Bio::SeqIO::game::featHandler(3pm)

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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