deprecated:

this attribute is not part of transcript anymore

Code:

public String Bio::EnsEMBL::Transcript::created_date

(

)

[inherited]

  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:

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

Code:

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

public String Bio::EnsEMBL::Transcript::description

(

)

[inherited]

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

Code:

public String Bio::EnsEMBL::PredictionTranscript::display_id

(

)

  Arg [1]    : none
  Example    : print $rf->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier. For prediction 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:

Reimplemented from Bio::EnsEMBL::Transcript.

public String Bio::EnsEMBL::PredictionTranscript::display_label

(

)

  Arg [1]    : string $newval (optional)
               The new value to set the display_label attribute to
  Example    : $display_label = $pt->display_label()
  Description: Getter/Setter for a displayable identifier for this
               prediction transcript.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

(

)

[inherited]

  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:

public Boolean Bio::EnsEMBL::Transcript::edits_enabled

(

)

[inherited]

  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:

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

Code:

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

(

)

[inherited]

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

Code:

public Boolean Bio::EnsEMBL::Transcript::equals

(

)

[inherited]

  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:

Reimplemented from Bio::EnsEMBL::Feature.

public Bio::EnsEMBL::PredictionTranscript::external_db

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::PredictionTranscript::external_name

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::PredictionTranscript::external_status

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

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

Code:

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

(

)

[inherited]

  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:

public void Bio::EnsEMBL::Transcript::flush_Exons

(

)

[inherited]

  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

Code:

public Bio::EnsEMBL::Feature::flush_sub_SeqFeature

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Transcript::flush_supporting_features

(

)

[inherited]

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

Code:

public Bio::EnsEMBL::Transcript::genomic2cdna

(

)

[inherited]

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

Code:

public Bio::EnsEMBL::Transcript::genomic2pep

(

)

[inherited]

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

Code:

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:

public Arrayref Bio::EnsEMBL::Transcript::get_all_alternative_translations

(

)

[inherited]

  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:

public EMPTY Bio::EnsEMBL::PredictionTranscript::get_all_Attributes

(

)

  Arg [1]    : none
  Example    :
  Description: DOES NOTHING, Returns empty listref. Provided here to prevent
               Transcript attributes being returned for PredictionTranscripts.
  Returntype : EMPTY listref Bio::EnsEMBL::Attribute
  Exceptions : none
  Caller     : general
  Status     : At risk

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Transcript::get_all_cdna_SNPs

(

)

[inherited]

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

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

Code:

public Listref Bio::EnsEMBL::Transcript::get_all_constitutive_Exons

(

)

[inherited]

  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:

public Hashref Bio::EnsEMBL::Transcript::get_all_DAS_Features

(

)

[inherited]

  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:

Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Transcript::get_all_DASFactories

(

)

[inherited]

  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:

public Bio::EnsEMBL::PredictionTranscript::get_all_DBEntries

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::PredictionTranscript::get_all_DBLinks

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public A Bio::EnsEMBL::PredictionTranscript::get_all_Exons

(

)

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

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Listref Bio::EnsEMBL::Transcript::get_all_Introns

(

)

[inherited]

  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:

public Listref Bio::EnsEMBL::Transcript::get_all_object_xrefs

(

)

[inherited]

  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:

public Bio::EnsEMBL::Transcript::get_all_peptide_variations

(

)

[inherited]

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

Code:

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

(

)

[inherited]

  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:

public Bio::EnsEMBL::Transcript::get_all_SNPs

(

)

[inherited]

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

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

Code:

public Listref Bio::EnsEMBL::Transcript::get_all_supporting_features

(

)

[inherited]

  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:

public Listref Bio::EnsEMBL::PredictionTranscript::get_all_translateable_Exons

(

)

  Arg [1]    : none
  Example    : $exons = $self->get_all_translateable_Exons
  Description: Retrieves the translateable portion of all exons in this
               transcript.  For prediction transcripts this means all exons
               since no UTRs are stored for them.
  Returntype : listref of Bio::EnsEMBL::PredictionExons
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Listref Bio::EnsEMBL::Transcript::get_all_xrefs

(

)

[inherited]

  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:

public Bio::EnsEMBL::PredictionTranscript::get_cdna

(

)

  Description :

Deprecated:

use spliced_seq() or translateable_seq instead

Code:

public Bio::EnsEMBL::PredictionTranscript::get_exon_count

(

)

  Description:

Deprecated:

use get_all_Exons instead

Code:

public Bio::EnsEMBL::Gene Bio::EnsEMBL::Transcript::get_Gene

(

)

[inherited]

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

Code:

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:

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:

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

(

)

[inherited]

  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:

public Bio::EnsEMBL::Feature::id

(

)

[inherited]

Undocumented method

Code:

public Boolean Bio::EnsEMBL::Transcript::is_canonical

(

)

[inherited]

  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:

public Int Bio::EnsEMBL::Transcript::is_current

(

)

[inherited]

  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:

public Bio::EnsEMBL::PredictionTranscript::is_known

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

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:

public Int Bio::EnsEMBL::Transcript::length

(

)

[inherited]

  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:

Reimplemented from Bio::EnsEMBL::Feature.

public void Bio::EnsEMBL::Transcript::load

(

)

[inherited]

  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:

public Bio::EnsEMBL::Transcript::modified

(

)

[inherited]

  Description:

Deprecated:

this attribute is not part of transcript anymore

Code:

public String Bio::EnsEMBL::Transcript::modified_date

(

)

[inherited]

  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:

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:

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

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::new

(

)

  Arg [-DISPLAY_LABEL]
    string - a displayable identifier for this prediction
  Arg [...]  : See Bio::EnsEMBL::Transcript superclass constructor
  Example    : $pt = Bio::EnsEMBL::PredictionTranscript->new
                  ( '-start'         =>  $seq_region_start,
                    '-end'           =>  $seq_region_end,
                    '-strand'        =>  $seq_region_strand,
                    '-adaptor'       =>  $self,
                    '-slice'         =>  $slice,
                    '-analysis'      =>  $analysis,
                    '-dbID'          =>  $prediction_transcript_id,
                    '-display_label' =>  $display_label);
  Description: Constructor. Creates a new Bio::EnsEMBL::PredictionTranscript
               object
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

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:

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:

public Bio::EnsEMBL::Transcript::pep2genomic

(

)

[inherited]

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

Code:

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:

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:

public Bio::EnsEMBL::Transcript::recalculate_coordinates

(

)

[inherited]

Undocumented method

Code:

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

(

)

[inherited]

  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:

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:

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:

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:

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:

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:

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:

public Bio::EnsEMBL::PredictionTranscript::set_exon_count

(

)

  Description:

Deprecated:

this method does nothing now

Code:

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:

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

public Bio::EnsEMBL::Transcript::sort

(

)

[inherited]

  Description:

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

Code:

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:

Reimplemented in Bio::EnsEMBL::FeaturePair.

public Text Bio::EnsEMBL::Transcript::spliced_seq

(

)

[inherited]

  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:

public String Bio::EnsEMBL::PredictionTranscript::stable_id

(

)

  Arg [1]    : none
  Example    : print $pt->stable_id();
  Description: Gets a 'stable' identifier for this prediction transcript.  Note
               that prediction transcripts do not have true *stable*
               identifiers (i.e. identifiers maintained between releases).
               This method chains to the display_label method and is intended
               to provide polymorphism with the Transcript class.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

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:

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

(

)

[inherited]

 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:

public String Bio::EnsEMBL::Transcript::status

(

)

[inherited]

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

Code:

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:

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:

public Hashref Bio::EnsEMBL::Transcript::summary_as_hash

(

)

[inherited]

  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:

Reimplemented from Bio::EnsEMBL::Feature.

public void Bio::EnsEMBL::Transcript::swap_exons

(

)

[inherited]

  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:

public Bio::EnsEMBL::Transcript::temporary_id

(

)

[inherited]

 Function:

Deprecated:
: Use dbID or stable_id or something else instead

Code:

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

(

)

[inherited]

  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:

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::transfer

(

)

  Arg  1     : Bio::EnsEMBL::Slice $destination_slice
  Example    : $ptrans = $ptrans->transfer($slice);
  Description: Moves this PredictionTranscript to the given slice.
               If this Transcripts has Exons attached, they move as well.
               If this transcript cannot be moved then undef is returned
               instead.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionTranscript::transform

(

)

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Example    : $ptrans = $ptrans->transform('chromosome', 'NCBI33');
               $ptrans = $ptrans->transform('clone');
  Description: Moves this PredictionTranscript to the given coordinate system.
               If this Transcript has Exons attached, they move as well.
               A new Transcript is returned or undefined if this PT is not
               defined in the new coordinate system.
  Returntype : Bio::EnsEMBL::PredictionTranscript
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public A Bio::EnsEMBL::PredictionTranscript::translate

(

)

  Args      : none
  Function  : Give a peptide translation of all exons currently in
              the PT. Gives empty string when none is in.
  Returntype: a Bio::Seq as in transcript->translate()
  Exceptions: none
  Caller    : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Text Bio::EnsEMBL::Transcript::translateable_seq

(

)

[inherited]

  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:

public Int Bio::EnsEMBL::PredictionTranscript::translation

(

)

  Arg [1]    : none
  Example    : $translation = $pt->translation();
  Description: Retrieves a Bio::EnsEMBL::Translation object for this prediction
               transcript.  Note that this translation is generated on the fly
               and is not stored in the database.  The translation always
               spans the entire transcript (no UTRs; all CDS) and does not
               have an associated dbID, stable_id or adaptor.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

Reimplemented from Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Transcript::type

(

)

[inherited]

  Description:

Deprecated:
. Use biotype() instead.

Code:

public String Bio::EnsEMBL::Transcript::version

(

)

[inherited]

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

Code:

---

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

• Bio/EnsEMBL/PredictionTranscript.pm