//Written by Paul Stothard, University of Alberta, Canada

function codonPlot (theDocument) {	
	var newDna = "";
	var maxInput = 50000;
	var codonTable;
	var title;

	if (testScript() == false) {
		return false;
	}

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkCodonTable (theDocument.forms[0].elements[4].value) == false))	{
		return false;
	}

	codonTable = makeCodonTable(theDocument.forms[0].elements[4].value);
	if (codonTable == false) {
		return false;
	}

	newDna = getSequenceFromFasta (theDocument.forms[0].elements[0].value);
	title = getTitleFromFasta (theDocument.forms[0].elements[0].value);
	verifyDna (newDna);
	newDna = removeNonDna(newDna);

	openWindow("Codon Plot");
	outputWindow.document.write(getInfoFromTitleAndSequence(title, newDna));
	openPre();	

	writeCodonPlot(codonTable, newDna);
	closePre();
	closeWindow();
	return true;	



}

function writeCodonPlot(codonTable, sequence) {

	var markString = "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";
	var codon;
	var perThou;
	var fraction;
	var yValue;
	var aminoAcid;

	//replace 'u' with 't'
	sequence = sequence.replace(/u/gi, "t");
	sequence = sequence.replace(/(...)/g,
                    function (str, p1, offset, s) {
			try {
				aminoAcid = codonTable[p1.toString().toLowerCase()].aminoAcid;
				yValue = codonTable[p1.toString().toLowerCase()].fraction;
			}

			catch (e) {
				aminoAcid = "???";
				yValue = 0;
			}
			return  "<b>" + p1.toString().toLowerCase() + ", " + (offset + 1) + " to " + (offset + 3) + " (" + aminoAcid + ")</b>\n" + markString.substring(0, Math.round(yValue * markString.length)) + " " + yValue.toFixed(2) + "\n\n";                     
                   }
                );
	
	outputWindow.document.write (sequence + "\n");

	return true;

}		

function makeCodonTable(gcgTable) {
	gcgTable = gcgTable.replace(/[^\.]*\.\./,"");
	var tableArray = gcgTable.split(/[\f\n\r]/);
	var re = /(\w+)\s+(\w+)\s+(\S+)\s+(\S+)\s+(\S+)/g;
	var matchArray;
	var codonTable = new CodonTable();
	
	for (var i = 0; i < tableArray.length; i++)	{
		while (matchArray = re.exec(tableArray[i])) {
			
			try {
				codonTable[matchArray[2].toLowerCase()].fillCodon(matchArray[1], parseFloat(matchArray[3]), parseFloat(matchArray[4]), parseFloat(matchArray[5]));
				codonTable.codons.push(matchArray[2].toLowerCase());
				}
			catch(e) {
				alert ("There is a problem with a line of the codon table: " + matchArray[1] + " " + matchArray[2] + " " + matchArray[3] + " " + matchArray[4] + " " + matchArray[5]);
				return false;
			}		
		}
	}
	
	codonTable.fixFraction();
	
	return codonTable;	
}

//class CodonTable
function CodonTable() {
	this.codons = new Array();
	this.ggg = new Codon();
	this.gga = new Codon();
	this.ggt = new Codon();
	this.ggc = new Codon();
	this.gag = new Codon();
	this.gaa = new Codon();
	this.gat = new Codon();
	this.gac = new Codon();
	this.gtg = new Codon();
	this.gta = new Codon();
	this.gtt = new Codon();
	this.gtc = new Codon();
	this.gcg = new Codon();
	this.gca = new Codon();
	this.gct = new Codon();
	this.gcc = new Codon();
	this.agg = new Codon();
	this.aga = new Codon();
	this.agt = new Codon();
	this.agc = new Codon();
	this.aag = new Codon();
	this.aaa = new Codon();
	this.aat = new Codon();
	this.aac = new Codon();
	this.atg = new Codon();
	this.ata = new Codon();
	this.att = new Codon();
	this.atc = new Codon();
	this.acg = new Codon();
	this.aca = new Codon();
	this.act = new Codon();
	this.acc = new Codon();
	this.tgg = new Codon();
	this.tga = new Codon();
	this.tgt = new Codon();
	this.tgc = new Codon();
	this.tag = new Codon();
	this.taa = new Codon();
	this.tat = new Codon();
	this.tac = new Codon();
	this.ttg = new Codon();
	this.tta = new Codon();
	this.ttt = new Codon();
	this.ttc = new Codon();
	this.tcg = new Codon();
	this.tca = new Codon();
	this.tct = new Codon();
	this.tcc = new Codon();
	this.cgg = new Codon();
	this.cga = new Codon();
	this.cgt = new Codon();
	this.cgc = new Codon();
	this.cag = new Codon();
	this.caa = new Codon();
	this.cat = new Codon();
	this.cac = new Codon();
	this.ctg = new Codon();
	this.cta = new Codon();
	this.ctt = new Codon();
	this.ctc = new Codon();
	this.ccg = new Codon();
	this.cca = new Codon();
	this.cct = new Codon();
	this.ccc = new Codon();
}

//class CodonTable method fixFraction()
//added to address bug in http://www.kazusa.or.jp/codon/ that causes fraction values to all be given as 0.
function fixFraction() {
	for (var i = 0; i < this.codons.length; i++) {
		var outerCodon = this.codons[i];
		var perThouTotal = 0;
		for (var j = 0; j < this.codons.length; j++) {
			var innerCodon = this.codons[j];
			if (this[outerCodon].aminoAcid == this[innerCodon].aminoAcid) {
				perThouTotal = perThouTotal + this[innerCodon].perThou;
			}
 		}
		this[outerCodon].fraction = this[outerCodon].perThou / perThouTotal;
	}
	return true;	
}

//create and throw away a prototype object
new CodonTable ();

// define object methods
CodonTable.prototype.fixFraction = fixFraction;

//class Codon method fillCodon()
function fillCodon(aminoAcid, number, perThou, fraction) {
	this.aminoAcid = aminoAcid;
	this.number = number;
	this.perThou = perThou;
	this.fraction = fraction;
}

//class Codon
function Codon() {
	this.aminoAcid;
	this.number;
	this.perThou;
	this.fraction;
}

//create and throw away a prototype object
new Codon ();

// define object methods
Codon.prototype.fillCodon = fillCodon;