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/wiki/Mailing_lists  - About the mailing lists

Support¶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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¶

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 the web:

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

new¶

 Title   : new
 Usage   : not used directly
 Returns : a gameHandler object
 Args    : an XML filename

go¶

 Title   : go
 Usage   : not used directly
 Function: starts PerlSAX XML parsing

start_document¶

 Title   : start_document
 Usage   : not used directly

end_document¶

 Title   : end_document
 Usage   : not used directly

start_element¶

 Title   : start_element
 Usage   : not used directly

end_element¶

 Title   : end_element
 Usage   : not used directly

characters¶

 Title   : characters
 Usage   : not used directly

strip_characters¶

 Title   : strip_characters
 Usage   : not used directly
 Function: cleans up XML element contents

curr_element¶

 Title   : curr_element
 Usage   : not used directly
 Function: returns the currently open element

flush¶

 Title   : flush
 Usage   : $self->flush($element) # or $element->flush
 Function: prune a branch from the XML tree
 Returns : true if successful
 Args    : an element object (optional)

complain¶

 Title   : complain
 Usage   : $self->complain("This is terrible; I am not happy")
 Function: throw a non-fatal warning, formats message for pretty-printing
 Returns : nothing
 Args    : a list of strings

dbxref¶

 Title   : dbxref
 Usage   : $self->db_xref($el, $tags) 
 Function: an internal method to flatten dbxref elements
 Returns : the db_xref (eg wormbase:C02D5.1)
 Args    : an element object (reqd) and a hash ref of tag/values (optional)

comment¶

 Title   : comment
 Usage   : $self->comment($comment_element)
 Function: a method to flatten comment elements
 Returns : a string
 Args    : an comment element (reqd) and a hash ref of tag/values (optional)
 Note    : The hope here is that we can unflatten structured comments
           in game-derived annotations happen to make a return trip

property¶

 Title   : property
 Usage   : $self->property($property_element)
 Function: an internal method to flatten property elements
 Returns : a hash reference
 Args    : an property/output element (reqd) and a hash ref of tag/values (optional)
 Note: This method is aliased to 'output' to handle structurally identical output elements

evidence¶

 Title   : evidence
 Usage   : $self->evidence($evidence_element)
 Function: a method to flatten evidence elements
 Returns : a string
 Args    : an evidence element

date¶

 Title   : date
 Usage   : $self->date($date_element)
 Function: a method to flatten date elements
 Returns : true if successful
 Args    : a date element

protein_id¶

 Title   : protein_id
 Usage   : $pid = $self->protein_id($cds, $standard_name)
 Function: a method to search for a protein name
 Returns : a string
 Args    : the CDS object plus the transcript\'s 'standard_name'