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

NAME

GO::IO::OBDXML;

SYNOPSIS

my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost);
my $term = $apph->get_term({acc=>00003677});

#### ">-" is STDOUT
my $out = new FileHandle(">-");

my $xml_out = GO::IO::OBDXML->new(-output=>$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 $xml_out = GO::IO::OBDXML(-output=>$out);
$xml_out->start_document();
$xml_out->draw_graph($term, 3677);
$xml_out->end_document();

DESCRIPTION

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

new

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

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

my $out = new FileHandle(">-"); my $xml_out = new GO::IO::OBDXML(-output=>$out);

cgi_header

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

cgi_header 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;
Returns - None
Args    - None

start_document 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.

start_graph

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

start_graph opens a new graph segment.

end_document

Usage   - $xml_out->end_document;

Call this when done.

end_graph

Usage   - $xml_out->end_graph;

Call this when done a graph segment.

draw_node_graph

Usage   - $xml_out->draw_node_graph(-graph=>$graph);
Returns - None
Args    -graph=>$graph,
        -show_associations=>'yes' or 'no', # optional, default 'yes'.
        -show_terms=>'yes' or 'no',        # optional, default 'yes'.
        -show_xrefs=>'yes' or 'no',        # optional, default 'yes'.
        -show_evidence=>'yes' or 'no',     # optional, default 'yes'.

draw_term

Usage   - $xml_out->draw_term();
Returns - None
Args    -term=>$term,
        -graph=>$graph,                    # optional
        -show_associations=>'yes' or 'no', # optional, default 'yes'.
        -show_terms=>'yes' or 'no',        # optional, default 'yes'.
        -show_xrefs=>'yes' or 'no',        # optional, default 'yes'.
        -show_evidence=>'yes' or 'no',     # optional, default 'yes'.