Bio::SeqIO::game::featHandler -- a class for handling feature elements

       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

perl v5.32.1                                       2021-08-15                 Bio::SeqIO::game::featHandler(3pm)

       Email mckays@cshl.edu

       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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       data examples if at all possible.

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       Bug reports can be submitted via the web:

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       Bio::SeqIO::game::featHandler -- a class for handling feature elements

       This module is not used directly