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

function revTrans (theDocument) {	
	var newProtein = "";
	var maxInput = 20000;

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

	var codonTable;

	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;
	}

	openWindow("Reverse Translate");
	openPre();
	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);

	for (var i = 0; i < arrayOfFasta.length; i++)	{
		newProtein = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);

		newProtein = removeNonProtein(newProtein);

		outputWindow.document.write(getInfoFromTitleAndSequence(title, newProtein));
		writeRevTransSeqNoDegen(newProtein, title, codonTable);
		outputWindow.document.write ("\n");
		writeRevTransSeqDegen(newProtein, title, codonTable);
		outputWindow.document.write ("\n");
		outputWindow.document.write ("Graph of base probabilities:\n");		
		writeRevTransGraph(newProtein, codonTable);
		
		outputWindow.document.write ('\n\n');
	}

	closePre();
	closeWindow();
	return true;
}

function writeRevTransSeqNoDegen(protein, title, codonTable) {
	var aminoAcid;

	protein = protein.replace(/\*/g,"z");

	protein = protein.replace(/(.)/g,
                    function (str, p1, offset, s) {
			aminoAcid = codonTable[p1.toString().toLowerCase()];
			return aminoAcid.mostCommonCodon;                 
                   }
                );
	outputWindow.document.write ('&gt;' + 'reverse translation of ' + title + ' to a ' + protein.length + ' base sequence of most likely codons.\n');
	outputWindow.document.write (addReturns(protein));
	outputWindow.document.write ("\n");
	return true;
}

function writeRevTransSeqDegen(protein, title, codonTable) {
	var aminoAcid;

	protein = protein.replace(/\*/g,"z");

	protein = protein.replace(/(.)/g,
                    function (str, p1, offset, s) {
			aminoAcid = codonTable[p1.toString().toLowerCase()];
			return aminoAcid.degenCodon;                 
                   }
                );
	outputWindow.document.write ('&gt;' + 'reverse translation of ' + title + ' to a ' + protein.length + ' base sequence of consensus codons.\n');
	outputWindow.document.write (addReturns(protein));
	outputWindow.document.write ("\n");
	return true;
}

function writeRevTransGraph(protein, codonTable) {
	
	var aminoAcid;

	protein = protein.replace(/\*/g,"z");

	protein = protein.replace(/(.)/g,
                    function (str, p1, offset, s) {
			aminoAcid = codonTable[p1.toString().toLowerCase()];
			return "<b>" + (offset + 1) + "_" + str + "_" + "first</b>\n" + aminoAcid.rulerPosOne + "<b>" + (offset + 1) + "_" + str + "_" + "second</b>\n" + aminoAcid.rulerPosTwo + "<b>" + (offset + 1) + "_" + str + "_" + "third</b>\n" + aminoAcid.rulerPosThree + "\n";                      
                   }
                );

	outputWindow.document.write (protein);

	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[1].toLowerCase()].addCodon(new Codon(matchArray[2], parseFloat(matchArray[3]), parseFloat(matchArray[4]), parseFloat(matchArray[5])));

				}
			catch(e) {
				
				alert ("There is a problem with a line of the codon table: " + matchArray[1] + " " + matchArray[2] + " " + matchArray[3] + " " + matchArray[4] + " " + matchArray[4]);
				return false;
			}		
		}
	}
	
	codonTable.a.fillRuler();
	codonTable.c.fillRuler();
	codonTable.d.fillRuler();
	codonTable.e.fillRuler();
	codonTable.f.fillRuler();
	codonTable.g.fillRuler();
	codonTable.h.fillRuler();
	codonTable.i.fillRuler();
	codonTable.k.fillRuler();
	codonTable.l.fillRuler();
	codonTable.m.fillRuler();
	codonTable.n.fillRuler();
	codonTable.p.fillRuler();
	codonTable.q.fillRuler();
	codonTable.r.fillRuler();
	codonTable.s.fillRuler();
	codonTable.t.fillRuler();
	codonTable.v.fillRuler();
	codonTable.w.fillRuler();
	codonTable.y.fillRuler();
	codonTable.z.fillRuler();	

	return codonTable;	
}

//class CodonTable
function CodonTable() {
	this.a = new AminoAcid();
	this.c = new AminoAcid();
	this.d = new AminoAcid();
	this.e = new AminoAcid();
	this.f = new AminoAcid();
	this.g = new AminoAcid();
	this.h = new AminoAcid();
	this.i = new AminoAcid();
	this.k = new AminoAcid();
	this.l = new AminoAcid();
	this.m = new AminoAcid();
	this.n = new AminoAcid();
	this.p = new AminoAcid();
	this.q = new AminoAcid();
	this.r = new AminoAcid();
	this.s = new AminoAcid();
	this.t = new AminoAcid();
	this.v = new AminoAcid();
	this.w = new AminoAcid();
	this.y = new AminoAcid();
	this.z = new AminoAcid();

	this.ala = this.a;
	this.cys = this.c;
	this.asp = this.d;
	this.glu = this.e;
	this.phe = this.f;
	this.gly = this.g;
	this.his = this.h;
	this.ile = this.i;
	this.lys = this.k;
	this.leu = this.l;
	this.met = this.m;
	this.asn = this.n;
	this.pro = this.p;
	this.gln = this.q;
	this.arg = this.r;
	this.ser = this.s;
	this.thr = this.t;
	this.val = this.v;
	this.trp = this.w;
	this.tyr = this.y;
	this.end = this.z;
}

//class AminoAcid method fillRuler()
function fillRuler() {

	var markG = "gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg";
	var markA = "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa";
	var markT = "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";
	var markC = "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";
	
	var markLength = markG.length;
	
	this.rulerPosOne = this.getRuler(this.baseFreqPosOne[0], markG) + 
			   this.getRuler(this.baseFreqPosOne[1], markA) + 
			   this.getRuler(this.baseFreqPosOne[2], markT) + 
			   this.getRuler(this.baseFreqPosOne[3], markC);

	this.rulerPosTwo = this.getRuler(this.baseFreqPosTwo[0], markG) + 
			   this.getRuler(this.baseFreqPosTwo[1], markA) + 
			   this.getRuler(this.baseFreqPosTwo[2], markT) + 
			   this.getRuler(this.baseFreqPosTwo[3], markC);

	this.rulerPosThree = this.getRuler(this.baseFreqPosThree[0], markG) + 
			   this.getRuler(this.baseFreqPosThree[1], markA) + 
			   this.getRuler(this.baseFreqPosThree[2], markT) + 
			   this.getRuler(this.baseFreqPosThree[3], markC);

	//calculate some other values
	this.setMostCommonCodon();
	this.setDegenCodon();
}

//class AminoAcid method getRuler()
function getRuler(freq, mark) {
	return mark.substring(0, 1) + mark.substring(0, freq * mark.length) + " " + (freq).toFixed(2) + "\n";	
}

//class AminoAcid method addCodon()
function addCodon(codon) {
	this.codons.push(codon);

	if (codon.sequence.charAt(0) == "g") {
		this.baseFreqPosOne[0] = this.baseFreqPosOne[0] + codon.fraction;
	}
	else if (codon.sequence.charAt(0) == "a") {
		this.baseFreqPosOne[1] = this.baseFreqPosOne[1] + codon.fraction;
	}
	else if (codon.sequence.charAt(0) == "t") {
		this.baseFreqPosOne[2] = this.baseFreqPosOne[2] + codon.fraction;
	}
	else if (codon.sequence.charAt(0) == "c") {
		this.baseFreqPosOne[3] = this.baseFreqPosOne[3] + codon.fraction;
	}

	if (codon.sequence.charAt(1) == "g") {
		this.baseFreqPosTwo[0] = this.baseFreqPosTwo[0] + codon.fraction;
	}
	else if (codon.sequence.charAt(1) == "a") {
		this.baseFreqPosTwo[1] = this.baseFreqPosTwo[1] + codon.fraction;
	}
	else if (codon.sequence.charAt(1) == "t") {
		this.baseFreqPosTwo[2] = this.baseFreqPosTwo[2] + codon.fraction;
	}
	else if (codon.sequence.charAt(1) == "c") {
		this.baseFreqPosTwo[3] = this.baseFreqPosTwo[3] + codon.fraction;
	}

	if (codon.sequence.charAt(2) == "g") {
		this.baseFreqPosThree[0] = this.baseFreqPosThree[0] + codon.fraction;
	}
	else if (codon.sequence.charAt(2) == "a") {
		this.baseFreqPosThree[1] = this.baseFreqPosThree[1] + codon.fraction;
	}
	else if (codon.sequence.charAt(2) == "t") {
		this.baseFreqPosThree[2] = this.baseFreqPosThree[2] + codon.fraction;
	}
	else if (codon.sequence.charAt(2) == "c") {
		this.baseFreqPosThree[3] = this.baseFreqPosThree[3] + codon.fraction;
	}	
}

//class AminoAcid method getMostCommonCodon()
function setMostCommonCodon() {
	var highestFraction = 0;
	var highestCodon = "nnn";
	for (var i = 0; i < this.codons.length; i++)	{
		if (this.codons[i].fraction > highestFraction) {
			highestFraction = this.codons[i].fraction;
			highestCodon = this.codons[i].sequence;
		}
	}
	this.mostCommonCodon =  highestCodon;
}

//class AminoAcid method getDegenCodon()
function setDegenCodon() {
	this.degenCodon = getConsensusBase(this.baseFreqPosOne) + getConsensusBase(this.baseFreqPosTwo) + getConsensusBase(this.baseFreqPosThree);
}

//class AminoAcid method getConsensusBase()
function getConsensusBase(baseFreq) {
	var g;
	var a;
	var t;
	var c;
	if (baseFreq[0] > 0) {
		g = true;
	}
	if (baseFreq[1] > 0) {
		a = true;
	}
	if (baseFreq[2] > 0) {
		t = true;
	}
	if (baseFreq[3] > 0) {
		c = true;
	}

	if (g && a && c && t) {
		return "n";
	}
	else if (a && c && t) {
		return "h";
	}
	else if (a && g && t) {
		return "d";
	}
	else if (c && g && t) {
		return "b";
	}
	else if (a && c) {
		return "m";
	}
	else if (g && t) {
		return "k";
	}
	else if (a && t) {
		return "w";
	}
	else if (g && c) {
		return "s";
	}
	else if (c && t) {
		return "y";
	}
	else if (a && g) {
		return "r";
	}
	else if (t) {
		return "t";
	}
	else if (g) {
		return "g";
	}
	else if (c) {
		return "c";
	}
	else if (a) {
		return "a";
	}
	return true;
}

//class AminoAcid
function AminoAcid() {
	this.codons = new Array();
	//g, a, t, c
	this.baseFreqPosOne = new Array (0, 0, 0, 0);
	this.baseFreqPosTwo = new Array (0, 0, 0, 0);
	this.baseFreqPosThree = new Array (0, 0, 0, 0);
	this.mostComonCodon;
	this.degenCodon;
	this.rulerPosOne;
	this.rulerPosTwo;
	this.rulerPosThree;
}

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

// define object methods
AminoAcid.prototype.fillRuler = fillRuler;
AminoAcid.prototype.getRuler = getRuler;
AminoAcid.prototype.addCodon = addCodon;
AminoAcid.prototype.setMostCommonCodon = setMostCommonCodon;
AminoAcid.prototype.setDegenCodon = setDegenCodon;
AminoAcid.prototype.getConsensusBase = getConsensusBase;

//class Codon
function Codon(sequence, number, perThou, fraction) {
	this.sequence = sequence.toLowerCase();
	this.number = number;
	this.perThou = perThou;
	this.fraction = fraction;
}