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

function pairwiseAlignDna (theDocument) {	

	//var MATCH_SCORE = 2;
	//var MISMATCH_SCORE = -1;
	//var GAP_PENALTY = 2;

	//var BEGIN_GAP_PENALTY = 0;
	//var END_GAP_PENALTY = 0;

	var newDnaOne = "";
	var titleOne = "";

	var newDnaTwo = "";
	var titleTwo = "";
	
	var maxInput = 2000;

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

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

	var MATCH_SCORE = parseInt(theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
	var MISMATCH_SCORE = parseInt(theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value);
	var BEGIN_GAP_PENALTY = parseInt(theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);
	var GAP_PENALTY = parseInt(theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value);
	var END_GAP_PENALTY = parseInt(theDocument.forms[0].elements[9].options[theDocument.forms[0].elements[9].selectedIndex].value);

	openWindow("Pairwise Align DNA");
	openPre();

	newDnaOne = getSequenceFromFasta(theDocument.forms[0].elements[0].value);
	newDnaOne = removeNonDna(newDnaOne);
	titleOne = getTitleFromFasta(theDocument.forms[0].elements[0].value);

	newDnaTwo = getSequenceFromFasta(theDocument.forms[0].elements[1].value);
	newDnaTwo = removeNonDna(newDnaTwo);
	titleTwo = getTitleFromFasta(theDocument.forms[0].elements[1].value);

	outputWindow.document.write(getPairwiseAlignTitle(titleOne, newDnaOne, titleTwo, newDnaTwo));

	//change to arrays for pass by reference, so that large sequence isn't copied
	if (newDnaOne.search(/./) != -1)	{
		newDnaOne = newDnaOne.match(/./g);
	}


	if (newDnaTwo.search(/./) != -1)	{
		newDnaTwo = newDnaTwo.match(/./g);
	}


	pairwiseDna (titleOne, newDnaOne, titleTwo, newDnaTwo, MATCH_SCORE, MISMATCH_SCORE, GAP_PENALTY, BEGIN_GAP_PENALTY, END_GAP_PENALTY);
	closePre();
	closeWindow();
	return true;
}	

function pairwiseDna (titleOne, newDnaOne, titleTwo, newDnaTwo, matchScore, mismatchScore, gapPenalty, beginGapPenalty, endGapPenalty)	{

	//can use one or both.
	//can compare scores (should be identical)
	var useLinearSpace = true;
	var useQuadraticSpace = false;
	
	var matrix = new Identity();
	matrix.setMatch(matchScore);
	matrix.setMismatch(mismatchScore);

	var scoreSet = new ScoreSet();
	scoreSet.setScoreSetParam(matrix, gapPenalty, beginGapPenalty, endGapPenalty);
	
	var alignment;
	
	if (useLinearSpace) {
		alignment = new AlignPairLinear();
		alignment.setAlignParam(newDnaOne, newDnaTwo, scoreSet);
		alignment.align();

		outputWindow.document.write(">" + titleOne + "\n");
		outputWindow.document.write(addReturns(alignment.getAlignedM()));
		outputWindow.document.write("\n");
		outputWindow.document.write("\n");
		outputWindow.document.write(">" + titleTwo + "\n");
		outputWindow.document.write(addReturns(alignment.getAlignedN()));
		outputWindow.document.write("\n\n");
		outputWindow.document.write("Alignment score: " + alignment.score + "\n\n");
	}

	if (useQuadraticSpace) {

		alignment = new AlignPairQuad();
		alignment.initializeMatrix(newDnaOne, newDnaTwo, scoreSet);
		alignment.fillMatrix();
		//alignment.dumpMatrix();
		alignment.align();	

		outputWindow.document.write(">" + titleOne + "\n");
		outputWindow.document.write(addReturns(alignment.getAlignedM()));
		outputWindow.document.write("\n");
		outputWindow.document.write("\n");
		outputWindow.document.write(">" + titleTwo + "\n");
		outputWindow.document.write(addReturns(alignment.getAlignedN()));
		outputWindow.document.write("\n\n");
		outputWindow.document.write("Alignment score: " + alignment.score + "\n\n");
	}
}



//------------------------------------ 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 == r2) {
		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;

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

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

//Identity class
function Identity () {
}

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