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 / 
go-perl-0.15
River stage one • 1 direct dependent • 1 total dependent
/ GO::IO::ObanOwl

NAME


            

              
              
GO::IO::ObanOwl;

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.