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

function pcrProducts (theDocument) {	
	var newDna = "";
	var maxInput = 500000;

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

	var re;
	var primers = new Array();
	var forwardMatches = new Array();
	var reverseMatches = new Array();
	var pcrProducts = new Array();	

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false) || (checkFormElement (theDocument.forms[0].elements[2]) == false) || (checkFormElement (theDocument.forms[0].elements[3]) == false) || (checkFormElement (theDocument.forms[0].elements[4]) == false))	{
		return false;
	}

	if (theDocument.forms[0].elements[2].value.replace(/[^A-Za-z]/g,"").length < 10) {
		alert ("Please enter primer sequences that are at least 10 bases long.");
		return false;	
	}

	if (theDocument.forms[0].elements[4].value.replace(/[^A-Za-z]/g,"").length < 10) {
		alert ("Please enter primer sequences that are at least 10 bases long.");
		return false;	
	}

	var primerOne = convertDegenerates(theDocument.forms[0].elements[2].value.replace(/[^A-Za-z]/g,""));
	var primerTwo = convertDegenerates(theDocument.forms[0].elements[4].value.replace(/[^A-Za-z]/g,""));
	
	try {
		re = eval("/" + primerOne + "/gi");
		var testString = "teststring";
		testString = testString.replace(re, "");
	}
	catch(e) {
		alert ("The first primer sequence is not formatted correctly.");
		return false;
	}

	try {
		re = eval("/" + primerTwo + "/gi");
		var testString = "teststring";
		testString = testString.replace(re, "");
	}
	catch(e) {
		alert ("The second primer sequence is not formatted correctly.");
		return false;
	}

	primers.push(new Primer(eval("/" + primerOne + "/gi"), theDocument.forms[0].elements[1].value));
	primers.push(new Primer(eval("/" + primerTwo + "/gi"), theDocument.forms[0].elements[3].value));

	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);
	for (var i = 0; i < arrayOfFasta.length; i++)	{
		newDna = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);
		newDna = removeNonDna(newDna);	
	
		//create matchedPrimer objects from sequences and add them to array
		forwardMatches = findMatches (primers, newDna, theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value);
		reverseMatches = findMatches (primers, reverse(complement(newDna)), theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value);
		makePcrProducts (newDna, title, forwardMatches, reverseMatches, theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value, pcrProducts);	
	}

	pcrProducts.sort(pcrProductSorter);

	openWindow("PCR Products");
	openPre();
	for (var i = 0; i < pcrProducts.length; i++)	{
		pcrProducts[i].writeProduct(theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value);
	}
	if (pcrProducts.length == 0) {
		outputWindow.document.write("No PCR products were obtained.\n\n");
	}
	closePre();
	closeWindow();
	return true;


}

function findMatches (primers, sequence, topology) {
	var matchArray;
	var matchPosition;
	var arrayOfMatches = new Array();
	var re;
	var originalLength = sequence.length;

	if (topology == "circular")	{
		var lookAhead = 50;
		var shiftValue = (sequence.substring(0, lookAhead)).length;
		var upperLimit = sequence.length + shiftValue;
		sequence = sequence.substring(sequence.length - lookAhead,sequence.length) + sequence + sequence.substring(0,lookAhead);
		var lowerLimit = 0 + shiftValue;
		
		for (var i = 0; i < primers.length; i++)	{
			re = primers[i].re;
			while (matchArray = re.exec(sequence)) {
				matchPosition = re.lastIndex;
				if ((matchPosition >= lowerLimit) && (matchPosition < upperLimit))	{
					matchPosition = matchPosition - shiftValue;
					if (matchPosition == 0) {
						matchPosition = originalLength;
					}
					arrayOfMatches.push(new Match(primers[i].name, matchArray[0], matchPosition));
				}		
			}
		}
	}
	else {
		for (var i = 0; i < primers.length; i++)	{
			re = primers[i].re;
			while (matchArray = re.exec(sequence)) {
				matchPosition = re.lastIndex;
				arrayOfMatches.push(new Match(primers[i].name, matchArray[0], matchPosition));			
			}
		}
	}
	return arrayOfMatches;
}

function makePcrProducts (newDna, title, forwardMatches, reverseMatches, topology, pcrProducts) {
	for (var i = 0; i < forwardMatches.length; i++)	{
		for (var j = 0; j < reverseMatches.length; j++)	{			
			
			if ((forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length) <= (newDna.length - reverseMatches[j].positionAfter)) {
				pcrProducts.push(new PcrProduct(title, forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length + 1, newDna.length - reverseMatches[j].positionAfter + reverseMatches[j].matchingText.length, forwardMatches[i].primerName, reverseMatches[j].primerName, forwardMatches[i].name, reverseMatches[j].name, newDna.substring(forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length, newDna.length - reverseMatches[j].positionAfter + reverseMatches[j].matchingText.length)));
			}
			
			else if ((topology == "circular") && ((forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length) > (newDna.length - reverseMatches[j].positionAfter + reverseMatches[j].matchingText.length - 1))) {
				pcrProducts.push(new PcrProduct(title, forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length + 1, newDna.length - reverseMatches[j].positionAfter + reverseMatches[j].matchingText.length, forwardMatches[i].primerName, reverseMatches[j].primerName, forwardMatches[i].name, reverseMatches[j].name, newDna.substring(forwardMatches[i].positionAfter - forwardMatches[i].matchingText.length, newDna.length) + newDna.substring(0, newDna.length - reverseMatches[j].positionAfter + reverseMatches[j].matchingText.length)));				
			}
		}
	}
}

//PcrProduct class writeProduct() method
function writeProduct(topology) {
	outputWindow.document.write ("&gt;" + this.sequence.length + " bp product from " + topology + " template " + this.template + ", base " + this.start + " to base " + this.stop + " (" + this.forwardName + " - " + this.reverseName + ").\n");
	outputWindow.document.write (addReturns(this.sequence) + "\n\n");
}

//PcrProduct class
function PcrProduct (template, start, stop, forwardName, reverseName, forwardPrimer, reversePrimer, sequence) {
   	this.template = template;
	this.start = start;
	this.stop = stop;
	this.forwardName = forwardName;
	this.reverseName = reverseName;
	this.forwardPrimer = forwardPrimer;
	this.reversePrimer = reversePrimer;
	this.sequence = sequence;
}

//create and throw away a prototype object
new PcrProduct("", 0, 0, "", "", "", "", "");

// define object methods
PcrProduct.prototype.writeProduct = writeProduct;


//Match class
function Match (primerName, matchingText, positionAfter) {
	this.primerName = primerName;
	this.matchingText = matchingText;
	this.positionAfter = positionAfter;
}

//Primer class
function Primer (re, name) {
	this.re = re;
	this.name = name;
}

function pcrProductSorter (a, b) {
   	if (a.sequence.length < b.sequence.length) {
      		return 1;
	}
   	if (a.sequence.length > b.sequence.length) {
      		return -1;
	}
	else {
		return 0;
	}
}