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Bio-EnsEMBL-112.0.0_57
River stage zero No dependents
/ Bio::EnsEMBL::SeqFeature

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::SeqFeature - Ensembl specific sequence feature.

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 It has been replaced by Bio::EnsEMBL::Feature.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::SeqFeatureI
  Bio::RangeI
  Bio::Root::RootI

The new Bio::EnsEMBL::Feature class is much shorter, and hopefully much easier to understand and maintain.

METHODS

start

 Title   : start
 Usage   : $start = $feat->start
           $feat->start(20)
 Function: Get/set on the start coordinate of the feature
 Returns : integer
 Args    : none

end

 Title   : end
 Usage   : $end = $feat->end
           $feat->end($end)
 Function: get/set on the end coordinate of the feature
 Returns : integer
 Args    : none

length

 Title   : length
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

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

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

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

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

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

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

analysis

 Title   : analysis
 Usage   : $sf->analysis();
 Function: Store details of the program/database
           and versions used to create this feature.

 Example :
 Returns :
 Args    :

validate

 Title   : validate
 Usage   : $sf->validate;
 Function: Checks whether all the data is present in the
           object.
 Example :
 Returns :
 Args    :

validate_prot_feature

 Title   : validate_prot_feature
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

has_tag

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

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)

each_tag_value

 Title   : each_tag_value
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

all_tags

 Title   : all_tags
 Usage   : @tags = $feat->all_tags()
 Function: gives all tags for this feature
 Returns : an array of strings
 Args    : none

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

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    :

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)

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    :

sub_SeqFeature

 Title   : sub_SeqFeature
 Usage   : @feats = $feat->sub_SeqFeature();
 Function: Returns an array of sub Sequence Features
 Returns : An array
 Args    : none

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

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

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

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

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.

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.

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

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