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rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

  https://github.com/bioperl/bioperl-live/issues

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
           optionally, an argument to set map_position to on.
           ( map => 1 ).  This will create a map_position elemant
           that will cause the feature coordinates to be remapped to
           a parent seqeunce.  A sequence name in the format seq:xxx-xxx
           is expected to determine the offset for the map_position.
           The default behavior is to have features mapped relative to 
           the sequence contained in the GAME-XML file

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_hierarchies

 Title   : _rearrange_hierarchies
 Usage   : $self->_rearrange_hierarchies($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
 Note    : Not currently used, may be removed

_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 
           a 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' or 'mRNA' 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 
           confounded by alternative splice variants.

_comp_analysis

  Usage:
  Desc :
  Ret  :
  Args :
  Side Effects:
  Example:

_comp_result

  Usage:
  Desc : recursively render a feature and its subfeatures as
         <result_set> and <result_span> elements
  Ret  : nothing meaningful
  Args : a feature

_comp_result_span

  Usage: _comp_result_span('foo12',$feature);
  Desc : write GAME XML for a Bio::SeqFeature::Computation feature
         that has no subfeatures
  Ret  : nothing meaningful
  Args : name for this span (some kind of identifier),
         SeqFeature object to put into this span
  Side Effects:
  Example:

_render_tags

  Usage:
  Desc :
  Ret  :
  Args :
  Side Effects:
  Example:

_render_output_tags

  Usage:
  Desc : print out <output> elements, with contents
         taken from the SeqFeature::Computation's 'output' tag
  Ret  : array of tag names this did not render
  Args : feature object, list of tag names to maybe render

  In game xml, only <result_span> and <result_set> elements can
  have <output> elements.

_render_tags_as_properties

  Usage:
  Desc :
  Ret  : empty array
  Args : feature object, array of tag names
  Side Effects:
  Example:

  In game xml, <annotation>, <computational_analysis>,
  and <feature_set> elements can have properties.

_render_comment_tags

  Usage:
  Desc :
  Ret  : names of tags that were not comment tags
  Args : feature object, tag names available for us to render
  Side Effects: writes XML
  Example:

  In game xml, <annotation> and <feature_set> elements can
  have comments.

_render_date_tags

  Usage:
  Desc :
  Ret  : names of tags that were not date tags
  Args : feature, list of tag names available for us to render
  Side Effects: writes XML for <date> elements
  Example:

  In game xml, <annotation>, <computational_analysis>,
  <transaction>, <comment>, and <feature_set> elements
  can have <date>s.

_render_dbxref_tags

  Desc : look for xref tags and render them if they are there
  Ret  : tag names that we didn't render
  Args : feature object, list of tag names to render
  Side Effects: writes a <dbxref> element if a tag with name
                matching /xref$/i is present


  In game xml, <annotation> and <seq> elements can have dbxrefs.

_render_target_tags

  Usage:
  Desc : process any 'Target' tags that would indicate a sequence alignment subject
  Ret  : array of tag names that we didn't render
  Args : feature object
  Side Effects: writes a <seq_relationship> of type 'subject' if it finds
                any properly formed tags named 'Target'
  Example:

  In game xml, <result_span>, <feature_span>, and <result_set> can have
  <seq_relationship>s.  <result_set> can only have one, a 'query' relation.

_property

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

_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, a Bio::LocationI-compliant object,
           (optional) sequence name (defaults to the query seq)
           and (optional) alignment string

_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