NAME
SYNOPSIS
my $apph = GO::AppHandle-> connect ( -d => $go , -dbhost => $dbhost );
my $term = $apph ->get_term({ acc =>00003677});
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();
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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();
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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
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Initializes the writer object. To write to standard out, do:
my $out = new FileHandle(">-"); my $xml_out = new GO::IO::XML(-output=>$out);
Usage - $xml_out ->xml_header;
Returns - None
Args - None
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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
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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();
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Call this when done.
draw_node_graph
Usage - $xml_out ->draw_node_graph( -graph => $graph );
Returns - None
Args -graph => $node_graph ,
-focus => $acc ,
-show_associations => "yes" or "no"
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draw_term
Usage - $xml_out ->draw_term();
Returns - None
Args -term => $term ,
-graph => $graph ,
-is_focus => "yes" or "no" ,
-show_associations => "yes" or "no" ,
-show_terms => "yes" or "no" ,
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sub characters
This is simply a wrapper to XML::Writer->characters
which strips out any non-ascii characters.
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sub dataElement
This is simply a wrapper to XML::Writer->dataElement
which strips out any non-ascii characters.
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