Bio::EnsEMBL::CDS Class Reference

Inheritance diagram for Bio::EnsEMBL::CDS:

Public Member Functions
public Bio::EnsEMBL::CDS	new ()
public Bio::EnsEMBL::Transcript	transcript ()
public Bio::EnsEMBL::Translation	translation ()
public String	seq_region_start ()
public String	seq_region_end ()
public Bio::EnsEMBL::Gene	get_Gene ()
public String	translation_id ()
public Int	phase ()
public Hash	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::CDS;
 
$feature = Bio::EnsEMBL::CDS->new(
  -start         => 100,
  -end           => 220,
  -strand        => -1,
  -slice         => $slice,
  -phase         => 1,
  -transcript    => $transcript
);

Description

This is a CDS feature within the Ensembl CDS.
It represents the coding regions of a transcript.

Definition at line 28 of file CDS.pm.

Member Function Documentation

get_Gene()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::CDS::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::CDS Bio::EnsEMBL::CDS::new

(

)

  Arg [...]  : Named arguments passed to superclass
  Example    :

$feature = Bio::EnsEMBL::CDS->new
                       (-start   => 1,
                        -end     => 100,
                        -strand  => 1,
                        -slice   => $slice,
                        -dbID    => 10,
                        -transcript  => $transcript,
                        -phase   => 1);

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

Code:

phase()

public Int Bio::EnsEMBL::CDS::phase

(

)

  Arg [1]    : (optional) string $phase
  Example    :

print $cds->phase();

  Description: This method returns an integer that describes
               the phase of the coding feature
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

seq_region_end()

public String Bio::EnsEMBL::CDS::seq_region_end

(

)

  Arg [1]    : (optional) string $seq_region_end
  Example    :

$seq_region_end = $cds->seq_region_end();

  Description: Getter/Setter for the seq_region_end for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

seq_region_start()

public String Bio::EnsEMBL::CDS::seq_region_start

(

)

  Arg [1]    : (optional) string $seq_region_start
  Example    :

$seq_region_start = $cds->seq_region_start();

  Description: Getter/Setter for the seq_region_start for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hash Bio::EnsEMBL::CDS::summary_as_hash

(

)

  Example    :

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

  Description: Generates a HashRef compatible with GFFSerializer. Adds
               Parent, source and phase to the basic feature hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transcript()

public Bio::EnsEMBL::Transcript Bio::EnsEMBL::CDS::transcript

(

)

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

$transcript = $cds->transcript();

  Description: Getter/Setter for the transcript associated with this
               CDS.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

translation()

public Bio::EnsEMBL::Translation Bio::EnsEMBL::CDS::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:

translation_id()

public String Bio::EnsEMBL::CDS::translation_id

(

)

  Arg [1]    : (optional) string $translation_id
  Example    :

$translation_id = $cds->translation_id();

  Description: Getter/Setter for the stable_id for the translation
               associated with this CDS.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/CDS.pm