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GO::IO::RDFXML.3pm

NAME

   GO::IO::RDFXML - dump GO terms as xml
 
 

SYNOPSIS

     my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
     my $term = $apph->get_term({acc=>00003677});
 
     #### ">-" is STDOUT
     my $out = new FileHandle(">-");  
     
     my $xml_out = GO::IO::XML->new(-output=>$out);
     $xml_out->start_document();
     $xml_out->draw_term($term);
     $xml_out->end_document();
 
 

OR:

     my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
     my $term = $apph->get_node_graph(-acc=>00003677, -depth=>2);
     my $out = new FileHandle(">-");  
     
     my $xml_out = GO::IO::XML(-output=>$out);
     $xml_out->start_document();
     $xml_out->draw_node_graph($term, 3677);
     $xml_out->end_document();
 
 

DESCRIPTION

Utility class to dump GO terms as xml. Currently you just call start_ducument, then draw_term for each term, then end_document.

If there's a need I'll add draw_node_graph, draw_node_list, etc.

new

     Usage   - my $xml_out = GO::IO::XML->new(-output=>$out);
     Returns - None
     Args    - Output FileHandle
 
 

Initializes the writer object. To write to standard out, do:

my $out = new FileHandle(``>-''); my $xml_out = new GO::IO::XML(-output=>$out);

xml_header

     Usage   - $xml_out->xml_header;
     Returns - None
     Args    - None
 
 

start_document prints the ``Content-type: text/xml'' statement. If creating a cgi script, you should call this before start_document.

start_document

     Usage   - $xml_out->start_document(-timestamp=>$time);
     Returns - None
     Args    - optional: timestamp string, pre-formatted
 
 

start_ducument takes care of the fiddly bits like xml declarations, namespaces, etc. It draws the initial tags and leaves the document ready to add go:term nodes.

end_document

     Usage   - $xml_out->end_document();
 
 

Call this when done.

draw_node_graph

     Usage   - $xml_out->draw_node_graph(-graph=>$graph);
     Returns - None
     Args    -graph=>$node_graph, 
             -focus=>$acc,                      ## optional
             -show_associations=>"yes" or "no"  ## optional
 
 

draw_term

     Usage   - $xml_out->draw_term();
     Returns - None
     Args    -term=>$term, 
             -graph=>$graph, 
             -is_focus=>"yes" or "no",    ## optional
             -show_associations=>"yes" or "no",    ## optional
             -show_terms=>"yes" or "no",    ## optional, just draws associations
 
 

sub characters

   This is simply a wrapper to XML::Writer->characters
   which strips out any non-ascii characters.
 
 

sub dataElement

   This is simply a wrapper to XML::Writer->dataElement
   which strips out any non-ascii characters.