(function ($) {
    
    function init() {
   
         // find all icon menu items and add event listeners
         $("#main-menu-links a.active").each(function(a) {
            $(this).width(190);
            $(this).hover(
              function () {
                 $(this).width(190);
              }, 
              function () {
                 $(this).width(76);
              }
            );
         });

         $("#main-menu-links").each(function(a) {
            $(this).hover(
              function () {
                 $("#main-menu-links a.active").width(76);
              }, 
              function () {
                 $("#main-menu-links a.active").width(190);
              }
            );
         });
         
         // Setup the Codon Optimizer
         $("#optimize-codons").click(function(c) {
         
            var map = Array();
            map['TTT'] = 'TTC';
            map['TTA'] = 'CTG';
            map['TTG'] = 'CTG';
            map['CTT'] = 'CTG';
            map['CTC'] = 'CTG';
            map['CTA'] = 'CTG';
            map['ATA'] = 'ATC';
            map['GTT'] = 'GTG';
            map['GTA'] = 'GTC';
            map['TCT'] = 'TCC';
            map['TCA'] = 'TCG';
            map['CCT'] = 'CCG';
            map['CCA'] = 'CCC';
            map['ACT'] = 'ACG';
            map['ACA'] = 'ACC';
            map['TAG'] = 'TGA';
            map['CAA'] = 'CAG';
            map['AAA'] = 'AAG';
            map['TGT'] = 'TGC';
            map['CGA'] = 'CGC';
            map['CGT'] = 'CGC';
            map['AGT'] = 'AGC';
            map['AGA'] = 'AGG';
            map['GGA'] = 'GGC';
            map['GGT'] = 'GGC';
            
            // Split the input string into chunks of 3
            var codons = $('#old-codons').val().match(/.{1,3}/g);
            
            // Loop through each set of 3 and check if they match our conditions
            $.each(codons, function(index, value) {
               if(map[value]) {
                  codons[index] = map[value];
               }
            });
            
            // Put our string back together and display it on the page
            $('#new-codons').html(codons.join(''));
         });

   
   }


    $(function () {
        init();
    });


})(jQuery);