| Bio::SeqIO::game::gameSubs(3pm) | User Contributed Perl Documentation | Bio::SeqIO::game::gameSubs(3pm) |
Bio::SeqIO::game::gameSubs -- a base class for game-XML parsing
Not used directly
A bag of tricks for game-XML parsing. The PerlSAX handler methods were stolen from Chris Mungall's XML base class, which he stole from Ken MacLeod's XML::Handler::Subs
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : not used directly Returns : a gameHandler object Args : an XML filename
Title : go Usage : not used directly Function: starts PerlSAX XML parsing
Title : start_document Usage : not used directly
Title : end_document Usage : not used directly
Title : start_element Usage : not used directly
Title : end_element Usage : not used directly
Title : characters Usage : not used directly
Title : strip_characters Usage : not used directly Function: cleans up XML element contents
Title : curr_element Usage : not used directly Function: returns the currently open element
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)
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
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)
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
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
Title : evidence Usage : $self->evidence($evidence_element) Function: a method to flatten evidence elements Returns : a string Args : an evidence element
Title : date Usage : $self->date($date_element) Function: a method to flatten date elements Returns : true if successful Args : a date element
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'
| 2021-08-15 | perl v5.32.1 |