plucky (3) Bio::SeqFeature::Annotated.3pm.gz
NAME
Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE
SYNOPSIS
# none yet, complain to authors
DESCRIPTION
None yet, complain to authors.
Implemented Interfaces
This class implements the following interfaces.
Bio::SeqFeatureI
Note that this includes implementing Bio::RangeI.
Bio::AnnotatableI
Bio::FeatureHolderI
Features held by a feature are essentially sub-features.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look
at the problem and quickly address it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug
reports can be submitted via the web:
http://bugzilla.open-bio.org/
AUTHOR - Allen Day
Allen Day <allenday at ucla.edu>
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded
with a _
PREAMBLE
Okay, where to start...
The original idea for this class appears to lump all SeqFeatureI data (primary_tag, source_tag, etc) into
AnnotationI objects into an Bio::Annotation::Collection. The type is then checked against SOFA.
There have been several requests to have type checking be optionally run.
Bio::FeatureHolderI::create_hierarchy_from_ParentIDs Bio::FeatureHolderI::feature_count
Bio::FeatureHolderI::get_all_SeqFeatures Bio::FeatureHolderI::set_ParentIDs_from_hierarchy
Bio::RangeI::contains Bio::RangeI::disconnected_ranges Bio::RangeI::equals Bio::RangeI::intersection
Bio::RangeI::offsetStranded Bio::RangeI::overlap_extent Bio::RangeI::overlaps Bio::RangeI::subtract
Bio::RangeI::union Bio::SeqFeature::Annotated::Dumper Bio::SeqFeature::Annotated::MAX_TYPE_CACHE_MEMBERS
Bio::SeqFeature::Annotated::add_Annotation Bio::SeqFeature::Annotated::add_SeqFeature
Bio::SeqFeature::Annotated::add_tag_value Bio::SeqFeature::Annotated::add_target
Bio::SeqFeature::Annotated::annotation Bio::SeqFeature::Annotated::attach_seq
Bio::SeqFeature::Annotated::display_name Bio::SeqFeature::Annotated::each_target
Bio::SeqFeature::Annotated::end Bio::SeqFeature::Annotated::entire_seq Bio::SeqFeature::Annotated::frame
Bio::SeqFeature::Annotated::from_feature Bio::SeqFeature::Annotated::get_Annotations
Bio::SeqFeature::Annotated::get_SeqFeatures Bio::SeqFeature::Annotated::get_all_tags
Bio::SeqFeature::Annotated::get_tag_values Bio::SeqFeature::Annotated::get_tagset_values
Bio::SeqFeature::Annotated::has_tag Bio::SeqFeature::Annotated::length
Bio::SeqFeature::Annotated::location Bio::SeqFeature::Annotated::name Bio::SeqFeature::Annotated::new
Bio::SeqFeature::Annotated::phase Bio::SeqFeature::Annotated::primary_tag
Bio::SeqFeature::Annotated::remove_Annotations Bio::SeqFeature::Annotated::remove_SeqFeatures
Bio::SeqFeature::Annotated::remove_tag Bio::SeqFeature::Annotated::score Bio::SeqFeature::Annotated::seq
Bio::SeqFeature::Annotated::seq_id Bio::SeqFeature::Annotated::source
Bio::SeqFeature::Annotated::source_tag Bio::SeqFeature::Annotated::start
Bio::SeqFeature::Annotated::strand Bio::SeqFeature::Annotated::type
Bio::SeqFeature::Annotated::uri_escape Bio::SeqFeature::Annotated::uri_unescape
Bio::SeqFeature::TypedSeqFeatureI::croak Bio::SeqFeature::TypedSeqFeatureI::ontology_term
Bio::SeqFeatureI::generate_unique_persistent_id Bio::SeqFeatureI::gff_string Bio::SeqFeatureI::primary_id
Bio::SeqFeatureI::spliced_seq
ATTRIBUTE ACCESSORS FOR Bio::SeqFeature::Annotated
from_feature
Usage: $obj->from_feature($myfeature);
Desc : initialize this object with the contents of another feature
object. Useful for converting objects like
L<Bio::SeqFeature::Generic> to this class
Ret : nothing meaningful
Args : a single object of some other feature type,
Side Effects: throws error on failure
Example:
seq_id()
Usage : $obj->seq_id($newval)
Function: holds a string corresponding to the unique
seq_id of the sequence underlying the feature
(e.g. database accession or primary key).
Returns : string representing the seq_id.
Args : on set, some string or a Bio::Annotation::SimpleValue object.
name()
Usage : $obj->name($newval)
Function: human-readable name for the feature.
Returns : value of name (a scalar)
Args : on set, new value (a scalar or undef, optional)
type()
Usage : $obj->type($newval)
Function: a SOFA type for the feature.
Returns : Bio::Annotation::OntologyTerm object representing the type.
NB: to get a string, use primary_tag().
Args : on set, Bio::Annotation::OntologyTerm object.
NB: to set a string (SOFA name or identifier), use primary_tag()
source()
Usage : $obj->source($newval)
Function: holds the source of the feature.
Returns : a Bio::Annotation::SimpleValue representing the source.
NB: to get a string, use source_tag()
Args : on set, a Bio::Annotation::SimpleValue object.
NB: to set a string, use source_tag()
score()
Usage : $score = $feat->score()
$feat->score($score)
Function: holds a value corresponding to the score of the feature.
Returns : a string representing the score.
Args : on set, a scalar or a Bio::Annotation::SimpleValue object.
phase()
Usage : $phase = $feat->phase()
$feat->phase($phase)
Function: get/set on phase information
Returns : a string 0,1,2,'.'
Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue
object holding one of 0,1,2,'.' as its value.
frame()
Usage : $frame = $feat->frame()
$feat->frame($phase)
Function: get/set on phase information
Returns : a string 0,1,2,'.'
Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue
object holding one of 0,1,2,'.' as its value.
SHORTCUT METHODS TO ACCESS Bio::AnnotatableI INTERFACE METHODS
add_Annotation()
Usage :
Function: $obj->add_Annotation() is a shortcut to $obj->annotation->add_Annotation
Returns :
Args :
remove_Annotations()
Usage :
Function: $obj->remove_Annotations() is a shortcut to $obj->annotation->remove_Annotations
Returns :
Args :
INTERFACE METHODS FOR Bio::SeqFeatureI
Note that no methods are deprecated. Any SeqFeatureI methods must return strings (no objects).
display_name()
primary_tag()
source_tag()
attach_seq()
Usage : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
Bio::Seq object is for the *entire* sequence: ie
from 1 to 10000
Returns : TRUE on success
Args : a Bio::PrimarySeqI compliant object
seq()
Usage : $tseq = $sf->seq()
Function: returns a truncated version of seq() with bounds matching this feature
Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence
bounded by start & end, or undef if there is no sequence attached
Args : none
entire_seq()
Usage : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
sequence attached
Args : none
INTERFACE METHODS FOR Bio::RangeI
as inherited via Bio::SeqFeatureI
length()
Usage : $feature->length()
Function: Get the feature length computed as $feat->end - $feat->start + 1
Returns : integer
Args : none
start()
Usage : $obj->start($newval)
Function: Get/set on the start coordinate of the feature
Returns : integer
Args : on set, new value (a scalar or undef, optional)
end()
Usage : $obj->end($newval)
Function: Get/set on the end coordinate of the feature
Returns : integer
Args : on set, new value (a scalar or undef, optional)
strand()
Usage : $strand = $feat->strand($newval)
Function: get/set on strand information, being 1,-1 or 0
Returns : -1,1 or 0
Args : on set, new value (a scalar or undef, optional)
INTERFACE METHODS FOR Bio::FeatureHolderI
This includes methods for retrieving, adding, and removing features. Since this is already a feature,
features held by this feature holder are essentially sub-features.
get_SeqFeatures
Usage : @feats = $feat->get_SeqFeatures();
Function: Returns an array of Bio::SeqFeatureI objects
Returns : An array
Args : none
add_SeqFeature()
Usage : $feat->add_SeqFeature($subfeat);
$feat->add_SeqFeature($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 parent''s start/end/strand will
be adjusted so that it grows to accommodate the new
subFeature
Example :
Returns : nothing
Args : a Bio::SeqFeatureI object
remove_SeqFeatures()
Usage : $obj->remove_SeqFeatures
Function: Removes all sub SeqFeatures. If you want to remove only a subset,
remove that subset from the returned array, and add back the rest.
Returns : The array of Bio::SeqFeatureI implementing sub-features that was
deleted from this feature.
Args : none
INTERFACE METHODS FOR Bio::AnnotatableI
annotation()
Usage : $obj->annotation($annot_obj)
Function: Get/set the annotation collection object for annotating this
feature.
Returns : A Bio::AnnotationCollectionI object
Args : newvalue (optional)
location()
Usage : my $location = $seqfeature->location()
Function: returns a location object suitable for identifying location
of feature on sequence or parent feature
Returns : Bio::LocationI object
Args : [optional] Bio::LocationI object to set the value to.
add_target()
Usage : $seqfeature->add_target(Bio::LocatableSeq->new(...));
Function: adds a target location on another reference sequence for this feature
Returns : true on success
Args : a Bio::LocatableSeq object
each_target()
Usage : @targets = $seqfeature->each_target();
Function: Returns a list of Bio::LocatableSeqs which are the locations of this object.
To obtain the "primary" location, see L</location()>.
Returns : a list of 0..N Bio::LocatableSeq objects
Args : none
_expand_region
Title : _expand_region
Usage : $self->_expand_region($feature);
Function: Expand the total region covered by this feature to
accomodate for the given feature.
May be called whenever any kind of subfeature is added to this
feature. add_SeqFeature() already does this.
Returns :
Args : A Bio::SeqFeatureI implementing object.
get_Annotations
Usage : my $parent = $obj->get_Annotations('Parent');
my @parents = $obj->get_Annotations('Parent');
Function: a wrapper around Bio::Annotation::Collection::get_Annotations().
Returns : returns annotations as
Bio::Annotation::Collection::get_Annotations() does, but
additionally returns a single scalar in scalar context
instead of list context so that if an annotation tag
contains only a single value, you can do:
$parent = $feature->get_Annotations('Parent');
instead of:
($parent) = ($feature->get_Annotations('Parent'))[0];
if the 'Parent' tag has multiple values and is called in a
scalar context, the number of annotations is returned.
Args : an annotation tag name.
Bio::SeqFeatureI implemented methods
These are specialized implementations of SeqFeatureI methods which call the internal
Bio::Annotation::AnnotationCollection object. Just prior to the 1.5 release the below methods were moved
from Bio::SeqFeatureI to Bio::AnnotatableI, and having Bio::SeqFeatureI inherit Bio::AnnotatableI. This
behavior forced all Bio::SeqFeatureI-implementing classes to use Bio::AnnotationI objects for any data.
It is the consensus of the core developers that this be rolled back in favor of a more flexible approach
by rolling back the above changes and making this class Bio::AnnotatableI. The SeqFeatureI tag-related
methods are reimplemented in order to approximate the same behavior as before.
The methods below allow mapping of the "get_tag_values()"-style annotation access to
Bio::AnnotationCollectionI. These need not be implemented in a Bio::AnnotationCollectionI compliant
class, as they are built on top of the methods. For usage, see Bio::SeqFeatureI.
has_tag
add_tag_value
get_tag_values
Usage : @annotations = $obj->get_tag_values($tag)
Function: returns annotations corresponding to $tag
Returns : a list of scalars
Args : tag name
get_tagset_values
Usage : @annotations = $obj->get_tagset_values($tag1,$tag2)
Function: returns annotations corresponding to a list of tags.
this is a convenience method equivalent to multiple calls
to get_tag_values with each tag in the list.
Returns : a list of Bio::AnnotationI objects.
Args : a list of tag names
get_all_tags
Usage : @tags = $obj->get_all_tags()
Function: returns a list of annotation tag names.
Returns : a list of tag names
Args : none
remove_tag
Usage : See remove_Annotations().
Function:
Returns :
Args :
Note : Contrary to what the name suggests, this method removes
all annotations corresponding to $tag, not just a
single anntoation.