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

function fuzzySearchProtein (theDocument) {	

	//var MATRIX = "blosum62";

	//var GAP_PENALTY = 2;
	//var HITS = 8;

	var targetSequence = "";
	var targetTitle = "";

	var querySequence = "";
	var queryTitle = "";
	
	var maxTarget = 2000;
	var maxQuery = 30;

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

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

	var MATRIX = theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value;
	var GAP_PENALTY = parseInt(theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value);
	var HITS = parseInt(theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);

	openWindow("Fuzzy Protein DNA");
	openPre();

	targetSequence = getSequenceFromFasta(theDocument.forms[0].elements[0].value);
	targetSequence = removeNonProtein(targetSequence);
	targetTitle = getTitleFromFasta(theDocument.forms[0].elements[0].value);

	querySequence = getSequenceFromFasta(theDocument.forms[0].elements[1].value);
	querySequence = removeNonProtein(querySequence);
	queryTitle = "query";

	outputWindow.document.write(getFuzzySearchTitle(targetTitle, targetSequence, queryTitle, querySequence));

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


	if (querySequence.search(/./) != -1)	{
		querySequence = querySequence.match(/./g);
	}
	
	if (targetSequence.length == 0) {
		alert("The sequence contains no protein residues.");
		return false;
	}

	if (querySequence.length == 0) {
		alert("The query sequence contains no protein residues.");
		return false;
	}

	_fuzzySearchProtein (queryTitle, querySequence, targetTitle, targetSequence, MATRIX, GAP_PENALTY, HITS);
	closePre();
	closeWindow();
	return true;
}	

function _fuzzySearchProtein (queryTitle, querySequence, targetTitle, targetSequence, matrix, gapPenalty, hits)	{

	//create scoringMatrix object
	var scoringMatrix;

	if (matrix == "pam30") {
		scoringMatrix = new Pam30();
	}
	else if (matrix == "pam70") {
		scoringMatrix = new Pam70();
	}
	else if (matrix == "blosum80") {
		scoringMatrix = new Blosum80();
	}
	else if (matrix == "blosum62") {
		scoringMatrix = new Blosum62();
	}
	else if (matrix == "blosum45") {
		scoringMatrix = new Blosum45();
	}

	var scoreSet = new ScoreSet();
	scoreSet.setScoreSetParam(scoringMatrix, gapPenalty, hits);
	
	var fuzzySearch = new FuzzySearch();
	fuzzySearch.initializeMatrix(querySequence, targetSequence, scoreSet);
	fuzzySearch.search();
	var hits = fuzzySearch.getHits();

	if (hits.length > 0) {

		for (var i = 0; i < hits.length; i++) {
			outputWindow.document.write(">" + queryTitle + " from " + hits[i].startM + " to " + hits[i].endM + "\n");
			outputWindow.document.write(hits[i].sequenceM + "\n");
			outputWindow.document.write(">" + targetTitle + " from " + hits[i].startN + " to " + hits[i].endN + "\n");
			outputWindow.document.write(hits[i].sequenceN + "\n");			
			outputWindow.document.write("Score: " + hits[i].score + "\n\n");			
		}

	}
	else {
			outputWindow.document.write("No hits were obtained.\n\n");
	}
}


//------------------------------------ ScoreSet class

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

//ScoreSet setScoreSetParam
function setScoreSetParam (scoringMatrix, gapPenalty, hits) {
	this.scoringMatrix = scoringMatrix;
	this.gap = gapPenalty;
	this.hits = hits;
}

//ScoreSet class
function ScoreSet () {
	this.scoringMatrix;
	this.gap;
	this.hits;
}

//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 (this.scoreHash[r1 + r2] == null) {
		throw "Unrecognized residue pair: " + r1 + ", " + r2 + "."; 
	}
	else {
		return this.scoreHash[r1 + r2];
	}
}

function scoringMatrix_fillHash(matrix) {
	var cols = matrix[0].split(/\s+/);
	var cells;
	//go through rows
	for (var i = 1; i < matrix.length; i++) {
		cells = matrix[i].split(/\s+/);	
		//go through cells in this row		
		for (var j = 1; j < cols.length + 1; j++) {
			this.scoreHash[cells[0].toLowerCase() + cols[j-1].toLowerCase()] = parseInt(cells[j]);
		}
	}
}

//ScoringMatrix class
function ScoringMatrix() {
	this.scoreHash = {};
}

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

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

//------------------------------------ Blosum62 Class extends ScoringMatrix Class
//constructor
function Blosum62 () {
	
	var matrix = new Array (
   "A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V",
"A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0",
"R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3",
"N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3",
"D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3",
"C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1",
"Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2",
"E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2",
"G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3",
"H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3",
"I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3",
"L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1",
"K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2",
"M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1",
"F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1",
"P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2",
"S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2",
"T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0",
"W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3",
"Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1",
"V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4");

	this.scoringMatrix_fillHash(matrix);
}

Blosum62.prototype = new ScoringMatrix();


//------------------------------------ Blosum45 Class extends ScoringMatrix Class
//constructor
function Blosum45 () {
	
	var matrix = new Array (
   "A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V",
"A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -2 -2  0",
"R -2  7  0 -1 -3  1  0 -2  0 -3 -2  3 -1 -2 -2 -1 -1 -2 -1 -2",
"N -1  0  6  2 -2  0  0  0  1 -2 -3  0 -2 -2 -2  1  0 -4 -2 -3", 
"D -2 -1  2  7 -3  0  2 -1  0 -4 -3  0 -3 -4 -1  0 -1 -4 -2 -3",
"C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1",
"Q -1  1  0  0 -3  6  2 -2  1 -2 -2  1  0 -4 -1  0 -1 -2 -1 -3",
"E -1  0  0  2 -3  2  6 -2  0 -3 -2  1 -2 -3  0  0 -1 -3 -2 -3",
"G  0 -2  0 -1 -3 -2 -2  7 -2 -4 -3 -2 -2 -3 -2  0 -2 -2 -3 -3",
"H -2  0  1  0 -3  1  0 -2 10 -3 -2 -1  0 -2 -2 -1 -2 -3  2 -3",
"I -1 -3 -2 -4 -3 -2 -3 -4 -3  5  2 -3  2  0 -2 -2 -1 -2  0  3",
"L -1 -2 -3 -3 -2 -2 -2 -3 -2  2  5 -3  2  1 -3 -3 -1 -2  0  1",
"K -1  3  0  0 -3  1  1 -2 -1 -3 -3  5 -1 -3 -1 -1 -1 -2 -1 -2",
"M -1 -1 -2 -3 -2  0 -2 -2  0  2  2 -1  6  0 -2 -2 -1 -2  0  1",
"F -2 -2 -2 -4 -2 -4 -3 -3 -2  0  1 -3  0  8 -3 -2 -1  1  3  0",
"P -1 -2 -2 -1 -4 -1  0 -2 -2 -2 -3 -1 -2 -3  9 -1 -1 -3 -3 -3",
"S  1 -1  1  0 -1  0  0  0 -1 -2 -3 -1 -2 -2 -1  4  2 -4 -2 -1",
"T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1  2  5 -3 -1  0",
"W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2  1 -3 -4 -3 15  3 -3",
"Y -2 -1 -2 -2 -3 -1 -2 -3  2  0  0 -1  0  3 -3 -2 -1  3  8 -1",
"V  0 -2 -3 -3 -1 -3 -3 -3 -3  3  1 -2  1  0 -3 -1  0 -3 -1  5");

	this.scoringMatrix_fillHash(matrix);	
}

Blosum45.prototype = new ScoringMatrix();


//------------------------------------ Blosum80 Class extends ScoringMatrix Class
//constructor
function Blosum80 () {
	
	var matrix = new Array (
   "A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V",
"A  5 -2 -2 -2 -1 -1 -1  0 -2 -2 -2 -1 -1 -3 -1  1  0 -3 -2  0",
"R -2  6 -1 -2 -4  1 -1 -3  0 -3 -3  2 -2 -4 -2 -1 -1 -4 -3 -3",
"N -2 -1  6  1 -3  0 -1 -1  0 -4 -4  0 -3 -4 -3  0  0 -4 -3 -4",
"D -2 -2  1  6 -4 -1  1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4",
"C -1 -4 -3 -4  9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1",
"Q -1  1  0 -1 -4  6  2 -2  1 -3 -3  1  0 -4 -2  0 -1 -3 -2 -3",
"E -1 -1 -1  1 -5  2  6 -3  0 -4 -4  1 -2 -4 -2  0 -1 -4 -3 -3",
"G  0 -3 -1 -2 -4 -2 -3  6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4",
"H -2  0  0 -2 -4  1  0 -3  8 -4 -3 -1 -2 -2 -3 -1 -2 -3  2 -4",
"I -2 -3 -4 -4 -2 -3 -4 -5 -4  5  1 -3  1 -1 -4 -3 -1 -3 -2  3",
"L -2 -3 -4 -5 -2 -3 -4 -4 -3  1  4 -3  2  0 -3 -3 -2 -2 -2  1",
"K -1  2  0 -1 -4  1  1 -2 -1 -3 -3  5 -2 -4 -1 -1 -1 -4 -3 -3",
"M -1 -2 -3 -4 -2  0 -2 -4 -2  1  2 -2  6  0 -3 -2 -1 -2 -2  1",
"F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1  0 -4  0  6 -4 -3 -2  0  3 -1",
"P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4  8 -1 -2 -5 -4 -3",
"S  1 -1  0 -1 -2  0  0 -1 -1 -3 -3 -1 -2 -3 -1  5  1 -4 -2 -2",
"T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2  1  5 -4 -2  0",
"W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2  0 -5 -4 -4 11  2 -3",
"Y -2 -3 -3 -4 -3 -2 -3 -4  2 -2 -2 -3 -2  3 -4 -2 -2  2  7 -2",
"V  0 -3 -4 -4 -1 -3 -3 -4 -4  3  1 -3  1 -1 -3 -2  0 -3 -2  4");

	this.scoringMatrix_fillHash(matrix);	
}

Blosum80.prototype = new ScoringMatrix();


//------------------------------------ Pam70 Class extends ScoringMatrix Class
//constructor
function Pam70 () {
	
	var matrix = new Array (
    "A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V",
"A   5  -4  -2  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -6   0   1   1  -9  -5  -1",
"R  -4   8  -3  -6  -5   0  -5  -6   0  -3  -6   2  -2  -7  -2  -1  -4   0  -7  -5",
"N  -2  -3   6   3  -7  -1   0  -1   1  -3  -5   0  -5  -6  -3   1   0  -6  -3  -5",
"D  -1  -6   3   6  -9   0   3  -1  -1  -5  -8  -2  -7 -10  -4  -1  -2 -10  -7  -5",
"C  -4  -5  -7  -9   9  -9  -9  -6  -5  -4 -10  -9  -9  -8  -5  -1  -5 -11  -2  -4",
"Q  -2   0  -1   0  -9   7   2  -4   2  -5  -3  -1  -2  -9  -1  -3  -3  -8  -8  -4",
"E  -1  -5   0   3  -9   2   6  -2  -2  -4  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4",
"G   0  -6  -1  -1  -6  -4  -2   6  -6  -6  -7  -5  -6  -7  -3   0  -3 -10  -9  -3",
"H  -4   0   1  -1  -5   2  -2  -6   8  -6  -4  -3  -6  -4  -2  -3  -4  -5  -1  -4",
"I  -2  -3  -3  -5  -4  -5  -4  -6  -6   7   1  -4   1   0  -5  -4  -1  -9  -4   3",
"L  -4  -6  -5  -8 -10  -3  -6  -7  -4   1   6  -5   2  -1  -5  -6  -4  -4  -4   0",
"K  -4   2   0  -2  -9  -1  -2  -5  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -7  -6",
"M  -3  -2  -5  -7  -9  -2  -4  -6  -6   1   2   0  10  -2  -5  -3  -2  -8  -7   0",
"F  -6  -7  -6 -10  -8  -9  -9  -7  -4   0  -1  -9  -2   8  -7  -4  -6  -2   4  -5",
"P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -5  -4  -5  -7   7   0  -2  -9  -9  -3",
"S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -6  -2  -3  -4   0   5   2  -3  -5  -3",
"T   1  -4   0  -2  -5  -3  -3  -3  -4  -1  -4  -1  -2  -6  -2   2   6  -8  -4  -1",
"W  -9   0  -6 -10 -11  -8 -11 -10  -5  -9  -4  -7  -8  -2  -9  -3  -8  13  -3 -10",
"Y  -5  -7  -3  -7  -2  -8  -6  -9  -1  -4  -4  -7  -7   4  -9  -5  -4  -3   9  -5",
"V  -1  -5  -5  -5  -4  -4  -4  -3  -4   3   0  -6   0  -5  -3  -3  -1 -10  -5   6");

	this.scoringMatrix_fillHash(matrix);	
}

Pam30.prototype = new ScoringMatrix();

//------------------------------------ Pam30 Class extends ScoringMatrix Class
//constructor
function Pam30 () {
	
	var matrix = new Array (
    "A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V",
"A   6  -7  -4  -3  -6  -4  -2  -2  -7  -5  -6  -7  -5  -8  -2   0  -1 -13  -8  -2",
"R  -7   8  -6 -10  -8  -2  -9  -9  -2  -5  -8   0  -4  -9  -4  -3  -6  -2 -10  -8",
"N  -4  -6   8   2 -11  -3  -2  -3   0  -5  -7  -1  -9  -9  -6   0  -2  -8  -4  -8",
"D  -3 -10   2   8 -14  -2   2  -3  -4  -7 -12  -4 -11 -15  -8  -4  -5 -15 -11  -8",
"C  -6  -8 -11 -14  10 -14 -14  -9  -7  -6 -15 -14 -13 -13  -8  -3  -8 -15  -4  -6",
"Q  -4  -2  -3  -2 -14   8   1  -7   1  -8  -5  -3  -4 -13  -3  -5  -5 -13 -12  -7",
"E  -2  -9  -2   2 -14   1   8  -4  -5  -5  -9  -4  -7 -14  -5  -4  -6 -17  -8  -6",
"G  -2  -9  -3  -3  -9  -7  -4   6  -9 -11 -10  -7  -8  -9  -6  -2  -6 -15 -14  -5",
"H  -7  -2   0  -4  -7   1  -5  -9   9  -9  -6  -6 -10  -6  -4  -6  -7  -7  -3  -6",
"I  -5  -5  -5  -7  -6  -8  -5 -11  -9   8  -1  -6  -1  -2  -8  -7  -2 -14  -6   2",
"L  -6  -8  -7 -12 -15  -5  -9 -10  -6  -1   7  -8   1  -3  -7  -8  -7  -6  -7  -2",
"K  -7   0  -1  -4 -14  -3  -4  -7  -6  -6  -8   7  -2 -14  -6  -4  -3 -12  -9  -9",
"M  -5  -4  -9 -11 -13  -4  -7  -8 -10  -1   1  -2  11  -4  -8  -5  -4 -13 -11  -1",
"F  -8  -9  -9 -15 -13 -13 -14  -9  -6  -2  -3 -14  -4   9 -10  -6  -9  -4   2  -8",
"P  -2  -4  -6  -8  -8  -3  -5  -6  -4  -8  -7  -6  -8 -10   8  -2  -4 -14 -13  -6",
"S   0  -3   0  -4  -3  -5  -4  -2  -6  -7  -8  -4  -5  -6  -2   6   0  -5  -7  -6",
"T  -1  -6  -2  -5  -8  -5  -6  -6  -7  -2  -7  -3  -4  -9  -4   0   7 -13  -6  -3",
"W -13  -2  -8 -15 -15 -13 -17 -15  -7 -14  -6 -12 -13  -4 -14  -5 -13  13  -5 -15",
"Y  -8 -10  -4 -11  -4 -12  -8 -14  -3  -6  -7  -9 -11   2 -13  -7  -6  -5  10  -7",
"V  -2  -8  -8  -8  -6  -7  -6  -5  -6   2  -2  -9  -1  -8  -6  -6  -3 -15  -7   7");

	this.scoringMatrix_fillHash(matrix);	
}

Pam30.prototype = new ScoringMatrix();