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

function pcrPrimerStats (theDocument) {	

	var newDna = "";
	var title = "";
	var maxInput = 5000;
	var maxPrimerLength = 50;
	var milliMolarSalt = 50;
	var milliMolarMagnesium = 1.5;
	var nanoMolarPrimerTotal = 200;
	var isPhosphorylated = false;

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

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

	molarSalt = (milliMolarSalt/1E3); //convert to molar from millimolar
	molarMagnesium = (milliMolarMagnesium/1E3); //convert to molar from millimolar
	molarPrimerTotal = (nanoMolarPrimerTotal/1E9); //convert to molar from nanomolar
	isPhosphorylated = false;

	//molarSalt affects Salt adjusted Tm and Tm (Nearest neighbor)
	//molarMagnesium affects Tm (Nearest neighbor)
	//molarPrimerTotal affects Tm (Nearest neighbor)
	//isPhosphorylated affects molecular weight

	openWindow("PCR Primer Stats");
	openPre();
	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);

	outputWindow.document.write("Global settings:\n");
	if (isPhosphorylated) {
		outputWindow.document.write("-The primers have a 5'-phosphate group.\n");
	}
	else {
		outputWindow.document.write("-The primers do not have a 5'-phosphate group.\n");
	}
	outputWindow.document.write("-Combined concentration of K+ and Na+ in the reaction = " + milliMolarSalt + " millimolar.\n");
	outputWindow.document.write("-Mg+2 concentration in the reaction = " + milliMolarMagnesium + " millimolar.\n");
	outputWindow.document.write("-Primer concentration in the reaction = " + nanoMolarPrimerTotal + " nanomolar.\n");
	outputWindow.document.write('\n');
	outputWindow.document.write('------------------------------------------------------------\n');

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

		newDna = _removeNonPrimer(newDna);

		if (newDna.length == 0) {
			continue;
		}

		if (newDna.length > maxPrimerLength) {
			continue;
		}

		var percentGC = _percentGC(newDna);
		var nearestNeighborTm = _nearestNeighborTm(newDna, molarSalt, molarPrimerTotal, molarMagnesium);
		var selfCompHash = _getSelfComplementarityReport(newDna, 3, 50);
		var hairpinHash = _getHairpinReport(newDna, 3, 50);

		outputWindow.document.write('------------------------------------------------------------\n');
		outputWindow.document.write ('General properties:\n');
		outputWindow.document.write ('-------------------\n');
		outputWindow.document.write(rightNum("Primer name:", "", 32, "") + title + "\n");
		outputWindow.document.write(rightNum("Primer sequence:", "", 32, "") + newDna + "\n");
		outputWindow.document.write(rightNum("Sequence length:", "", 32, "") + newDna.length + "\n");
		outputWindow.document.write(rightNum("Base counts:", "", 32, "") + _baseCounts(newDna) + "\n");
		outputWindow.document.write(rightNum("GC content (%):", "", 32, "") + percentGC + "\n");
		outputWindow.document.write(rightNum("Molecular weight (Daltons):", "", 32, "") + _molecularWeight(newDna, isPhosphorylated) + "\n");
		outputWindow.document.write(rightNum("nmol/A260:", "", 32, "") + _nmolPerA260(newDna) + "\n");
		outputWindow.document.write(rightNum("micrograms/A260:", "", 32, "") + _microgramsPerA260(newDna, isPhosphorylated) + "\n");
		outputWindow.document.write(rightNum("Basic Tm (degrees C):", "", 32, "") + _basicTm(newDna) + "\n");
		outputWindow.document.write(rightNum("Salt adjusted Tm (degrees C):", "", 32, "") + _molarSaltAdjustedTm(newDna, molarSalt) + "\n");
		outputWindow.document.write(rightNum("Nearest neighbor Tm (degrees C):", "", 32, "") + nearestNeighborTm + "\n");
		
		outputWindow.document.write ('\n');
		outputWindow.document.write ('PCR suitability tests (Pass / Warning):\n');
		outputWindow.document.write ('------------------------------------\n');			
		outputWindow.document.write(rightNum("Single base runs:", "", 32, "") + _getBaseRunsReport(newDna, 5) + "\n");
		outputWindow.document.write(rightNum("Dinucleotide base runs:", "", 32, "") + _getDiNucleotideRunsReport(newDna, 5) + "\n");
		outputWindow.document.write(rightNum("Length:", "", 32, "") + _getSuitableLengthReport(newDna, 14, 30) + "\n");
		outputWindow.document.write(rightNum("Percent GC:", "", 32, "") + _getSuitableGCReport(newDna, percentGC, 40, 60) + "\n");
		outputWindow.document.write(rightNum("Tm (Nearest neighbor):", "", 32, "") + _getSuitableTmReport(newDna, nearestNeighborTm, 50, 58) + "\n");
		outputWindow.document.write(rightNum("GC clamp:", "", 32, "") + _getSuitableThreePrimeGC(newDna, 1, 3) + "\n");
		outputWindow.document.write(rightNum("Self-annealing:", "", 32, "") + selfCompHash['report'] + "\n");
		if (selfCompHash['report'] != "Pass") {
			outputWindow.document.write(rightNum(":", "", 32, "") + selfCompHash['upper'] + "\n");
			outputWindow.document.write(rightNum(":", "", 32, "") + selfCompHash['divider'] + "\n");
			outputWindow.document.write(rightNum(":", "", 32, "") + selfCompHash['lower'] + "\n");
		}
		outputWindow.document.write(rightNum("Hairpin formation:", "", 32, "") + hairpinHash['report'] + "\n");
		if (hairpinHash['report'] != "Pass") {
			outputWindow.document.write(rightNum(":", "", 32, "") + hairpinHash['upper']  + "\n");
			outputWindow.document.write(rightNum(":", "", 32, "") + hairpinHash['divider'] + "\n");
			outputWindow.document.write(rightNum(":", "", 32, "") + hairpinHash['lower'] + "\n");
		}
		outputWindow.document.write('------------------------------------------------------------\n');
		outputWindow.document.write('\n');
	}
	closePre();
	closeWindow();
	return true;
}


//Nucleotide Code: Base:
//---------------- -----
//A.................Adenine
//C.................Cytosine
//G.................Guanine
//T (or U)..........Thymine (or Uracil)
//R.................A or G
//Y.................C or T
//S.................G or C
//W.................A or T
//K.................G or T
//M.................A or C
//B.................C or G or T
//D.................A or G or T
//H.................A or C or T
//V.................A or C or G
//N.................any base


function _removeNonPrimer (sequence) {
	return sequence.replace(/[^gatcryswkmbdhvnGATCRYSWKMBDHVN]/g, "");
}

function _containsOnlyNonDegenerates (sequence) {
    	if (sequence.search(/[^gatc]/i) == -1)	{
 		return true;
    	}
	return false;
}

function _baseCounts (sequence) {
	var numG = _getBaseCount(sequence, "g");
	var numA = _getBaseCount(sequence, "a");
	var numT = _getBaseCount(sequence, "t");
	var numC = _getBaseCount(sequence, "c");
	var numOther = sequence.length - (numG + numA + numT + numC);
	return "G=" + numG + "; A=" + numA + "; T=" + numT + "; C=" + numC + "; Other=" + numOther + ";";
}

function _microgramsPerA260 (sequence, isPhosphorylated) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _microgramsPerA260NonDegen (sequence, isPhosphorylated);
	}
	else {
		return _microgramsPerA260Degen (sequence, isPhosphorylated);
	}
}

function _microgramsPerA260NonDegen(sequence, isPhosphorylated) {

	var mw = _mw(sequence, isPhosphorylated)
	var result = mw / _getExtinctionCoefficient(sequence);
	return result.toFixed(2);
}

function _microgramsPerA260Degen(sequence, isPhosphorylated) {
	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace all other degenerates with the base with lowest value in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "g");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "c");

	//replace all other degenerates with base with highest value in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "t");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "a");

	//swap upper and lower because of how downstream calculation is done
	//return _microgramsPerA260NonDegen(lowerBoundsSequence, isPhosphorylated) + " to " + _microgramsPerA260NonDegen(upperBoundsSequence, isPhosphorylated);

	return _microgramsPerA260NonDegen(upperBoundsSequence, isPhosphorylated) + " to " + _microgramsPerA260NonDegen(lowerBoundsSequence, isPhosphorylated);	

}

function _nmolPerA260 (sequence) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _nmolPerA260NonDegen (sequence);
	}
	else {
		return _nmolPerA260Degen (sequence);
	}
}

function _nmolPerA260NonDegen(sequence) {
		
	var result = _getExtinctionCoefficient(sequence);
	result = 1 / result * 1000;
	return result.toFixed(2);
}

function _getExtinctionCoefficient(sequence) {
	var dimerValues = _getDimerExtinctionCoefficients();
	var singleValues = _getSingleExtinctionCoefficients();
	var dimerSum = 0;
	var singleSum = 0;

	for (var i = 0; i < sequence.length - 1; i++) {
		dimerSum = dimerSum + dimerValues[sequence.charAt(i) + sequence.charAt(i + 1)];
	}

	for (var i = 1; i < sequence.length - 1; i++) {
		singleSum = singleSum + singleValues[sequence.charAt(i)];
	}
	return (2 * dimerSum - singleSum);
}

function _nmolPerA260Degen(sequence) {
	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace all other degenerates with the base with lowest value in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "g");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "c");

	//replace all other degenerates with base with highest value in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "t");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "a");

	//swap upper and lower because of how downstream calculation is done
	//return _nmolPerA260NonDegen(lowerBoundsSequence) + " to " + _nmolPerA260NonDegen(upperBoundsSequence);
	return _nmolPerA260NonDegen(upperBoundsSequence) + " to " + _nmolPerA260NonDegen(lowerBoundsSequence);
}

function _percentGC (sequence) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _percentGCNonDegen (sequence);
	}
	else {
		return _percentGCDegen (sequence);
	}
}

function _percentGCNonDegen (sequence) {

	var numHits = _getBaseCount(sequence, "g") + _getBaseCount(sequence, "c");
	return ((numHits / sequence.length) * 100).toFixed(2);
}

function _percentGCDegen (sequence) {

	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace degenerates that must be g or c with g in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");

	//replace degenerates that must be a or t with a in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");

	//replace all other degenerates with a or t in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "a");

	//replace all other degenerates with g or c in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "g");

	return _percentGCNonDegen(lowerBoundsSequence) + " to " + _percentGCNonDegen(upperBoundsSequence);
}

function _molecularWeight (sequence, isPhosphorylated) {

	if (_containsOnlyNonDegenerates(sequence)) {
		return _molecularWeightNonDegen (sequence, isPhosphorylated);
	}
	else {
		return _molecularWeightDegen (sequence, isPhosphorylated);
	}
}

function _molecularWeightNonDegen (sequence, isPhosphorylated) {
	return _mw(sequence, isPhosphorylated).toFixed(2);
}

function _mw(sequence, isPhosphorylated) {
	//DNA molecular weight for synthesized oligonucleotides
	//Anhydrous Molecular Weight = (An x 313.21) + (Tn x 304.2) + (Cn x 289.18) + (Gn x 329.21) - 61.96
	//An, Tn, Cn, and Gn are the number of each respective nucleotide within the polynucleotide.
	//The subtraction of 61.96 gm/mole from the oligonucleotide molecular weight takes into account
	//the removal of HPO2 (63.98) and the addition of two hydrogens (2.02).
	var g = _getBaseCount(sequence, "g");
	var a = _getBaseCount(sequence, "a");
	var t = _getBaseCount(sequence, "t");
	var c = _getBaseCount(sequence, "c");
	var phosAdjust = 0;
	if (isPhosphorylated) {
		phosAdjust = 78 //79 for the phosphate (PO3), -1 for the hydrogen that is lost
	}
	return ((g * 329.21) + (a * 313.21) + (t * 304.20) + (c * 289.18) - 61.96 + phosAdjust)
}

function _molecularWeightDegen (sequence, isPhosphorylated) {

	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace all other degenerates with lightest base possible in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "c");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "c");

	//replace all other degenerates with heaviest base possible in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "t");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "g");

	return _molecularWeightNonDegen(lowerBoundsSequence, isPhosphorylated) + " to " + _molecularWeightNonDegen(upperBoundsSequence, isPhosphorylated);
}

function _basicTm (sequence) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _basicTmNonDegen (sequence);
	}
	else {
		return _basicTmDegen (sequence);
	}
}

function _basicTmNonDegen (sequence) {
	//Simple formula when primer length < 14 bases from
	//Rychlik, W. and Rhoads, R.E. (1989) Nucleic Acids Research 17, 8543
	//Tm = 4C x (number of G's and C's in the primer) + 2C x (number of A's and T's in the primer)
	//
	//When longer use:
	//tm = 64.9C + 41C * (number of G's and C's in the primer - 16.4)/ primer length
	//
	//both assume reaction is carried out in the presence of 50mM monovalent cations
	
	if (sequence.length < 14) {
		var numG = _getBaseCount(sequence, "g");
		var numC = _getBaseCount(sequence, "c");
		var numA = _getBaseCount(sequence, "a");
		var numT = _getBaseCount(sequence, "t");
		return (4 * (numG + numC) + 2 * (numA + numT)).toFixed(0);
	}
	else {
		var numG = _getBaseCount(sequence, "g");
		var numC = _getBaseCount(sequence, "c");
		return (64.9 + 41 * (numG + numC - 16.4) / sequence.length).toFixed(0);	
	}
}

function _basicTmDegen (sequence) {

	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace degenerates that must be g or c with g in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");

	//replace degenerates that must be a or t with a in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");

	//replace all other degenerates with a or t in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "a");

	//replace all other degenerates with g or c in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "g");

	return _basicTmNonDegen(lowerBoundsSequence) + " to " + _basicTmNonDegen(upperBoundsSequence);

}

//molarSalt in molar concentration
function _molarSaltAdjustedTm (sequence, molarSalt) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _molarSaltAdjustedTmNonDegen (sequence, molarSalt);
	}
	else {
		return _molarSaltAdjustedTmDegen (sequence, molarSalt);
	}
}

function _molarSaltAdjustedTmNonDegen (sequence, molarSalt) {
	//commonly used formula takes into account the molarSalt concentration of the reaction:
	//Tm = 81.5C + 7.21C x Math.log(molarSalt) + (0.41 x GC) - (675 / primer length);
	//see refs
	//Rychlik, W. and Rhoads, R.E. (1989) Nucl. Acids Res. 17, 8543.
	//PCR Core Systems Technical Bulletin #TB254, Promega Corporation.
	//Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
	//Mueller, P.R. et al. (1993) In: Current Protocols in Molecular Biology 15.5, Greene Publishing Associates, Inc. and John Wiley and Sons, New York.

	var gcHits = _getBaseCount(sequence, "g") + _getBaseCount(sequence, "c");
	var pGC = (gcHits / sequence.length) * 100;	
	return (81.5 + 7.21 * Math.log(molarSalt) + (0.41 * pGC) - (675 / sequence.length)).toFixed(0);
		
	
}

function _molarSaltAdjustedTmDegen (sequence, molarSalt) {

	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace degenerates that must be g or c with g in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");

	//replace degenerates that must be a or t with a in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");

	//replace all other degenerates with a or t in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "a");

	//replace all other degenerates with g or c in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "g");

	return _molarSaltAdjustedTmNonDegen(lowerBoundsSequence, molarSalt) + " to " + _molarSaltAdjustedTmNonDegen(upperBoundsSequence, molarSalt);
}

function _nearestNeighborTm (sequence, molarSalt, molarPrimerTotal, molarMagnesium) {
	if (_containsOnlyNonDegenerates(sequence)) {
		return _nearestNeighborTmNonDegen (sequence, molarSalt, molarPrimerTotal, molarMagnesium);
	}
	else {
		return _nearestNeighborTmDegen (sequence, molarSalt, molarPrimerTotal, molarMagnesium);
	}
}

function _nearestNeighborTmNonDegen (sequence, molarSalt, molarPrimerTotal, molarMagnesium) {
	//The most sophisticated Tm calculations take into account the exact sequence and base stacking parameters, not just the base composition.
	//Tm = ((1000* dh)/(ds+(R * Math.log(primer concentration))))-273.15;
	//Borer P.N. et al. (1974)  J. Mol. Biol. 86, 843.
	//SantaLucia, J. (1998) Proc. Nat. Acad. Sci. USA 95, 1460.
	//Allawi, H.T. and SantaLucia, J. Jr. (1997) Biochemistry 36, 10581.
	//von Ahsen N. et al. (1999) Clin. Chem. 45, 2094.

	sequence = sequence.toLowerCase();

	var R = 1.987; //universal gas constant in Cal/degrees C * mol
	var ds = 0;    //cal/Kelvin/mol
	var dh = 0;    //kcal/mol

	//perform salt correction
	var correctedSalt = molarSalt + molarMagnesium * 140; //adjust for greater stabilizing effects of Mg compared to Na or K. See von Ahsen et al 1999
	ds = ds + 0.368 * (sequence.length - 1) * Math.log(correctedSalt); //from von Ahsen et al 1999

	//perform terminal corrections
	var termDsCorr = _getTerminalCorrectionsDsHash();
	ds = ds + termDsCorr[sequence.charAt(0)];
	ds = ds + termDsCorr[sequence.charAt(sequence.length - 1)];

	var termDhCorr = _getTerminalCorrectionsDhHash();
	dh = dh + termDhCorr[sequence.charAt(0)];
	dh = dh + termDhCorr[sequence.charAt(sequence.length - 1)];

	var dsValues = _getDsHash();
	var dhValues = _getDhHash();

	for (var i = 0; i < sequence.length - 1; i++) {
		ds = ds + dsValues[sequence.charAt(i) + sequence.charAt(i + 1)];
		dh = dh + dhValues[sequence.charAt(i) + sequence.charAt(i + 1)];
	}
	return (((1000 * dh) / (ds + (R * Math.log(molarPrimerTotal / 2)))) - 273.15).toFixed(2);
}

function _nearestNeighborTmDegen (sequence, molarSalt, molarPrimerTotal, molarMagnesium) {

	var lowerBoundsSequence = sequence;
	var upperBoundsSequence = sequence;

	//replace degenerates that must be g or c with g in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/s/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/s/gi, "g");

	//replace degenerates that must be a or t with a in both sequences
	lowerBoundsSequence = lowerBoundsSequence.replace(/w/gi, "a");
	upperBoundsSequence = upperBoundsSequence.replace(/w/gi, "a");

	//replace all other degenerates with a or t in lowerBoundsSequence
	lowerBoundsSequence = lowerBoundsSequence.replace(/r/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/y/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/k/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/m/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/b/gi, "t");
	lowerBoundsSequence = lowerBoundsSequence.replace(/d/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/h/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/v/gi, "a");
	lowerBoundsSequence = lowerBoundsSequence.replace(/n/gi, "a");

	//replace all other degenerates with g or c in upperBoundsSequence
	upperBoundsSequence = upperBoundsSequence.replace(/r/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/y/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/k/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/m/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/b/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/d/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/h/gi, "c");
	upperBoundsSequence = upperBoundsSequence.replace(/v/gi, "g");
	upperBoundsSequence = upperBoundsSequence.replace(/n/gi, "g");

	return _nearestNeighborTmNonDegen(lowerBoundsSequence, molarSalt, molarPrimerTotal, molarMagnesium) + " to " + _nearestNeighborTmNonDegen(upperBoundsSequence, molarSalt, molarPrimerTotal, molarMagnesium);

}

function _getBaseCount (sequence, base) {
	var basePattern = new RegExp (base, "gi");
	if (sequence.search(basePattern) != -1)	{
		return (sequence.match(basePattern)).length;
	}
	else {
		return 0;
	}
}

function _getTerminalCorrectionsDsHash() {
	//SantaLucia, J. (1998) Proc. Nat. Acad. Sci. USA 95, 1460.
	var hash = {};
	hash['g'] = -2.8;
	hash['a'] = 4.1;
	hash['t'] = 4.1;
	hash['c'] = -2.8;
	return hash;
}

function _getTerminalCorrectionsDhHash() {
	//SantaLucia, J. (1998) Proc. Nat. Acad. Sci. USA 95, 1460.
	var hash = {};
	hash['g'] = 0.1;
	hash['a'] = 2.3;
	hash['t'] = 2.3;
	hash['c'] = 0.1;
	return hash;
}

function _getDsHash() {
	//SantaLucia, J. (1998) Proc. Nat. Acad. Sci. USA 95, 1460.
	var hash = {};
	hash['gg'] = -19.9;
	hash['ga'] = -22.2;
	hash['gt'] = -22.4;
	hash['gc'] = -27.2;

	hash['ag'] = -21.0;
	hash['aa'] = -22.2;
	hash['at'] = -20.4;
	hash['ac'] = -22.4;

	hash['tg'] = -22.7;
	hash['ta'] = -21.3;
	hash['tt'] = -22.2;
	hash['tc'] = -22.2;

	hash['cg'] = -27.2;
	hash['ca'] = -22.7;
	hash['ct'] = -21.0;
	hash['cc'] = -19.9;

	return hash;
}

function _getDhHash() {
	//SantaLucia, J. (1998) Proc. Nat. Acad. Sci. USA 95, 1460.
	var hash = {};
	hash['gg'] = -8.0;
	hash['ga'] = -8.2;
	hash['gt'] = -8.4;
	hash['gc'] = -10.6;

	hash['ag'] = -7.8;
	hash['aa'] = -7.9;
	hash['at'] = -7.2;
	hash['ac'] = -8.4;

	hash['tg'] = -8.5;
	hash['ta'] = -7.2;
	hash['tt'] = -7.9;
	hash['tc'] = -8.2;

	hash['cg'] = -10.6;
	hash['ca'] = -8.5;
	hash['ct'] = -7.8;
	hash['cc'] = -8.0;

	return hash;
}

function _getDimerExtinctionCoefficients() {
	//netprimer documentation
	var hash = {};
	hash['gg'] = 10.8;
	hash['ga'] = 12.6;
	hash['gt'] = 10.0;
	hash['gc'] = 8.8;

	hash['ag'] = 12.5;
	hash['aa'] = 13.7;
	hash['at'] = 11.4;
	hash['ac'] = 10.6;

	hash['tg'] = 9.5;
	hash['ta'] = 11.7;
	hash['tt'] = 8.4;
	hash['tc'] = 8.1;

	hash['cg'] = 9.0;
	hash['ca'] = 10.6;
	hash['ct'] = 7.6;
	hash['cc'] = 7.3;

	return hash;
}

function _getSingleExtinctionCoefficients() {
	//netprimer documentation
	var hash = {};
	hash['g'] = 11.5;
	hash['a'] = 15.4;
	hash['t'] = 8.7;
	hash['c'] = 7.4;

	return hash;
}

function _getBaseRunsReport(sequence, minRunLength) {
	var report = "";
	var hasRun = false;
	var nucleotides = ['G', 'A', 'T', 'C'];

	for (var i = 0; i < nucleotides.length; i++) {
		if (_hasRunOfBases(sequence, nucleotides[i], minRunLength)) {
			hasRun = true;
			report = report + "Contains run of " + nucleotides[i] + "'s; ";
		}
	}

	if (hasRun) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}

}

function _getDiNucleotideRunsReport(sequence, minRunLength) {
	var report = "";
	var hasRun = false;
	var diNucleotides = ['GA', 'GT', 'GC', 'AG', 'AT', 'AC', 'TG', 'TA', 'TC', 'CG', 'CA', 'CT'];

	for (var i = 0; i < diNucleotides.length; i++) {
		if (_hasRunOfBases(sequence, diNucleotides[i], minRunLength)) {
			hasRun = true;
			report = report + "Contains run of " + diNucleotides[i] + "'s; ";
		}
	}

	if (hasRun) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}

}

function _hasRunOfBases(sequence, base, minRunLength) {
	var basePattern = new RegExp ("(?:" + base + "){" + minRunLength + ",}", "gi");
	if (sequence.search(basePattern) != -1)	{
		return (sequence.match(basePattern)).length;
	}
	else {
		return 0;
	}	
}

function _getSuitableLengthReport(sequence, minSuitableLength, maxSuitableLength) {
	var report = "";
	var hasProblem = false;
	
	if (sequence.length < minSuitableLength) {
		hasProblem = true;
		report = report + "Contains fewer than " + minSuitableLength + " bases; ";
	}

	if (sequence.length > maxSuitableLength) {
		hasProblem = true;
		report = report + "Contains more than " + maxSuitableLength + " bases; ";
	}

	if (hasProblem) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}	
}

function _getSuitableGCReport(sequence, percentGCRange, minSuitableGC, maxSuitableGC) {
	var report = "";
	var hasProblem = false;
	var lowerCalculated;
	var upperCalculated;
	
	//percentGCRange may be a single number or a string containing something like "40 to 60";
	var rangePattern = new RegExp ("([\d\.]+)\D+([\d\.]+)", "gi");
	if (percentGCRange.search(rangePattern) != -1)	{
		lowerCalculated = parseFloat($1);
		upperCalculated = parseFloat($2);
	}
	else {
		lowerCalculated = parseFloat(percentGCRange);
		upperCalculated = parseFloat(percentGCRange);
	}
	
	if (lowerCalculated < minSuitableGC) {
		hasProblem = true;
		report = report + "%GC is less than " + minSuitableGC + "; ";
	}

	if (upperCalculated > maxSuitableGC) {
		hasProblem = true;
		report = report + "%GC is greater than " + maxSuitableGC + "; ";
	}

	if (hasProblem) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}	
}


function _getSuitableLengthReport(sequence, minSuitableLength, maxSuitableLength) {
	var report = "";
	var hasProblem = false;
	
	if (sequence.length < minSuitableLength) {
		hasProblem = true;
		report = report + "Contains fewer than " + minSuitableLength + " bases; ";
	}

	if (sequence.length > maxSuitableLength) {
		hasProblem = true;
		report = report + "Contains more than " + maxSuitableLength + " bases; ";
	}

	if (hasProblem) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}	
}

function _getSuitableTmReport(sequence, range, minSuitable, maxSuitable) {
	var report = "";
	var hasProblem = false;
	var lowerCalculated;
	var upperCalculated;
	
	//range may be a single number or a string containing something like "40 to 60";
	var rangePattern = new RegExp ("([\d\.]+)\D+([\d\.]+)", "gi");
	if (range.search(rangePattern) != -1)	{
		lowerCalculated = parseFloat($1);
		upperCalculated = parseFloat($2);
	}
	else {
		lowerCalculated = parseFloat(range);
		upperCalculated = parseFloat(range);
	}
	
	if (lowerCalculated < minSuitable) {
		hasProblem = true;
		report = report + "Tm is less than " + minSuitable + "; ";
	}

	if (upperCalculated > maxSuitable) {
		hasProblem = true;
		report = report + "Tm is greater than " + maxSuitable + "; ";
	}

	if (hasProblem) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}	
}

function _getSuitableThreePrimeGC(sequence, minSuitable, maxSuitable) {
	var threePrimeEnd;
	var desiredThreePrimeEndSize = 5;
	var report = "";
	var gcCounts;
	var hasProblem = false;
	if (sequence.length >= desiredThreePrimeEndSize) {
		threePrimeEnd = sequence.substr(sequence.length - desiredThreePrimeEndSize, 5);
	}
	else {
		threePrimeEnd = sequence;
	}

	gcCounts = _getBaseCount(threePrimeEnd, "g") + _getBaseCount(threePrimeEnd, "c");

	if (gcCounts < minSuitable) {
		hasProblem = true;
		report = report + "There are less than " + minSuitable + " G's or C's in the last " + threePrimeEnd.length + " bases; ";		
	}

	if (gcCounts > maxSuitable) {
		hasProblem = true;
		report = report + "There are more than " + maxSuitable + " G's or C's in the last " + threePrimeEnd.length + " bases; ";
	}

	if (hasProblem) {
		return "Warning: " + report;
	}
	else {
		return "Pass";
	}

}

function _getSelfComplementarityReport(sequence, maxContig, maxPercentIdent) {
	var matchScore = 1;
	var mismatchScore = -1;
	var gapPenalty = 99;
	var beginGapPenalty = 0;
	var endGapPenalty = 0;

	var returnHash = {};
	returnHash['report'] = "";
	returnHash['upper'] = "";
	returnHash['lower'] = "";
	returnHash['divider'] = "";

	var report = "";
	var hasProblem = false;
	var sequenceLength = sequence.length;

	var matrix = new Complementarity();
	matrix.setMatch(matchScore);
	matrix.setMismatch(mismatchScore);

	var scoreSet = new ScoreSet();
	scoreSet.setScoreSetParam(matrix, gapPenalty, beginGapPenalty, endGapPenalty);

	var rev = reverse(sequence);
	//convert String to Array
	sequence = sequence.match(/./g);
	rev = rev.match(/./g);

	//align_pair_quad.js
	alignment = new AlignPairQuad();
	alignment.initializeMatrix(sequence, rev, scoreSet);
	alignment.fillMatrix();
	alignment.align();

	//aligned output will be something like:
	//cttttgagcaagttcagcctggttaag--
	//--gaattggtccgacttgaacgagttttc
	var seqAligned = (alignment.getAlignedM()).replace(/\-/g," ");
	var revAligned = (alignment.getAlignedN()).replace(/\-/g," ");	
	
	var score = alignment.score;

	var divider = new Array();
	var maxContiguous = 0;
	var totalMatches = 0;
	var contiguous = 0;
	for (var i = 0; i < seqAligned.length; i++)	{
		if (scoreSet.getScore(seqAligned.charAt(i), revAligned.charAt(i)) == matchScore) {
			divider.push("|");
			contiguous++;
			totalMatches++;
		}
		else {
			divider.push(" ");
			contiguous = 0;
		}
		
		if (contiguous > maxContiguous) {
			maxContiguous = contiguous;	
		}
	}

	if (maxContiguous > maxContig) {
		hasProblem = true;
		report = report + "There are more than " + maxContig + " self-annealing bases in a row; ";
	}

	if (((totalMatches / sequenceLength) * 100) > maxPercentIdent) {
		hasProblem = true;
		report = report + "More than " + maxPercentIdent  + " percent of the bases are self-annealing; ";
	}

	if (hasProblem) {
		report = "Warning: " + report;
	}
	else {
		report = "Pass";
	}

	returnHash['report'] = report;
	returnHash['upper'] = seqAligned;
	returnHash['lower'] = revAligned;
	returnHash['divider'] = divider.join("");

	return returnHash;

}

function _getHairpinReport(sequence, maxContig, maxPercentIdent) {
	
	var upper = sequence;
	upper = upper.match(/./g);
	var loop = "";
	var lower = new Array();

	var returnHash = {};
	returnHash['report'] = "";
	returnHash['upper'] = "";
	returnHash['lower'] = "";
	returnHash['divider'] = "";
	
	var topScore = 0;
	var score;
	var u;
	var l;
	var topScoreUpper = sequence;
	var topScoreLower = "";
	var topScoreLoop = "";	

	var matchScore = 1;
	var mismatchScore = -1;
	var gapPenalty = 99;
	var beginGapPenalty = 0;
	var endGapPenalty = 0;

	var report = "";
	var hasProblem = false;
	var sequenceLength = sequence.length;

	var matrix = new Complementarity();
	matrix.setMatch(matchScore);
	matrix.setMismatch(mismatchScore);

	var scoreSet = new ScoreSet();
	scoreSet.setScoreSetParam(matrix, gapPenalty, beginGapPenalty, endGapPenalty);
	
	while(upper.length > 0) {
		score = 0;
		if (loop == "") {
			loop = upper.pop();
		}
		else {
			lower.push(loop);
			loop = "";
		}

		//determine score
		u = upper.length - 1;
		l = lower.length - 1;
		while ((u >= 0) && (l >= 0)) {
			score = score + scoreSet.getScore(upper[u], lower[l]);
			u--;
			l--;
		}

		if (score > topScore) {
			topScore = score;
			topScoreUpper = upper.join("");
			topScoreLower = lower.join("");
			topScoreLoop = loop;				
		}	

	}

	//format top scoring hit and return

	var upperLowerDiff = topScoreUpper.length - topScoreLower.length;
	if (upperLowerDiff > 0) {
		for (var i = 0; i < upperLowerDiff; i++)	{
			topScoreLower = " " + topScoreLower;
		}
	}
	else if (upperLowerDiff < 0) {
		for (var i = upperLowerDiff; i < 0; i++)	{
			topScoreUpper = " " + topScoreUpper;
		}
	}

	var maxContiguous = 0;
	var totalMatches = 0;
	var contiguous = 0;
	var divider = new Array();
	//add vertical lines between matches
	for (var i = 0; i < topScoreUpper.length; i++)	{
		if (scoreSet.getScore(topScoreUpper.charAt(i), topScoreLower.charAt(i)) == matchScore) {
			divider.push("|");
			contiguous++;
			totalMatches++;
		}
		else {
			divider.push(" ");		
			contiguous = 0;
		}
		
		if (contiguous > maxContiguous) {
			maxContiguous = contiguous;	
		}
	}

	if (maxContiguous > maxContig) {
		hasProblem = true;
		report = report + "There are more than " + maxContig + " hairpin bases in a row; ";
	}

	if (((totalMatches / sequenceLength) * 100) > maxPercentIdent) {
		hasProblem = true;
		report = report + "More than " + maxPercentIdent  + " percent of the bases are in a hairpin; ";
	}

	if (hasProblem) {
		report = "Warning: " + report;
	}
	else {
		report = "Pass";
	}

	if (topScoreLoop == "") {
		topScoreLoop = ")";
	}

	returnHash['report'] = report;
	returnHash['upper'] = topScoreUpper;
	returnHash['divider'] = divider.join("") + topScoreLoop;
	returnHash['lower'] = topScoreLower;

	return returnHash;	
}


//I wrote these classes originally in pairwise_align_dna.js
//------------------------------------ ScoreSet class

//ScoreSet getScore
function getScore (r1, r2) {
	return this.scoringMatrix.scoringMatrix_getScore(r1, r2);	
}

//ScoreSet setScoreSetParam
function setScoreSetParam (scoringMatrix, gapPenalty, beginGapPenalty, endGapPenalty) {
	this.scoringMatrix = scoringMatrix;
	this.gap = gapPenalty;
	this.beginGap = beginGapPenalty;
	this.endGap = endGapPenalty;
}

//ScoreSet class
function ScoreSet () {
	this.scoringMatrix;
	this.gap;
	this.beginGap;
	this.endGap;
	this.useBeginGapTop = true;
	this.useBeginGapLeft = true;
	this.useEndGapBottom = true;
	this.useEndGapRight = true;
}

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

//define object methods
ScoreSet.prototype.getScore = getScore;
ScoreSet.prototype.setScoreSetParam = setScoreSetParam;

//------------------------------------


//------------------------------------ ScoringMatrix abstract class
//ScoringMatrix getScore method
function scoringMatrix_getScore(r1, r2) {
	r1 = r1.toLowerCase();
	r2 = r2.toLowerCase();
	if (((r1 == "g") && (r2 == "c")) || ((r2 == "g") && (r1 == "c"))) {
		return this.match;
	}
	else if (((r1 == "a") && (r2 == "t")) || ((r2 == "a") && (r1 == "t"))) {
		return this.match;
	}
	else {
		return this.mismatch;
	}
}

//ScoringMatrix class
function ScoringMatrix() {
	this.mismatch;
	this.match;
}

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

//define object methods
ScoringMatrix.prototype.scoringMatrix_getScore = scoringMatrix_getScore;

//------------------------------------ Complementarity class extends ScoringMatrix Class
//Complementarity class setMismatch method
function setMismatch(mismatchScore) {
	this.mismatch = mismatchScore;
}

//Complementarity class setMatch method
function setMatch(matchScore) {
	this.match = matchScore;
}

//Complementarity class
function Complementarity () {
}

Complementarity.prototype = new ScoringMatrix();
Complementarity.prototype.setMismatch = setMismatch;
Complementarity.prototype.setMatch = setMatch;