[nexml]
phylogenetic data in xmlThe future data exchange standard is here!
nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process.
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| Tue Jan 6 02:08:03 2009 —
Nexml JavaScript libraries
The JS libraries are a port of a subset of Bio::Phylo's functionality. In particular, they implement most of the tree API, with the characters API in early development.
The libraries are useful for client side data pre- and post processing, for example in the widget on the front page, where these JS libraries interact with the Tree of Life web service through AJAX, parse the xml the service returns, reformat it to a newick string and pass it to the visualization widget.
Tree and node objects
Some neat things are possible, for example:
// instantiate node object
var root = new Phylo.Forest.Node( { 'name' : 'root' } );
// instantiate tree object
var tree = new Phylo.Forest.Tree( { 'name' : 'tree' } );
// add root node to tree
tree.insert(root);
// build tree recursively, up to a depth of maxdepth
var maxdepth = 5;
var nodecounter = 1;
tree.visit_depth_first({
'pre' : function (node) {
if ( node.calc_nodes_to_root() < maxdepth ) {
var left = new Phylo.Forest.Node( { 'name' : 'left' + nodecounter++ } );
var right = new Phylo.Forest.Node( { 'name' : 'right' + nodecounter } );
node.set_child(left);
node.set_child(right);
left.set_parent(node);
right.set_parent(node);
tree.insert(left,right);
}
}
});
alert(tree.to_newick());
Containers and nexml
// now, create a "forest" object, a container for trees
var forest = new Phylo.Forest({ 'name' : 'forest' });
// add the tree to the forest container
forest.insert(tree);
// create a taxa container
var taxa = new Phylo.Taxa({ 'name' : 'taxa' });
// create a link between taxa and forest
forest.set_taxa(taxa);
// create taxon objects for all tips
tree.get_terminals().map(
function(tip) {
var taxon = new Phylo.Taxa.Taxon({ 'name' : tip.get_name() });
tip.set_taxon(taxon);
taxa.insert(taxon);
}
);
// and serialize to xml
var xml = taxa.get_root_open_tag()
+ taxa.to_xml()
+ forest.to_xml()
+ forest.get_root_close_tag();
alert(xml);
Round-tripping trees nexml
// now parse the xml, this returns an array of top level container objects
var blocks = Phylo.IO.parse( { 'format' : 'nexml', 'string' : xml } );
// find the forest object, get the parsed tree
var parsed_tree;
for ( var i = 0; i < blocks.length; i++ ) {
// each "class" has a unique constant
if ( blocks[i]._type() == Phylo.Util.CONSTANT._FOREST_() ) {
parsed_tree = blocks[i].first();
break;
}
}
// ...and write out the round trip
alert(parsed_tree.to_newick());
The code blocks above were all evaluated concatenated (to maintain scope). Below, we start with a fresh slate to work on character data.
Character data
// create a matrix object
var matrix = new Phylo.Matrices.Matrix({
'name':'matrix',
'type':'Dna'
});
// create a datum object
var datum = new Phylo.Matrices.Datum({
'name':'datum',
'type':'Dna'
});
// add some data
datum.set_char(['acgt']);
// add datum to matrix
matrix.insert(datum);
var taxa = new Phylo.Taxa();
matrix.set_taxa(taxa);
// write xml
var xml = taxa.get_root_open_tag()
+ taxa.to_xml()
+ matrix.to_xml({'compact':false}) // when set to 'true', creates <seq> elements
+ taxa.get_root_close_tag();
alert(xml);
Round-tripping characters nexml
// now parse the taxa block and characters matrix
var blocks = Phylo.IO.parse({
'format':'nexml',
'string':xml
});
// now loop over the blocks
for ( var i in blocks ) {
if ( blocks[i] == Phylo.Util.CONSTANT._TAXA_() ) {
taxa = blocks[i];
}
else if ( blocks[i] == Phylo.Util.CONSTANT._MATRIX_() ) {
matrix = blocks[i];
}
}
// writes out the same info set as the input
var xml = taxa.get_root_open_tag()
+ taxa.to_xml()
+ matrix.to_xml({'compact':false}) // when set to 'true', creates <seq> elements
+ taxa.get_root_close_tag();
alert(xml);
The Project object
// the project object is a convenient container to clump data together
var p = new Phylo.Project();
Phylo.IO.parse({
'format' :'nexml',
'string' : xml,
'project' : p,
});
alert(p.to_xml());
Name Last modified Size Description
Parent Directory 17-Dec-2008 14:31 - Folder
Phylo.js 17-Dec-2008 14:31 2k Javascript
Phylo/ 17-Dec-2008 14:31 - Folder
phylo.html 17-Dec-2008 14:31 1k HTML document