hierarchy.js

"buildTaxonHierarchy": function(data) {
      var occurrenceTree = {"phyla": []};

      // Some preproccessing
      data.records.forEach(function(d) {
        d.rank = (d.rnk) ? taxaBrowser.rankMap(d.rnk) : "Unknown";
        d.itallics = (d.rnk < 6) ? "itallics" : "";
        d.old_name = (d.tna.split(" ")[0] != d.idt) ? d.tna : "";
        d.display_name1 = (d.tna === (d.idt + " " + d.ids)) ? d.tna : d.idt;
        d.display_name2 = (d.tna === (d.idt + " " + d.ids)) ? d.tna : d.ids;
      });

      // Find unique phyla
      data.records.forEach(function(d) {
        var phyla = [];
        for (var i = 0; i < occurrenceTree.phyla.length; i++) {
          phyla.push(occurrenceTree.phyla[i].phylum);
        }

        if (phyla.indexOf(d.phl) < 0) {
          var newPhylum = {"phylum": d.phl, "classes": []};
          occurrenceTree.phyla.push(newPhylum);
        }
          
      });

      // Find unique phylum/class combinations
      data.records.forEach(function(d) {
        var phyla_classes = [];
        for (var i = 0; i < occurrenceTree.phyla.length; i++) {
          for (var j = 0; j < occurrenceTree.phyla[i].classes.length; j++) {
            phyla_classes.push(occurrenceTree.phyla[i].phylum + "-" + occurrenceTree.phyla[i].classes[j].nameClass);
          }
        }

        if (phyla_classes.indexOf(d.phl + "-" + d.cll) < 0) {
          var newClass = {"nameClass": d.cll, "families": []},
              phylumIndex = navMap.getIndex(occurrenceTree.phyla, d.phl, "phylum");
          occurrenceTree.phyla[phylumIndex]["classes"].push(newClass);
        }
      });

      // Find unique phylum/class/family combinations
      data.records.forEach(function(d) {
        var phyla_class_family = [];
        for (var i = 0; i < occurrenceTree.phyla.length; i++) {
          for (var j = 0; j < occurrenceTree.phyla[i].classes.length; j++) {
            for (var k = 0; k < occurrenceTree.phyla[i].classes[j].families.length; k++) {
              phyla_class_family.push(occurrenceTree.phyla[i].phylum + "-" + occurrenceTree.phyla[i].classes[j].nameClass + "-" + occurrenceTree.phyla[i].classes[j].families[k].family);
            }
          }
        }

        if (phyla_class_family.indexOf(d.phl + "-" + d.cll + "-" + d.fml) < 0) {
          var newFamily = {"family": d.fml, "genera": []},
              phylumIndex = navMap.getIndex(occurrenceTree.phyla, d.phl, "phylum"),
              classIndex = navMap.getIndex(occurrenceTree.phyla[phylumIndex].classes, d.cll, "nameClass");
          occurrenceTree.phyla[phylumIndex].classes[classIndex]["families"].push(newFamily);
        }
      });
      
      // Place genera into the right phylum/class/family
      data.records.forEach(function(d) {
        var phylumIndex = navMap.getIndex(occurrenceTree.phyla, d.phl, "phylum"),
            classIndex = navMap.getIndex(occurrenceTree.phyla[phylumIndex].classes, d.cll, "nameClass"),
            familyIndex = navMap.getIndex(occurrenceTree.phyla[phylumIndex].classes[classIndex].families, d.fml, "family");
        occurrenceTree.phyla[phylumIndex].classes[classIndex].families[familyIndex].genera.push(d);
      });

      occurrenceTree.phyla.forEach(function(d) {
        if (typeof(d.phylum) === "undefined") {
          d.phylum = "Unranked taxa";
          d.unranked = true;
        }
      });

      return occurrenceTree;
    }