Bio::EnsEMBL::PredictionExon Class Reference

Inheritance diagram for Bio::EnsEMBL::PredictionExon:

Public Member Functions
public Bio::EnsEMBL::PredictionExon	new ()
public String	score ()
public String	p_value ()
public Int	end_phase ()
public Bio::EnsEMBL::Exon	transform ()
public Bio::EnsEMBL::Gene	transfer ()
public Hashref	summary_as_hash ()
public Bio::EnsEMBL::PredictionTranscript	transcript ()
public Bio::EnsEMBL::PredictionTranscript	prediction_transcript ()
public void	add_supporting_features ()
public Empty	get_all_supporting_features ()
public Empty	find_supporting_evidence ()
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

$exon = new Bio::EnsEMBL::PredictionExon(
  -START   => 100,
  -END     => 200,
  -STRAND  => 1,
  -SLICE   => $slice,
  -DBID    => $dbID,
  -P_VALUE => 23.5,
  -SCORE   => 99
);
 
# seq() returns a Bio::Seq
my $seq = $exon->seq->seq();
 
# peptide() only makes sense within transcript context
my $pep = $exon->peptide($transcript)->seq();
 
# Normal feature operations can be performed:
$exon = $exon->transform('clone');
$exon->move( $new_start, $new_end, $new_strand );
print $exon->slice->seq_region_name();

Description

This is a class which represents an prediction exon which is part of a
predcition transcript. See Bio::EnsEMBL:PredictionTranscript

Definition at line 38 of file PredictionExon.pm.

Member Function Documentation

add_supporting_features()

public void Bio::EnsEMBL::PredictionExon::add_supporting_features

(

)

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : none
  Status     : Stable

Code:

end_phase()

public Int Bio::EnsEMBL::PredictionExon::end_phase

(

)

  Arg [1]    : (optional) int $end_phase
  Example    :

$end_phase = $feat->end_phase;

  Description: Gets/Sets the end phase of the exon.
               end_phase = number of bases from the last incomplete codon of 
               this exon.
               Usually, end_phase = (phase + exon_length)%3
               but end_phase could be -1 if the exon is half-coding and its 3 
               prime end is UTR.
  Returntype : int
  Exceptions : warning if end_phase is called without an argument and the
               value is not set.
  Caller     : general
  Status     : Stable

Code:

find_supporting_evidence()

public Empty Bio::EnsEMBL::PredictionExon::find_supporting_evidence

(

)

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : empty list.
  Status     : Stable

Code:

get_all_supporting_features()

public Empty Bio::EnsEMBL::PredictionExon::get_all_supporting_features

(

)

  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing and returns empty list
  Returntype : empty list.
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::PredictionExon Bio::EnsEMBL::PredictionExon::new

(

)

  Args       : see SUPERCLASS Bio::EnsEMBL::Exon
  Example    :

none

  Description: create an Exon object
  Returntype : Bio::EnsEMBL::PredictionExon 
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

p_value()

public String Bio::EnsEMBL::PredictionExon::p_value

(

)

  Arg [1]    : string $newval (optional) 
               The new value to set the p_value attribute to
  Example    :

$p_value = $obj->p_value()

  Description: Getter/Setter for the p_value attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

prediction_transcript()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionExon::prediction_transcript

(

)

  Example     :

$prediction_transcript = $exon->prediction_transcript;

  Description : Locates the parent prediction transcript using an exon dbID
  Returns     : Bio::EnsEMBL::PredictionTranscript

Code:

score()

public String Bio::EnsEMBL::PredictionExon::score

(

)

  Arg [1]    : string $newval (optional) 
               The new value to set the score attribute to
  Example    :

$score = $obj->score()

  Description: Getter/Setter for the score attribute
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

summary_as_hash()

public Hashref Bio::EnsEMBL::PredictionExon::summary_as_hash

(

)

  Example       :

$exon_summary = $exon->summary_as_hash();

  Description   : Extends Feature::summary_as_hash
                  Retrieves a summary of this prediction exon.
  Returns       : hashref of descriptive strings
  Status        : Intended for internal use
 

Code:

transcript()

public Bio::EnsEMBL::PredictionTranscript Bio::EnsEMBL::PredictionExon::transcript

(

)

  Example     :

$prediction_transcript = $exon->transcript;

  Description : Locates the parent prediction transcript using an exon dbID
                Same as prediction_transcript, duplicated for compatibility
                with Exon feature
  Returns     : Bio::EnsEMBL::PredictionTranscript

Code:

transfer()

public Bio::EnsEMBL::Gene Bio::EnsEMBL::PredictionExon::transfer

(

)

  Arg [1]    : Bio::EnsEMBL::Slice $destination_slice
  Example    :

none

  Description: Moves this Exon to given target slice coordinates. If Features
               are attached they are moved as well. Returns a new exon.
  Returntype : Bio::EnsEMBL::Gene
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

transform()

public Bio::EnsEMBL::Exon Bio::EnsEMBL::PredictionExon::transform

(

)

  Arg  1     : String $coordinate_system_name
  Arg [2]    : String $coordinate_system_version
  Description: moves this exon to the given coordinate system. If this exon has
               attached supporting evidence, they move as well.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : wrong parameters
  Caller     : general
  Status     : Stable

Code:

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

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