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Bio::EnsEMBL::PredictionExon Class Reference
Inheritance diagram for Bio::EnsEMBL::PredictionExon:

List of all members.


Class Summary

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.

Available Methods

protected _deprecated_transform ()
protected _get_stable_entry_info ()
protected
Bio::EnsEMBL::Mapper::Coordinate 
_merge_ajoining_coords ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public add_sub_SeqFeature ()
public void add_supporting_features ()
public Bio::EnsEMBL::Exon adjust_start_end ()
public Bio::EnsEMBL::Analysis analysis ()
public Int cdna_coding_end ()
public Int cdna_coding_start ()
public Int cdna_end ()
public Int cdna_start ()
public Int coding_region_end ()
public Int coding_region_start ()
public contig ()
public String coord_system_name ()
public created ()
public String created_date ()
public Int dbID ()
public String display_id ()
public Int end ()
public Int end_phase ()
public Boolean equals ()
public Bio::EnsEMBL::Slice feature_Slice ()
public Empty find_supporting_evidence ()
public flush_sub_SeqFeature ()
public flush_supporting_features ()
public Int frame ()
public Reference get_all_alt_locations ()
public get_all_DAS_Features ()
public Empty get_all_supporting_features ()
public Bio::EnsEMBL::Gene get_nearest_Gene ()
public List get_overlapping_Genes ()
public String hashkey ()
public id ()
public Int is_constitutive ()
public Int is_current ()
public Boolean is_stored ()
public Int length ()
public Nothing load ()
public modified ()
public String modified_date ()
public void move ()
public Bio::EnsEMBL::PredictionExon new ()
public Bio::EnsEMBL::Feature new_fast ()
public Boolean overlaps ()
public String p_value ()
public Bio::Seq peptide ()
public Int phase ()
public List project ()
public List project_to_slice ()
public String score ()
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 String species ()
public String stable_id ()
public Int start ()
public Int strand ()
public sub_SeqFeature ()
public Hashref summary_as_hash ()
public temporary_id ()
public Bio::EnsEMBL::Gene transfer ()
public Bio::EnsEMBL::Exon transform ()
public type ()
public String version ()

Method Documentation

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

Undocumented method

Code:
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protected Bio::EnsEMBL::Exon::_get_stable_entry_info ( ) [inherited]
  Description:

Deprecated:
.
 
Code:
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protected Bio::EnsEMBL::Mapper::Coordinate Bio::EnsEMBL::Exon::_merge_ajoining_coords ( ) [inherited]
 
   Arg [1]     : ArrayRef of Bio::EnsEMBL::Mapper::Coordinate objects
   Example     : 
   Description : Merges coords which are ajoining or overlapping
   Returntype  : Bio::EnsEMBL::Mapper::Coordinate or undef if it cannot happen
   Exceptions  : Exception if the cooords cannot be condensed into one location
   Caller      : internal
   Status      : Development
 
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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
 
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public Bio::EnsEMBL::Feature::add_sub_SeqFeature ( ) [inherited]

Undocumented method

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public void Bio::EnsEMBL::PredictionExon::add_supporting_features ( )
  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : none
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Exon.

public Bio::EnsEMBL::Exon Bio::EnsEMBL::Exon::adjust_start_end ( ) [inherited]
  Arg  1     : int $start_adjustment
  Arg  2     : int $end_adjustment
  Example    : none
  Description: returns a new Exon with this much shifted coordinates
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : none
  Caller     : Transcript->get_all_translateable_Exons()
  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 Int Bio::EnsEMBL::Exon::cdna_coding_end ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     : $cdna_coding_end = $exon->cdna_coding_end($transcript);
    Description : Returns the end position of the coding region of the
                  exon in cDNA coordinates.  Returns undef if the whole
                  exon is non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::cdna_coding_start ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     : $cdna_coding_start = $exon->cdna_coding_start($transcript);
    Description : Returns the start position of the coding region of the
                  exon in cDNA coordinates.  Returns undef if the whole
                  exon is non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::cdna_end ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     : $cdna_end = $exon->cdna_end($transcript);
    Description : Returns the end position of the exon in cDNA
                  coordinates.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer
    Exceptions  : Throws if the given argument is not a transcript.
                  Throws if the last part of the exon maps into a gap.
                  Throws if the exon can not be mapped at all.
    Caller      : General
    Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::cdna_start ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
                  The transcript for which cDNA coordinates should be
                  relative to.
    Example     : $cdna_start = $exon->cdna_start($transcript);
    Description : Returns the start position of the exon in cDNA
                  coordinates.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer
    Exceptions  : Throws if the given argument is not a transcript.
                  Throws if the first part of the exon maps into a gap.
                  Throws if the exon can not be mapped at all.
    Caller      : General
    Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::coding_region_end ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
    Example     : $coding_region_end =
                    $exon->coding_region_end($transcript);
    Description : Returns the end position of the coding region of
                  the exon in slice-relative coordinates on the
                  forward strand.  Returns undef if the whole exon is
                  non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::coding_region_start ( ) [inherited]
    Arg [1]     : Bio::EnsEMBL::Transcript $transcript
    Example     : $coding_region_start =
                    $exon->coding_region_start($transcript);
    Description : Returns the start position of the coding region
                  of the exon in slice-relative coordinates on the
                  forward strand.  Returns undef if the whole exon is
                  non-coding.
                  Since an exon may be part of one or more transcripts,
                  the relevant transcript must be given as argument to
                  this method.
    Return type : Integer or undef
    Exceptions  : Throws if the given argument is not a transcript.
    Caller      : General
    Status      : Stable
 
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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::Exon::created ( ) [inherited]
  Description:

Deprecated:
. Do not use.
 
Code:
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public String Bio::EnsEMBL::Exon::created_date ( ) [inherited]
  Arg [1]    : string $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
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::Exon::display_id ( ) [inherited]
  Arg [1]    : none
  Example    : print $exons->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier. For exons 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.

public Int Bio::EnsEMBL::Exon::end ( ) [inherited]
  Arg [1]    : int $end (optional)
  Example    : $end = $exon->end();
  Description: Getter/Setter for the end of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

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:
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Reimplemented from Bio::EnsEMBL::Exon.

public Boolean Bio::EnsEMBL::Exon::equals ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::Exon exon
  Example       : if ($exonA->equals($exonB)) { ... }
  Description   : Compares two exons 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 exons are *not* equal.
                  2. If both exons have stable IDs: if these are the
                     same, the exons are equal, otherwise not.
                  3. If the exons have the same start, end, strand, and
                     phase, 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 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 Empty Bio::EnsEMBL::PredictionExon::find_supporting_evidence ( )
  Description: For compatibility with Bio::EnsEMBL::Exon
               Does nothing.
  Returntype : empty list.
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Exon.

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

Undocumented method

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public Bio::EnsEMBL::Exon::flush_supporting_features ( ) [inherited]
  Example     : $exon->flush_supporting_features;
  Description : Removes all supporting evidence from the exon.
  Return type : (Empty) listref
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::frame ( ) [inherited]
  Arg [1]    : none
  Example    : $frame = $exon->frame
  Description: Gets the frame of this exon
  Returntype : int
  Exceptions : thrown if an arg is passed
               thrown if frame cannot be calculated due to a bad phase value
  Caller     : general
  Status     : Stable
 
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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
 
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

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:
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Reimplemented from Bio::EnsEMBL::Exon.

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
 
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public String Bio::EnsEMBL::Exon::hashkey ( ) [inherited]
  Arg [1]    : none
  Example    : if(exists $hash{$exon->hashkey}) { do_something(); }
  Description: Returns a unique hashkey that can be used to uniquely identify
               this exon.  Exons are considered to be identical if they share
               the same seq_region, start, end, strand, phase, end_phase.
               Note that this will consider two exons on different slices
               to be different, even if they actually are not. 
  Returntype : string formatted as slice_name-start-end-strand-phase-end_phase
  Exceptions : thrown if not all the necessary attributes needed to generate
               a unique hash value are set
               set
  Caller     : general
  Status     : Stable
 
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public Bio::EnsEMBL::Feature::id ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::Exon::is_constitutive ( ) [inherited]
  Arg [1]    : Boolean $is_constitutive
  Example    : $exon->is_constitutive(0)
  Description: Getter/setter for is_constitutive state of this exon.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public Int Bio::EnsEMBL::Exon::is_current ( ) [inherited]
  Arg [1]    : Boolean $is_current
  Example    : $exon->is_current(1)
  Description: Getter/setter for is_current state of this exon.
  Returntype : Int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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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
 
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public Int Bio::EnsEMBL::Feature::length ( ) [inherited]
  Arg [1]    : none
  Example    : $length = $feat->length();
  Description: Returns the length of this feature
  Returntype : Integer
  Exceptions : Throws if end < start and the feature is not on a
               circular slice
  Caller     : general
  Status     : Stable
 
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Reimplemented in Bio::EnsEMBL::Intron, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Upstream.

public Nothing Bio::EnsEMBL::Exon::load ( ) [inherited]
  Args          : None
  Example       : $exon->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.
  Returns       : Nothing.
 
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public Bio::EnsEMBL::Exon::modified ( ) [inherited]
  Description:

Deprecated:
. Do not use.
 
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public String Bio::EnsEMBL::Exon::modified_date ( ) [inherited]
  Arg [1]    : string $modified_date
  Example    : none
  Description: get/set for attribute modified_date
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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public void Bio::EnsEMBL::Exon::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.  This overrides the superclass
               move() method so that the internal sequence cache can be
               flushed if the exon if moved.
  Returntype : none
  Exceptions : Thrown is invalid arguments are provided
  Caller     : general
  Status     : Stable
 
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Reimplemented from Bio::EnsEMBL::Feature.

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:
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Reimplemented from Bio::EnsEMBL::Exon.

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
 
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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
 
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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
 
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public Bio::Seq Bio::EnsEMBL::Exon::peptide ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Transcript $tr
  Example    : my $pep_str = $exon->peptide($transcript)->seq; 
  Description: Retrieves the portion of the transcripts peptide
               encoded by this exon.  The transcript argument is necessary
               because outside of the context of a transcript it is not
               possible to correctly determine the translation.  Note that
               an entire amino acid will be present at the exon boundaries
               even if only a partial codon is present.  Therefore the 
               concatenation of all of the peptides of a transcripts exons 
               is not the same as a transcripts translation because the 
               summation may contain duplicated amino acids at splice sites.
               In the case that this exon is entirely UTR, a Bio::Seq object 
               with an empty sequence string is returned.
  Returntype : Bio::Seq
  Exceptions : thrown if transcript argument is not provided
  Caller     : general
  Status     : Stable
 
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public Int Bio::EnsEMBL::Exon::phase ( ) [inherited]
  Arg [1]    : (optional) int $phase
  Example    :  my $phase = $exon->phase;
                $exon->phase(2);
  Description: Gets/Sets the phase of the exon.
  Returntype : int
  Exceptions : throws if phase is not (0, 1 2 or -1).
  Caller     : general
  Status     : Stable
Get or set the phase of the Exon, which tells the
translation machinery, which makes a peptide from
the DNA, where to start.
The Ensembl phase convention can be thought of as
"the number of bases of the first codon which are
on the previous exon".  It is therefore 0, 1 or 2
(or -1 if the exon is non-coding).  In ascii art,
with alternate codons represented by ### and
+++:
       Previous Exon   Intron   This Exon
    ...-------------            -------------...
    5'                    Phase                3'
    ...#+++###+++###          0 +++###+++###+...
    ...+++###+++###+          1 ++###+++###++...
    ...++###+++###++          2 +###+++###+++...
Here is another explanation from Ewan:
Phase means the place where the intron lands
inside the codon - 0 between  codons, 1 between
the 1st and second base, 2 between the second and
3rd  base. Exons therefore have a start phase and
a end phase, but introns have just one phase.
 
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 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:
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public Bio::Seq Bio::EnsEMBL::Exon::seq ( ) [inherited]
  Arg [1]    : none
  Example    : my $seq_str = $exon->seq->seq;
  Description: Retrieves the dna sequence of this Exon.
               Returned in a Bio::Seq object.  Note that the sequence may
               include UTRs (or even be entirely UTR).
  Returntype : Bio::Seq or undef
  Exceptions : warning if argument passed,
               warning if exon does not have attatched slice
               warning if exon strand is not defined (or 0)
  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::Exon::slice ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::Slice
  Example    : $slice = $exon->slice();
  Description: Getter/Setter for the slice this exon is on.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : Bio::EnsEMBL::Slice
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

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 String Bio::EnsEMBL::Exon::stable_id ( ) [inherited]
  Arg [1]    : string $stable_id
  Example    : none
  Description: get/set for attribute stable_id
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Exon::start ( ) [inherited]
  Arg [1]    : int $start (optional)
  Example    : $start = $exon->start();
  Description: Getter/Setter for the start of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

public Int Bio::EnsEMBL::Exon::strand ( ) [inherited]
  Arg [1]    : int $strand (optional)
  Example    : $start = $exon->strand();
  Description: Getter/Setter for the strand of this exon.  The superclass
               implmentation is overridden to flush the internal sequence
               cache if this value is altered
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Feature.

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

Undocumented method

Code:
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public Hashref Bio::EnsEMBL::Feature::summary_as_hash ( ) [inherited]
  Example       : $feature_summary = $feature->summary_as_hash();
  Description   : Retrieves a textual summary of this Feature.
	              Should be overidden by subclasses for specific tweaking
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use
 
Code:
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Reimplemented in Bio::EnsEMBL::Gene, and Bio::EnsEMBL::Transcript.

public Bio::EnsEMBL::Exon::temporary_id ( ) [inherited]
  Description:

Deprecated:
. This should not be necessary.
 
Code:
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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:
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Reimplemented from Bio::EnsEMBL::Exon.

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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Reimplemented from Bio::EnsEMBL::Exon.

public Bio::EnsEMBL::Exon::type ( ) [inherited]
  Description:

Deprecated:
. Do not use.
 
Code:
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public String Bio::EnsEMBL::Exon::version ( ) [inherited]
  Arg [1]    : string $version
  Example    : none
  Description: get/set for attribute version
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: