Bio::SeqIO::game::gameWriter -- a class for writing game-XML # insert sample code here # Description goes here

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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 $writer = Bio::SeqIO::game::gameWriter->new($seq); Function: constructor method for gameWriter Returns : a game writer object Args : a Bio::SeqI implementing object

write_to_game
Title : write_to_game Usage : $writer->write_to_game Function: writes the sequence object to game-XML Returns : xml as a multiline string Args : none

_rearrange
Title : _rearrange Usage : $self->_rearrange($seq) Function: internal method to rearrange gene containment hierarchies so that snRNA or transposon features contain their genes rather than the other way around Returns : nothing Args : a Bio::RichSeq object

_write_feature
Title : _write_feature Usage : $seld->_write_feature($feat, 1) Function: internal method for writing generic features as <annotation> elements Returns : nothing Args : a Bio::SeqFeature::Generic object and an optional flag to write a bare feature set with no annotation wrapper

_write_gene
Title : _write_gene Usage : $self->_write_gene($feature) Function: internal method for rendering gene containment hierarchies into an nested <annotation> element Returns : nothing Args : a nested Bio::SeqFeature::Generic gene feature Note : A nested gene hierarchy (gene->mRNA->CDS->exon) is expected. If other gene subfeatures occur as level one subfeatures (same level as mRNA subfeats) an attempt will be made to link them to transcripts via the 'standard_name' qualifier

_check_cds
Title : _check_cds Usage : $self->_check_cds($cds, $name) Function: internal method to check if the CDS associated with an mRNA is the correct alternative splice variant Returns : a Bio::SeqFeature::Generic CDS object Args : the CDS object plus the transcript\'s 'standard_name' Note : this method only works if alternatively spliced transcripts are bound together by a 'standard_name' qualifier. If none is present, we will hope that the exons were derived from a segmented RNA or a CDS with no associated mRNA feature. Neither of these two cases would be confused by alternative splice variants.

_feature_set_tags
Title : _feature_set_tags Usage : $self->_feature_set_tags($feature) Function: an internal method to handle tag/value attributes for a feature set element Returns : nothing Args : a Bio::SeqFeatureI-compliant object

_property
Title : _property Usage : $self->_property($tag => $value); Function: an internal method to write property XML elements Returns : nothing Args : a tag/value pair

_tags
Title : _tags Usage : $self->_tags($feat) Function: an internal method to intercept GO terms and db_xrefs and handle generic tag/value pairs for a gene Returns : nothing Args : a Bio::SeqFeatureI-compliant object

_unflatten_attribute
Title : _unflatten_attribute Usage : $self->_unflatten_attribute($name, $value) Function: an internal method to unflatten and write comment or evidence elements Returns : nothing Args : a list of strings

_xref
Title : _xref Usage : $self->_xref($value) Function: an internal method to write db_xref elements Returns : nothing Args : a list of strings

_feature_span
Title : _feature_span Usage : $self->_feature_span($name, $type, $loc) Function: an internal method to write a feature_span element (the actual feature with coordinates) Returns : nothing Args : a feature name and Bio::SeqFeatureI-compliant object

_seq_relationship
Title : _seq_relationship Usage : $self->_seq_relationship($type, $loc) Function: an internal method to handle feature_span sequence relationships Returns : nothing Args : feature type and a Bio::LocationI-compliant object

_element
Title : _element Usage : $self->_element($name, $chars, $atts) Function: an internal method to generate 'generic' XML elements Example : my $name = 'foo'; my $content = 'bar'; my $attributes = { baz => 1 }; # print the element $self->_element($name, $content, $attributes); Returns : nothing Args : the element name and content plus a ref to an attribute hash

_span
Title : _span Usage : $self->_span($loc) Function: an internal method to write the 'span' element Returns : nothing Args : a Bio::LocationI-compliant object

_seq
Title : _seq Usage : $self->_seq($seq, $dna) Function: an internal method to print the 'sequence' element Returns : nothing Args : and Bio::SeqI-compliant object and a reference to an attribute hash

_find_name
Title : _find_name Usage : my $name = $self->_find_name($feature) Function: an internal method to look for a gene name Returns : a string Args : a Bio::SeqFeatureI-compliant object