var colors = {
    "protein coding"       : d3.rgb('#A00000'),
    "pseudogene"           : d3.rgb('#666666'),
    "processed transcript" : d3.rgb('#0033FF'),
    "ncRNA"                : d3.rgb('#8B668B'),
    "antisense"            : d3.rgb('#CBDD8B'),
};

var biotype_to_legend = {
    "protein_coding"       : "protein coding",
    "pseudogene"           : "pseudogene",
    "processed_pseudogene" : "pseudogene",
    "processed_transcript" : "processed transcript",
    "miRNA"                : "ncRNA",
    "lincRNA"              : "ncRNA",
    "misc_RNA"             : "ncRNA",
    "snoRNA"               : "ncRNA",
    "snRNA"                : "ncRNA",
    "rRNA"                 : "ncRNA",
    "antisense"            : "antisense",
    "sense_intronic"       : "antisense"
};

var render = function (div) {
    // legend placeholder
    var legend_div = d3.select(div)
        .append("div")
        .attr("class", "tnt_legend_div");

    legend_div
        .append("text")
        .text("Gene legend:");

    // Gene track
    var gene_track = tnt.board.track()
        .height(200)
        .color("white")
        .display(tnt.board.track.feature.genome.gene()
             .color("#550055")
        )
        .data(tnt.board.track.data.genome.gene());

    d3.selectAll("tnt_biotype")
        .data(gene_track.data().elements());

    // Get the default data updater...
    var gene_updater = gene_track.data().retriever();
    // ... and create a new updater that calls the orig one + populates the legend dynamically
    gene_track.data().retriever (function (obj) {
        return gene_updater.call(gene_track, obj)
            .then (function (genes) {
                genes.map(gene_color);

                // And we setup/update the legend
                var biotypes_array = genes.map(function(e){
                    return biotype_to_legend[e.biotype];
                });
                var biotypes_hash = {};
                for (var i=0; i<biotypes_array.length; i++) {
                    biotypes_hash[biotypes_array[i]] = 1;
                }
                var biotypes = [];
                for (var p in biotypes_hash) {
                    if (biotypes_hash.hasOwnProperty(p)) {
                        biotypes.push(p);
                    }
                }
                var biotype_legend = legend_div.selectAll(".tnt_biotype_legend")
                    .data(biotypes, function(d){
                        return d;
                    });

                var new_legend = biotype_legend
                    .enter()
                    .append("div")
                    .attr("class", "tnt_biotype_legend")
                    .style("display", "inline");

                new_legend
                    .append("div")
                    .style("display", "inline-block")
                    .style("margin", "0px 2px 0px 15px")
                    .style("width", "10px")
                    .style("height", "10px")
                    .style("border", "1px solid #000")
                    .style("background", function(d){return colors[d];});
                new_legend
                    .append("text")
                .text(function(d){return d;});
                biotype_legend
                    .exit()
                    .remove();

                return genes;
            });
    });

    var gene_color =  function (gene) {
        gene.color = colors[biotype_to_legend[gene.biotype]];
        return;
    };

    var genome = tnt.board.genome().species("human").gene("brca2").width(950);
    genome.add_track(gene_track);
    genome(div);
    genome.start();
};