var sort_nodes = function (div) {

    // Selection of sorting criteria
    var menu_pane1 = d3.select(div)
        .append("div")
        .append("span")
        .text("Sort By:  ");

    var sel1 = menu_pane1
        .append("select")
        .on("change", function (d) {
            var prop = this.value;
            tree.root().sort(function(node1, node2) {
                var highest1 = get_highest_val(node1, prop);
                var highest2 = get_highest_val(node2, prop);
                return get_highest_val(node1, prop) - get_highest_val(node2, prop);
            });
            tree.update();
        });

    sel1
        .append("option")
        .attr("value", "Chromosome pairs")
        .attr("selected", 1)
        .text("Number of chromosome pairs");

    sel1
        .append("option")
        .attr("value", "Protein-coding genes")
        .text("Number of protein-coding genes");

    sel1
        .append("option")
        .attr("value", "Genome length")
        .text("Genome length");

    sel1
        .append("option")
        .attr("value", "Cuteness factor")
        .text("Cuteness factor");

    // Selection of coloring criteria
    var menu_pane2 = d3.select(div)
        .append("div")
        .append("span")
        .text("Color by: ");

    var sel2 = menu_pane2
        .append("select")
        .on("change", function (d) {
            // Create a new color scale
            var prop = this.value;
            var vals = [];
            for (var sp in species_data) {
                vals.push(species_data[sp][prop]);
            }
            var extent = d3.extent(vals);
            var scale = d3.scale.linear()
                .domain(extent)
                .range(["steelblue", "red"]);

            tree.node_display(tree.node_display()
                .fill(function (node) {
                    if (node.is_leaf()) {
                        return scale(species_data[node.node_name()][prop]);
                    }
                    return "black";
                })
            );

            tree.update_nodes();
        });

    sel2
        .append("option")
        .attr("value", "Chromosome pairs")
        .attr("selected", 1)
        .text("Number of chromosome pairs");

    sel2
        .append("option")
        .attr("value", "Protein-coding genes")
        .text("Number of protein-coding genes");

    sel2
        .append("option")
        .attr("value", "Genome length")
        .text("Genome length");

    sel2
        .append("option")
        .attr("value", "Cuteness factor")
        .text("Cuteness factor");



    var tree_data = tnt.tree.parse_newick(newick);

    var prop = "Chromosome pairs";
    var vals = [];

    for (var sp in species_data) {
        vals.push(species_data[sp][prop]);
    }

    var extent = d3.extent(vals);

    var scale = d3.scale.linear()
        .domain(extent)
        .range(["steelblue", "red"]);

    var tree = tnt.tree();
    tree
        .data(tree_data)
        .duration(1000)
        .layout(tnt.tree.layout.vertical()
            .width(600)
            .scale(false)
        )
        .node_display(tree.node_display()
            .size(7)
            .fill (function(node) {
                if (node.is_leaf()) {
                    return scale(species_data[node.node_name()][prop]);
                }
                return "black";
            })
        );

    // Increase the separation between nodes
    tree
        .label()
        .height(function(){
            return 20;
        });

    var root = tree.root();
    root.sort (function (node1, node2) {
        var highest1 = get_highest_val(node1, 'Chromosome pairs');
        var highest2 = get_highest_val(node2, 'Chromosome pairs');
        return highest1 - highest2;
    });

    // The visualization is started at this point
    tree(div);
};

// Helper function to get the lowest value in
// the subnode -- this is used in the sort cbak
var get_highest_val = function (node, prop) {
    var highest = 0;
    node.apply(function (n) {
        if (species_data[n.node_name()] === undefined) {
            return;
        }
        var val = parseFloat(species_data[n.node_name()][prop]);
        if (val > highest) {
            highest = val;
        }
    });
    return highest;
};

var newick = "(((((((Mus musculus:0.0845,Rattus norvegicus:0.0916):0.2567,Oryctolagus cuniculus:0.2157):0.0153,(((((Pan troglodytes:0.0067,Homo sapiens:0.0067):0.0022,Gorilla gorilla:0.0088):0.0097,Pongo abelii:0.0183):0.0143,Macaca mulatta:0.0375):0.0220,Callithrix jacchus:0.0661):0.0891):0.0206,(((Felis catus:0.0986,Canis familiaris:0.1025):0.0498,Equus caballus:0.1094):0.0107,((Ovis aries:0.0618,Bos taurus:0.0618):0.0869,Sus scrofa:0.1073):0.0403):0.0329):0.2584,Monodelphis domestica:0.3408):0.0717,Ornithorhynchus anatinus:0.4566):0.1095,(((Gallus gallus:0.0414,Meleagris gallopavo:0.0414):0.1242,Taeniopygia guttata:0.1715):0.3044,Anolis carolinensis:0.4989):0.1700)";

var species_data = {
    'Homo sapiens' : {
        'Chromosome pairs' : 23,
        'Protein-coding genes' : 20805,
        'Genome length' : 3.1,
        'Ensembl date' : new Date(2001, 07),
        'Cuteness factor' : 6
    },
    'Tetraodon nigroviridis' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 19602,
        'Genome length' : 0.36,
        'Ensembl date' : new Date(2004, 09),
        'Cuteness factor' : 10
    },
    'Monodelphis domestica' : {
        'Chromosome pairs' : 11,
        'Protein-coding genes' : 21327,
        'Genome length' : 3.6,
        'Ensembl date' : new Date(2005, 11),
        'Cuteness factor' : 9
    },
    'Mus musculus' : {
        'Chromosome pairs' : 20,
        'Protein-coding genes' : 23148,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2002,01),
        'Cuteness factor' : 7
    },
    'Ornithorhynchus anatinus' : {
        'Chromosome pairs' : 26,
        'Protein-coding genes' : 21698,
        'Genome length' : 2.1,
        'Ensembl date' : new Date(2006,12),
        'Cuteness factor' : 9
    },
    'Pan troglodytes' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 18759,
        'Genome length' : 3.3,
        'Ensembl date' : new Date(2004,05),
        'Cuteness factor' : 6
    },
    'Macaca mulatta' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 21905,
        'Genome length' : 3.1,
        'Ensembl date' : new Date(2005,12),
        'Cuteness factor' : 6
    },
    'Ovis aries' : {
        'Chromosome pairs' : 27,
        'Protein-coding genes' : 20921,
        'Genome length' : 2.6,
        'Ensembl date' : new Date(2013,12),
        'Cuteness factor' : 6
    },
    'Sus scrofa' : {
        'Chromosome pairs' : 19,
        'Protein-coding genes' : 21630,
        'Genome length' : 2.8,
        'Ensembl date' : new Date(2009,09),
        'Cuteness factor' : 5
    },
    'Ciona intestinalis' : {
        'Chromosome pairs' : 14,
        'Protein-coding genes' : 16658,
        'Genome length' : 0.1,
        'Ensembl date' : new Date(2005,05),
        'Cuteness factor' : 3
    },
    'Rattus norvegicus' : {
        'Chromosome pairs' : 21,
        'Protein-coding genes' : 22941,
        'Genome length' : 2.9,
        'Ensembl date' : new Date(2002,11),
        'Cuteness factor' : 5
    },
    'Anolis carolinensis' : {
        'Chromosome pairs' : 14,
        'Protein-coding genes' : 18596,
        'Genome length' : 1.8,
        'Ensembl date' : new Date(2009,03),
        'Cuteness factor' : 7
    },
    'Bos taurus' : {
        'Chromosome pairs' : 30,
        'Protein-coding genes' : 19994,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2005,07),
        'Cuteness factor' : 6
    },
    'Pongo abelii' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 20424,
        'Genome length' : 3.4,
        'Ensenbl date' : new Date(2011,04),
        'Cuteness factor' : 8
    },
    'Callithrix jacchus' : {
        'Chromosome pairs' : 23,
        'Protein-coding genes' : 20993,
        'Genome length' : 2.9,
        'Ensembl date' : new Date(2009,09),
        'Cuteness factor' : 8
    },
    'Equus caballus' : {
        'Chromosome pairs' : 32,
        'Protein-coding genes' : 20449,
        'Genome length' : 2.5,
        'Ensembl date' : new Date(2008,03),
        'Cuteness factor' : 6
    },
    'Taeniopygia guttata' : {
        'Chromosome pairs' : 40,
        'Protein-coding genes' : 17488,
        'Genome length' : 1.2,
        'Ensembl date' : new Date(2009,03),
        'Cuteness factor' : 8
    },
    'Gasterosteus aculeatus' : {
        'Chromosome pairs' : 22,
        'Protein-coding genes' : 20787,
        'Genome length' : 0.46,
        'Ensembl date' : new Date(2006,08),
        'Cuteness factor' : 3
    },
    'Gallus gallus' : {
        'Chromosome pairs' : 39,
        'Protein-coding genes' : 15508,
        'Genome length' : 1,
        'Ensembl date' : new Date(2004,06),
        'Cuteness factor' : 4
    },
    'Felis catus' : {
        'Chromosome pairs' : 19,
        'Protein-coding genes' : 19493,
        'Genome length' : 2.5,
        'Ensembl date' : new Date(2007,02),
        'Cuteness factor' : 9
    },
    'Gorilla gorilla' : {
        'Chromosome pairs' : 24,
        'Protein-coding genes' : 20962,
        'Genome length' : 3,
        'Ensembl date' : new Date(2008,12),
        'Cuteness factor' : 4
    },
    'Oryctolagus cuniculus' : {
        'Chromosome pairs' : 22,
        'Protein-coding genes' : 19293,
        'Genome length' : 2.7,
        'Ensembl date' : new Date(2006,08),
        'Cuteness factor' : 10
    },
    'Meleagris gallopavo' : {
        'Chromosome pairs' : 40,
        'Protein-coding genes' : 14125,
        'Genome length' : 1.1,
        'Ensembl date' : new Date(2010,03),
        'Cuteness factor' : 2
    },
    'Canis familiaris' : {
        'Chromosome pairs' : 39,
        'Protein-coding genes' : 19856,
        'Genome length' : 2.4,
        'Ensembl date' : new Date(2004,12),
        'Cuteness factor' : 6
    }
};