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

List of all members.


Class Summary

Description

Do not use this module if you can avoid it. It has been replaced by
Bio::EnsEMBL::Feature.  This module has a long history of usage but has
become very bloated, and quite unweildy.  It was decided to replace
it completely with a smaller, light-weight feature class rather than
attempting to refactor this class, and maintain strict backwards
compatibility.
Part of the complexity of this class was in its extensive
inheritance. As an example the following is a simplified inheritance
heirarchy that was present for Bio::EnsEMBL::DnaAlignFeature:
  Bio::EnsEMBL::DnaAlignFeature
  Bio::EnsEMBL::BaseAlignFeature
  Bio::EnsEMBL::FeaturePair
  Bio::EnsEMBL::SeqFeature
  Bio::EnsEMBL::SeqFeatureI
  Bio::SeqFeatureI
  Bio::RangeI
  Bio::Root::RootI
The new Bio::EnsEMBL::Feature class is much shorter, and hopefully much
easier to understand and maintain.
 

Definition at line 33 of file SeqFeature.pm.

Available Methods

protected _rearrange ()
protected _rearrange ()
protected _transform_between_Slices ()
protected _transform_to_RawContig ()
protected _transform_to_Slice ()
public Nothing add_sub_SeqFeature ()
public Nothing add_tag_value ()
public An all_tags ()
public analysis ()
public attach_seq ()
public Bio::PrimarySeqI contig ()
public Float e_value ()
public each_tag_value ()
public Int end ()
public end_phase ()
public entire_seq ()
public external_db ()
public void flush_sub_SeqFeature ()
public frame ()
public gffstring ()
public has_tag ()
public id ()
public is_splittable ()
public length ()
public location ()
public void move ()
public new ()
public Float p_value ()
public Float percent_id ()
public phase ()
public A primary_tag ()
public Float score ()
public A seq ()
public String seqname ()
public A source_tag ()
public stack_trace ()
public stack_trace ()
public stack_trace_dump ()
public stack_trace_dump ()
public Int start ()
public strand ()
public An sub_SeqFeature ()
public throw ()
public throw ()
public transform ()
public validate ()
public validate_prot_feature ()
public verbose ()
public verbose ()
public vthrow ()
public warn ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
Code:
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protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
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protected Bio::EnsEMBL::SeqFeature::_transform_between_Slices ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::SeqFeature::_transform_to_RawContig ( )

Undocumented method

Code:
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protected Bio::EnsEMBL::SeqFeature::_transform_to_Slice ( )

Undocumented method

Code:
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public Nothing Bio::EnsEMBL::SeqFeature::add_sub_SeqFeature ( )
 Title   : add_sub_SeqFeature
 Usage   : $feat->add_sub_SeqFeature($subfeat);
           $feat->add_sub_SeqFeature($subfeat,'EXPAND')
 Function: adds a SeqFeature into the subSeqFeature array.
           with no 'EXPAND' qualifer, subfeat will be tested
           as to whether it lies inside the parent, and throw
           an exception if not.
           If EXPAND is used, the parents start/end/strand will
           be adjusted so that it grows to accommodate the new
           subFeature
 Returns : nothing
 Args    : An object which has the SeqFeatureI interface
 
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public Nothing Bio::EnsEMBL::SeqFeature::add_tag_value ( )
 Title   : add_tag_value
 Usage   : $self->add_tag_value('note',"this is a note");
 Returns : nothing
 Args    : tag (string) and value (any scalar)
 
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public An Bio::EnsEMBL::SeqFeature::all_tags ( )
 Title   : all_tags
 Usage   : @tags = $feat->all_tags()
 Function: gives all tags for this feature
 Returns : an array of strings
 Args    : none
 
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public Bio::EnsEMBL::SeqFeature::analysis ( )
 Title   : analysis
 Usage   : $sf->analysis();
 Function: Store details of the program/database
           and versions used to create this feature.
 Example :
 Returns :
 Args    :
 
Code:
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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public Bio::EnsEMBL::SeqFeature::attach_seq ( )
 Title   : attach_seq
 Usage   : $sf->attach_seq($seq)
 Function: Attaches a Bio::PrimarySeqI object to this feature. This
           Bio::PrimarySeqI object is for the *entire* sequence: ie
           from 1 to 10000
 Example :
 Returns :
 Args    :
 
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public Bio::PrimarySeqI Bio::EnsEMBL::SeqFeature::contig ( )
  Arg [1]    : Bio::PrimarySeqI $seq
  Example    : $seq = $self->contig;
  Description: Accessor to attach/retrieve a sequence to/from a feature
  Returntype : Bio::PrimarySeqI
  Exceptions : none
  Caller     : general
 
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public Float Bio::EnsEMBL::SeqFeatureI::e_value ( ) [inherited]
 Title   : p_value
 Usage   : $p_val = $feat->p_value()
           $feat->p_value($p_val)
 Function: get/set on p value information
 Returns : float
 Args    : none if get, the new value if set
 
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public Bio::EnsEMBL::SeqFeature::each_tag_value ( )
 Title   : each_tag_value
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
 
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public Int Bio::EnsEMBL::SeqFeature::end ( )
 Title   : end
 Usage   : $end = $feat->end
           $feat->end($end)
 Function: get/set on the end coordinate of the feature
 Returns : integer
 Args    : none
 
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public Bio::EnsEMBL::SeqFeature::end_phase ( )
 Title   : end_phase
 Usage   : $end_phase = $feat->end_phase()
           $feat->end_phase($end_phase)
 Function: returns end_phase based on phase and length of feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.
 
Code:
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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public Bio::EnsEMBL::SeqFeature::entire_seq ( )
 Title   : entire_seq
 Usage   : $whole_seq = $sf->entire_seq()
 Function: gives the entire sequence that this seqfeature is attached to
 Example :
 Returns :
 Args    :
 
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public Bio::EnsEMBL::SeqFeature::external_db ( )
 Title   : external_db
 Usage   : $pid = $feat->external_db()
           $feat->external_db($dbid)
 Function: get/set for an external db accession number (e.g.: Interpro)
 Returns :
 Args    : none if get, the new value if set
 
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public void Bio::EnsEMBL::SeqFeature::flush_sub_SeqFeature ( )
 Title   : flush_sub_SeqFeature
 Usage   : $sf->flush_sub_SeqFeature
 Function: Removes all sub SeqFeature
           (if you want to remove only a subset, take
            an array of them all, flush them, and add
            back only the guys you want)
 Example :
 Returns : none
 Args    : none
 
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public Bio::EnsEMBL::SeqFeature::frame ( )
 Title   : frame
 Usage   : $frame = $feat->frame()
           $feat->frame($frame)
 Function: get/set on frame information
 Returns : 0,1,2
 Args    : none if get, the new value if set
 
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public Bio::EnsEMBL::SeqFeature::gffstring ( )

Undocumented method

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public Bio::EnsEMBL::SeqFeature::has_tag ( )
 Title   : has_tag
 Usage   : $value = $self->has_tag('some_tag')
 Function: Returns the value of the tag (undef if
           none)
 Returns :
 Args    :
 
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public Bio::EnsEMBL::SeqFeature::id ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public Bio::EnsEMBL::SeqFeature::is_splittable ( )

Undocumented method

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public Bio::EnsEMBL::SeqFeature::length ( )
 Title   : length
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
 
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public Bio::EnsEMBL::SeqFeatureI::location ( ) [inherited]

Undocumented method

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public void Bio::EnsEMBL::SeqFeature::move ( )
  Arg [1]    : int $start
  Arg [2]    : int $end
  Arg [3]    : (optional) int $strand 
  Example    : $feature->move(100, 200, -1);
  Description: Moves a feature to a different location.  This is faster
               then calling 3 seperate accesors in a large loop.
  Returntype : none
  Exceptions : none
  Caller     : BaseFeatureAdaptor
 
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public Bio::EnsEMBL::SeqFeature::new ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Root.

public Float Bio::EnsEMBL::SeqFeature::p_value ( )
 Title   : p_value
 Usage   : $p_val = $feat->p_value()
           $feat->p_value($p_val)
 Function: get/set on p value information
 Returns : float
 Args    : none if get, the new value if set
 
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public Float Bio::EnsEMBL::SeqFeature::percent_id ( )
 Title   : percent_id
 Usage   : $pid = $feat->percent_id()
           $feat->percent_id($pid)
 Function: get/set on percentage identity information
 Returns : float
 Args    : none if get, the new value if set
 
Code:
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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public Bio::EnsEMBL::SeqFeature::phase ( )
 Title   : phase
 Usage   : $phase = $feat->phase()
           $feat->phase($phase)
 Function: get/set on start phase of predicted exon feature
 Returns : [0,1,2]
 Args    : none if get, 0,1 or 2 if set.
 
Code:
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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public A Bio::EnsEMBL::SeqFeature::primary_tag ( )
 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
           $feat->primary_tag('exon')
 Function: get/set on the primary tag for a feature,
           eg 'exon'
 Returns : a string
 Args    : none
 
Code:
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public Float Bio::EnsEMBL::SeqFeature::score ( )
 Title   : score
 Usage   : $score = $feat->score()
           $feat->score($score)
 Function: get/set on score information
 Returns : float
 Args    : none if get, the new value if set
 
Code:
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public A Bio::EnsEMBL::SeqFeature::seq ( )
 Example : $tseq = $sf->seq()
 Function: returns the sequence (if any ) for this feature truncated to the range spanning the feature
 Returns : a Bio::PrimarySeq object (I reckon)
 
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public String Bio::EnsEMBL::SeqFeature::seqname ( )
  Arg [1]    : string $seqname
  Example    : $seqname = $self->seqname();
  Description: Obtains the seqname of this features sequence.  This is set
               automatically when a sequence with a name is attached, or may
               be set manually.
  Returntype : string
  Exceptions : none
  Caller     : general, attach_seq
 
Code:
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public A Bio::EnsEMBL::SeqFeature::source_tag ( )
 Title   : source_tag
 Usage   : $tag = $feat->source_tag()
           $feat->source_tag('genscan');
 Function: Returns the source tag for a feature,
           eg, 'genscan'
 Returns : a string
 Args    : none
 
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public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
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public Int Bio::EnsEMBL::SeqFeature::start ( )
 Title   : start
 Usage   : $start = $feat->start
           $feat->start(20)
 Function: Get/set on the start coordinate of the feature
 Returns : integer
 Args    : none
 
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public Bio::EnsEMBL::SeqFeature::strand ( )
 Title   : strand
 Usage   : $strand = $feat->strand()
           $feat->strand($strand)
 Function: get/set on strand information, being 1,-1 or 0
 Returns : -1,1 or 0
 Args    : none
 
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public An Bio::EnsEMBL::SeqFeature::sub_SeqFeature ( )
 Title   : sub_SeqFeature
 Usage   : @feats = $feat->sub_SeqFeature();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none
 
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public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::SeqFeature::transform ( )

Undocumented method

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public Bio::EnsEMBL::SeqFeature::validate ( )
 Title   : validate
 Usage   : $sf->validate;
 Function: Checks whether all the data is present in the
           object.
 Example :
 Returns :
 Args    :
 
Code:
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Reimplemented from Bio::EnsEMBL::SeqFeatureI.

public Bio::EnsEMBL::SeqFeature::validate_prot_feature ( )
 Title   : validate_prot_feature
 Usage   :
 Function:
 Example :
 Returns :
 Args    :
 
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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::SeqFeature::vthrow ( )

Undocumented method

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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
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The documentation for this class was generated from the following file: