Bio::EnsEMBL::ExonTranscript Class Reference

Inheritance diagram for Bio::EnsEMBL::ExonTranscript:

Public Member Functions
public Bio::EnsEMBL::ExonTranscript	new ()
public Bio::EnsEMBL::Exon	exon ()
public Bio::EnsEMBL::Transcript	transcript ()
public Bio::EnsEMBL::Translation	translation ()
public Bio::EnsEMBL::Gene	get_Gene ()
public String	rank ()
public Hash	summary_as_hash ()
Public Member Functions inherited from Bio::EnsEMBL::Exon
public Bio::EnsEMBL::Exon	new ()
public Int	end_phase ()
public Int	phase ()
public Int	frame ()
public Int	start ()
public Int	end ()
public Int	strand ()
public Int	cdna_start ()
public Int	cdna_end ()
public Int	cdna_coding_start ()
public Int	cdna_coding_end ()
public Int	coding_region_start ()
public Int	coding_region_end ()
public Int	rank ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean	equals ()
public void	move ()
public Bio::EnsEMBL::Exon	transform ()
public Bio::EnsEMBL::Exon	transfer ()
public void	add_supporting_features ()
public	flush_supporting_features ()
public Listreference	get_all_supporting_features ()
public void	find_supporting_evidence ()
public String	stable_id ()
public String	created_date ()
public String	modified_date ()
public String	version ()
public String	stable_id_version ()
public Int	is_current ()
public Int	is_constitutive ()
public Int	is_coding ()
public Bio::EnsEMBL::Exon	adjust_start_end ()
public Bio::Seq	peptide ()
protected Bio::EnsEMBL::Mapper::Coordinate	_merge_ajoining_coords ()
public Bio::Seq	seq ()
public String	hashkey ()
public String	display_id ()
public Nothing	load ()
public Hashref	summary_as_hash ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Synopsis

use Bio::EnsEMBL::ExonTranscript;
 
$feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);

Description

This is a feature which extends the Exon class to add
the relation to a specific transcript.

Definition at line 20 of file ExonTranscript.pm.

Member Function Documentation

exon()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::ExonTranscript::exon

(

)

  Arg [1]    : (optional) Bio::EnsEMBL::Exon
  Example    :

$exon = $exon_transcript->exon();

  Description: Getter/Setter for the exon forming this
               ExonTranscript.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

get_Gene()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::ExonTranscript::get_Gene

(

)

  Description: Get the gene associated with the ExonTranscript,
               if a transcript has been set
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::ExonTranscript Bio::EnsEMBL::ExonTranscript::new

(

)

  Arg [Exon]: The Exon object
  Arg [Transcript]: The Transcript object the exon belongs to
  Example    :

$feature = Bio::EnsEMBL::ExonTranscript->new(-exon => $exon, -transcript => $transcript);

  Description: Constructs a new Bio::EnsEMBL::ExonTranscript.
  Returntype : Bio::EnsEMBL::ExonTranscript
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable

Code:

rank()

public String Bio::EnsEMBL::ExonTranscript::rank

(

)

  Example    :

print $et->rank();

  Description: Getter/Setter for the exon rank
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hash Bio::EnsEMBL::ExonTranscript::summary_as_hash

(

)

  Example    :

my $hash = $utr->summary_as_hash();

  Description: Generates a HashRef compatible with GFFSerializer. Adds
               rank and transcript attributes to the basic Feature
               hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transcript()

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::ExonTranscript::transcript

(

)

  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    :

print $utr->type();

  Description: Getter/Setter for the parent transcript
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

translation()

public Bio::EnsEMBL::Translation Bio::EnsEMBL::ExonTranscript::translation

(

)

    Description: Fetch the translation associated with
                 this transcript, if it exists. Return undef
                 if there is no translation, ie. a pseudogene
    Returntype : Bio::EnsEMBL::Translation or undef
    Caller     : general
    Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/ExonTranscript.pm