/ 
bioperl-1.4
/ Bio::SeqIO::game::gameWriter

NAME

Bio::SeqIO::game::gameWriter -- a class for writing game-XML

SYNOPSIS

# insert sample code here

DESCRIPTION

# Description goes here

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.

Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/MailList.shtml      - About the mailing lists

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/

AUTHOR - Sheldon McKay

Email smckay@bcgsc.bc.ca

APPENDIX

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