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

function multiRevTrans (theDocument) {	
	var newProtein = "";
	var maxInput = 20000;
	var codonTable;
	var alignArray = new Array();
	var titleArray = new Array();
	var sequenceArray = new Array();

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

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

	theAlignment = "X" + theDocument.forms[0].elements[0].value;
	alignArray = theAlignment.split(/[>%#]/);

	if (earlyCheckAlign (alignArray) == false)	{
		return false;
	}

	for (var i = 1; i < alignArray.length; i++)	{
		titleArray[i-1] = alignArray[i].match(/[^\f\n\r]+[\f\n\r]/);
		titleArray[i-1] = filterFastaTitle(titleArray[i-1].toString()).replace(/[\f\n\r]/g, "");
		titleArray[i-1] = titleArray[i-1].substring(0, 20);
		if (i == 1) {
			longestTitle = titleArray[i-1].length;
		}
		else if (titleArray[i-1].length > longestTitle)	{
			longestTitle = titleArray[i-1].length;
		}
		sequenceArray[i-1] = alignArray[i].replace(/[^\f\n\r]+[\f\n\r]/,"");
		sequenceArray[i-1] = filterAlignSeq (sequenceArray[i-1]);
	}

	codonTable = makeCodonTable(theDocument.forms[0].elements[4].value);
	if (codonTable == false) {
		return false;
	}
	openWindow("Multi Rev Trans");
	for (var i = 0; i < titleArray.length; i++)	{
		outputWindow.document.write(getInfoFromTitleAndSequence(titleArray[i], sequenceArray[i]));
		if (i < titleArray.length - 1) {
			outputWindow.document.write("<div class=\"info\">Combined with:</div>\n");
		}	
	}
	openPre();
	writeConsensusSeq(sequenceArray, codonTable);
	outputWindow.document.write ("\n");
	writeMultiRevTrans(sequenceArray, codonTable);
	closePre();
	closeWindow();
	return true;
}

function writeConsensusSeq(sequenceArray, codonTable) {

	var consensusSeq = new Array();
	var aminoAcid;
	var firstG;
	var firstA;
	var firstT;
	var firstC;

	var secondG;
	var secondA;
	var secondT;
	var secondC;

	var thirdG;
	var thirdA;
	var thirdT;
	var thirdC;

	//go through each position in the alignment and fill 12 variables with the sum of the 
	for (var i = 0; i < sequenceArray[0].length; i++)	{
		
		firstG = 0;
		firstA = 0;
		firstT = 0;
		firstC = 0;

		secondG = 0;
		secondA = 0;
		secondT = 0;
		secondC = 0;

		thirdG = 0;
		thirdA = 0;
		thirdT = 0;
		thirdC = 0;

		for (var j = 0; j < sequenceArray.length; j++) {
			if ((sequenceArray[j].charAt(i) == "-") || (sequenceArray[j].charAt(i) == ".")) {
				firstG = firstG + 0.25;
				firstA = firstA + 0.25;
				firstT = firstT + 0.25;
				firstC = firstC + 0.25;

				secondG = secondG + 0.25;
				secondA = secondA + 0.25;
				secondT = secondT + 0.25;
				secondC = secondC + 0.25;

				thirdG = thirdG + 0.25;
				thirdA = thirdA + 0.25;
				thirdT = thirdT + 0.25;
				thirdC = thirdC + 0.25;
			}
			else {
				try {
					aminoAcid = codonTable[sequenceArray[j].charAt(i).toString().toLowerCase()];
				}
				catch (e) {				
					alert ("A codon table entry wasn't found for " + sequenceArray[j].charAt(i));
					return false;				
				}
				
				firstG = firstG + aminoAcid.baseFreqPosOne[0];
				firstA = firstA + aminoAcid.baseFreqPosOne[1];
				firstT = firstT + aminoAcid.baseFreqPosOne[2];
				firstC = firstC + aminoAcid.baseFreqPosOne[3];

				secondG = secondG + aminoAcid.baseFreqPosTwo[0];
				secondA = secondA + aminoAcid.baseFreqPosTwo[1];
				secondT = secondT + aminoAcid.baseFreqPosTwo[2];
				secondC = secondC + aminoAcid.baseFreqPosTwo[3];

				thirdG = thirdG + aminoAcid.baseFreqPosThree[0];
				thirdA = thirdA + aminoAcid.baseFreqPosThree[1];
				thirdT = thirdT + aminoAcid.baseFreqPosThree[2];
				thirdC = thirdC + aminoAcid.baseFreqPosThree[3];
			}
		}

		consensusSeq.push(_getConsensusBase([firstG, firstA, firstT, firstC]));
		consensusSeq.push(_getConsensusBase([secondG, secondA, secondT, secondC]));
		consensusSeq.push(_getConsensusBase([thirdG, thirdA, thirdT, thirdC]));
	}
	
	outputWindow.document.write ('&gt;' + 'reverse translation of alignment to a ' + consensusSeq.length + ' base sequence of consensus codons.\n');
	outputWindow.document.write (addReturns(consensusSeq.join("")));
	outputWindow.document.write ("\n");
	
	return true;
}



function writeMultiRevTrans(sequenceArray, codonTable) {

	var markG = "gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg";
	var markA = "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa";
	var markT = "TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";
	var markC = "CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC";

	var markLength = markG.length;

	var aminoAcid;
	var columnSeq;
	var firstG;
	var firstA;
	var firstT;
	var firstC;

	var secondG;
	var secondA;
	var secondT;
	var secondC;

	var thirdG;
	var thirdA;
	var thirdT;
	var thirdC;

	//go through each position in the alignment and fill 12 variables with the sum of the 
	for (var i = 0; i < sequenceArray[0].length; i++)	{

		columnSeq = "";	

		firstG = 0;
		firstA = 0;
		firstT = 0;
		firstC = 0;

		secondG = 0;
		secondA = 0;
		secondT = 0;
		secondC = 0;

		thirdG = 0;
		thirdA = 0;
		thirdT = 0;
		thirdC = 0;

		for (var j = 0; j < sequenceArray.length; j++) {
			columnSeq = columnSeq + sequenceArray[j].charAt(i);
			if ((sequenceArray[j].charAt(i) == "-") || (sequenceArray[j].charAt(i) == ".")) {
				firstG = firstG + 0.25;
				firstA = firstA + 0.25;
				firstT = firstT + 0.25;
				firstC = firstC + 0.25;

				secondG = secondG + 0.25;
				secondA = secondA + 0.25;
				secondT = secondT + 0.25;
				secondC = secondC + 0.25;

				thirdG = thirdG + 0.25;
				thirdA = thirdA + 0.25;
				thirdT = thirdT + 0.25;
				thirdC = thirdC + 0.25;
			}
			else {
				try {
					aminoAcid = codonTable[sequenceArray[j].charAt(i).toString().toLowerCase()];
				}
				catch (e) {				
					alert ("A codon table entry wasn't found for " + sequenceArray[j].charAt(i));
					return false;				
				}
				
				firstG = firstG + aminoAcid.baseFreqPosOne[0];
				firstA = firstA + aminoAcid.baseFreqPosOne[1];
				firstT = firstT + aminoAcid.baseFreqPosOne[2];
				firstC = firstC + aminoAcid.baseFreqPosOne[3];

				secondG = secondG + aminoAcid.baseFreqPosTwo[0];
				secondA = secondA + aminoAcid.baseFreqPosTwo[1];
				secondT = secondT + aminoAcid.baseFreqPosTwo[2];
				secondC = secondC + aminoAcid.baseFreqPosTwo[3];

				thirdG = thirdG + aminoAcid.baseFreqPosThree[0];
				thirdA = thirdA + aminoAcid.baseFreqPosThree[1];
				thirdT = thirdT + aminoAcid.baseFreqPosThree[2];
				thirdC = thirdC + aminoAcid.baseFreqPosThree[3];
			}
		}

		firstG = Math.round(markLength * firstG / sequenceArray.length);
		firstA = Math.round(markLength * firstA / sequenceArray.length);
		firstT = Math.round(markLength * firstT / sequenceArray.length);
		firstC = Math.round(markLength * firstC / sequenceArray.length);

		secondG = Math.round(markLength * secondG / sequenceArray.length);
		secondA = Math.round(markLength * secondA / sequenceArray.length);
		secondT = Math.round(markLength * secondT / sequenceArray.length);
		secondC = Math.round(markLength * secondC / sequenceArray.length);

		thirdG = Math.round(markLength * thirdG / sequenceArray.length);
		thirdA = Math.round(markLength * thirdA / sequenceArray.length);
		thirdT = Math.round(markLength * thirdT / sequenceArray.length);
		thirdC = Math.round(markLength * thirdC / sequenceArray.length);

		outputWindow.document.write("<b>" + (i + 1) + "_" + columnSeq + "_" + "first</b>\n");
		outputWindow.document.write( "g" + markG.substring(0, firstG) + " " + (firstG / markLength).toFixed(2) + "\n" + "a" + markA.substring(0, firstA) + " " + (firstA / markLength).toFixed(2) + "\n" + "T" + markT.substring(0, firstT) + " " + (firstT / markLength).toFixed(2) + "\n" + "C" + markC.substring(0, firstC) + " " + (firstC / markLength).toFixed(2) + "\n");


		outputWindow.document.write("<b>" + (i + 1) + "_" + columnSeq + "_" + "second</b>\n");
		outputWindow.document.write( "g" + markG.substring(0, secondG) + " " + (secondG / markLength).toFixed(2) + "\n" + "a" + markA.substring(0, secondA) + " " + (secondA / markLength).toFixed(2) + "\n" + "T" + markT.substring(0, secondT) + " " + (secondT / markLength).toFixed(2) + "\n" + "C" + markC.substring(0, secondC) + " " + (secondC / markLength).toFixed(2) + "\n");

		outputWindow.document.write("<b>" + (i + 1) + "_" + columnSeq + "_" + "third</b>\n");
		outputWindow.document.write( "g" + markG.substring(0, thirdG) + " " + (thirdG / markLength).toFixed(2) + "\n" + "a" + markA.substring(0, thirdA) + " " + (thirdA / markLength).toFixed(2) + "\n" + "T" + markT.substring(0, thirdT) + " " + (thirdT / markLength).toFixed(2) + "\n" + "C" + markC.substring(0, thirdC) + " " + (thirdC / markLength).toFixed(2) + "\n");

		outputWindow.document.write("\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[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.determineBaseFreq();
	codonTable.c.determineBaseFreq();
	codonTable.d.determineBaseFreq();
	codonTable.e.determineBaseFreq();
	codonTable.f.determineBaseFreq();
	codonTable.g.determineBaseFreq();
	codonTable.h.determineBaseFreq();
	codonTable.i.determineBaseFreq();
	codonTable.k.determineBaseFreq();
	codonTable.l.determineBaseFreq();
	codonTable.m.determineBaseFreq();
	codonTable.n.determineBaseFreq();
	codonTable.p.determineBaseFreq();
	codonTable.q.determineBaseFreq();
	codonTable.r.determineBaseFreq();
	codonTable.s.determineBaseFreq();
	codonTable.t.determineBaseFreq();
	codonTable.v.determineBaseFreq();
	codonTable.w.determineBaseFreq();
	codonTable.y.determineBaseFreq();
	codonTable.z.determineBaseFreq();

	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 addCodon()
function addCodon(codon) {
	this.codons.push(codon);	
}

//class AminoAcid method determineBaseFreq()
function determineBaseFreq() {
	this.fixFraction();
	for (var i = 0; i < this.codons.length; i++) {
	    if (this.codons[i].sequence.charAt(0) == "g") {
		    this.baseFreqPosOne[0] = this.baseFreqPosOne[0] + this.codons[i].fraction;
	    }
	    else if (this.codons[i].sequence.charAt(0) == "a") {
		    this.baseFreqPosOne[1] = this.baseFreqPosOne[1] + this.codons[i].fraction;
	    }
	    else if (this.codons[i].sequence.charAt(0) == "t") {
		    this.baseFreqPosOne[2] = this.baseFreqPosOne[2] + this.codons[i].fraction;
	    }
	    else if (this.codons[i].sequence.charAt(0) == "c") {
		    this.baseFreqPosOne[3] = this.baseFreqPosOne[3] + this.codons[i].fraction;
	    }

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

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

//class AminoAcid 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() {
	var perThouTotal = 0;
	for (var i = 0; i < this.codons.length; i++) {
		perThouTotal = perThouTotal + this.codons[i].perThou;
	}

	if (perThouTotal == 0) {
		return false;
	}

	for (var i = 0; i < this.codons.length; i++) {
		this.codons[i].fraction = this.codons[i].perThou / perThouTotal;
	}
	return true;	
}


//class AminoAcid
function AminoAcid() {
	this.codons = new Array();
	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.rulerPosOne;
	this.rulerPosTwo;
	this.rulerPosThree;
}

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

// define object methods
AminoAcid.prototype.addCodon = addCodon;
AminoAcid.prototype.determineBaseFreq = determineBaseFreq;
AminoAcid.prototype.fixFraction = fixFraction;


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

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";	
	}
	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 "?";
}