|$id = $feature->id([$newid])||Get or set the feature ID. This is an identifier for the feature, unique across the DAS server from which it was retrieved.|
|$label = $feature->label([$newlabel])||Get or set the label for the feature. This is an optional human-readable label that may be used to display the feature in text form. You may use the ID if label() returns undef.|
|$type = $feature->type([$newtype])||Get or set the type of the feature. This is a required attribute. The value returned is an object of type Bio::Das::Type, which contains information about the type of the annotation and the method used to derive it.|
|$segment = $feature->([$newsegment])||Get or set the Bio::Das::Segment from which this feature was derived.|
|$source = $feature->source||Get the Bio::Das object from which this feature was retrieved. This method is a front end to the associated segments source() method, and is therefore read-only.|
|$refseq = $feature->refseq||Get the reference sequence on which this features coordinates are based. This method is a front end to the associated segments refseq() method, and is therefore read-only.|
|$start = $feature->start([$newstart])||Get or set the starting position of the feature, in refseq coordinates.|
|$stop = $feature->stop([$newstop])||Get or set the stopping position of the feature, in refseq coordinates.|
|$isreference = $feature->stop([$newreference])||Get or set the value of the reference flag, which is true if the feature can be used as a sequence coordinate landmark.|
|$method = $feature->method||Return the ID of the method used to derive this feature. This is a front end to the feature types method() method (redundancy intended) and is therefore read-only.|
|$category = $feature->category||Return the ID of the category in which this feature calls. This is a front end to the feature types category() method and is therefore read-only.|
|$score = $feature->score([$newscore])||Get or set the score of this feature, a floating point number which might mean something in the right context.|
|$orientation = $feature->orientation([$neworientation])||Get or set the orientation of this feature relative to the genomic reference sequence. This is one of the values +1, 0 or -1.|
|$phase = $feature->phase([$newphase])||Get or set the phase of the feature (its position relative to a reading frame). The returned value can be 0, 1, 2 or undef if the phase is irrelevant to this feature type.|
|$group = $feature->group([$newgroup])||Get or set the group ID for the feature. Groups are used to group together logically-related features, such as the exons of a gene model.|
|$url = $feature->link([$newurl])||Get or set the URL that will return additional information about the feature.|
|$label = $feature->link_label([$newlabel])||Get or set the label that the DAS server recommends should be used for the link.|
|$note = $feature->note([$newnote])||Get or set the human-readable note associated with the feature.|
|$feature->each_tag_value() =item $feature->all_tags() =item $feature->add_tag_value() =item $feature->remove_tag() =item $feature->attributes()||The tag* methods work just like they do in Bio::SeqFeatureI. The attributes() method follows the conventions in Bio::DB::SeqFeature.|
|$target = $feature->target|
|($target,$start,$stop) = $feature->target|
These three methods get or set the target that is optionally
associated with alignments. In a scalar context, target() returns the
ID of the target, while in an array context, the method returns a
three-element list consisting of the target ID, and the start and end
position of the alignment.
You may pass a three-element list to change the target and range.
|$target_label = $feature->target_label([$newlabel])||This method returns an optional label assigned to the target.|
|$description = $feature->description||This method returns a human-readable description of the feature. It returns the value of note(), link_label() or target_label(), in that priority.|
|@segments = $feature->segments|
|@segments = $feature->sub_seqFeature||These methods are aliases. Both return an array of sub-parts of the feature in the form of Das::Sequence::Feature objects. Currently (March 2001) this is only implemented for grouped objects of type similarity and for transcripts (the union of introns and exons in a group).|
In addition to the methods listed above, Bio::Das::Segment::Feature implements all the methods required for the Bio::SeqFeatureI class.
Title : get_SeqFeatures Usage : @feat = $feature->get_SeqFeatures([$method]) Function: get subfeatures Returns : a list of Bio::DB::GFF::Feature objects Args : a feature method (optional) Status : Public
This method returns a list of any subfeatures that belong to the main feature. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on.
Title : add_subfeature Usage : $feature->add_subfeature($feature) Function: add a subfeature to the feature Returns : nothing Args : a Bio::DB::GFF::Feature object Status : Public
This method adds a new subfeature to the object. It is used internally by aggregators, but is available for public use as well.
Title : sort_features Usage : $feature->sort_features Function: sort features Returns : nothing Args : none Status : Public
This method sorts subfeatures in ascending order by their start position. For reverse strand features, it sorts subfeatures in descending order. After this is called sub_SeqFeature will return the features in order.
This method is called internally by merged_segments().
Title : compound Usage : $flag = $f->compound([$newflag]) Function: get or set the compound flag Returns : a boolean Args : a new flag (optional) Status : Public
This method gets or sets a flag indicated that the feature is not a primary one from the DAS server, but the result of aggregation.
When used in a string context, Bio::Das::Segment::Feature objects invoke the toString() method. This returns the value of the features label, or invokes the inherited Bio::Das::Segment->toString() method if no label is available.
Lincoln Stein <firstname.lastname@example.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
Bio::Das, Bio::Das::Type, Bio::Das::Segment, Bio::Das::Transcript, Bio::Das::Segment::GappedAlignment, Bio::RangeI
Hey! <B>The above document had some coding errors, which are explained below:B>
Around line 709: You forgot a =back before =head2
|perl v5.20.3||DAS::FEATURE (3)||2009-08-26|