Bio::SeqIO::game::featHandler -- a class for handling feature elements This module is not used directly Bio::SeqIO::game::featHandler converts game XML <annotation> elements into flattened Bio::SeqFeature::Generic objects to be added to the sequence

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. _Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email smckay@bcgsc.bc.ca The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l) Function: creates an object to deal with sequence features Returns : a handler object Args : $seq -- a Bio::SeqI compliant object $seq_h -- ref. to a hash of other sequences associated with the main sequence (proteins, etc) $ann_l -- ref. to a list of annotations

add_source
Title : add_source Usage : $featHandler->add_source($seq->length, \%tags); Function: creates a source feature Returns : a Bio::SeqFeature::Generic object Args : sequence length and a ref. to a hash of tag/value attributes

has_gene
Title : has_gene Usage : my $gene = $self->_has_gene($gene, $gname, $id) Function: method to get/set the current gene feature Returns : a Bio::SeqFeature::Generic object (if there is a gene) Args : (optional) $gene -- an XML element for the annotation $gname -- gene name $id -- gene ID (not always the same as the name)

_has_CDS
Title : _has_CDS Usage : my $cds = $self->_has_CDS Function: internal getter/setter for CDS features Returns : a Bio::SeqFeature::Generic transcript object (or nothing) Args : a Bio::SeqFeature::Generic transcript feature

add_annotation
Title : add_annotation Usage : $featHandler->add_annotation($seq, $type, $id, $tags, $feats) Function: converts a containment hierarchy into an ordered list of flat features Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects

_add_generic_annotation
Title : _add_generic_annotation Usage : $self->_add_generic_annotation($seq, $type, $id, $tags, $feats) Function: an internal method to handle non-gene annotations Returns : nothing Args : $seq -- a Bio::SeqI compliant object $type -- the annotation type $id -- the anotation ID $tags -- ref. to a hash of tag/value attributes $feats -- ref to an array of Bio::SeqFeature::Generic objects

feature_set
Title : feature_set Usage : push @feats, $featHandler->feature_set($id, $gname, $set, $anntype); Function: handles <feature_span> hierarchies (usually a transcript) Returns : a list of Bio::SeqFeature::Generic objects Args : $id -- ID of the feature set $gname -- name of the gene $set -- the <feature_set> object $anntype -- type of the parent annotation

_build_feature_set
Title : _build_feature_set Usage : $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat Function: an internal method to process attributes and subfeats of a feature set Returns : nothing Args : $set -- a <feature_set> element 1 -- optional flag to retain exons as subfeats. Otherwise, they will be converted to sublocations of a parent CDS feature

_add_feature_span
Title : _add_feature_span Usage : $self->_add_feature_span($el, 1) Function: an internal method to process <feature_span> elements Returns : nothing Args : $el -- a <feature_span> element 1 -- an optional flag to retain exons as subfeatures

_add_CDS
Title : _add_CDS Usage : my $cds = $self->_add_CDS($transcript, $tags) Function: an internal method to create a CDS feature from a transcript feature Returns : a Bio::SeqFeature::Generic object Args : $transcript -- a Bio::SeqFeature::Generic object for a transcript $tags -- ref. to a hash of tag/value attributes