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

function mutateForDigest (theDocument) {	

	var newDna = "";
	var mutatedDna = "";
	var title = "";
	var maxInput = 10000;
	var TOPOLOGY = "linear";

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

	var restrictionSiteCollection;
	var mutatedRestrictionSitesCollection;

	var geneticCode = getGeneticCodeString(theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);

	var restrictionSites = theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value;	

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

	geneticCode = geneticCode.split(/,/);

	if (checkGeneticCode(geneticCode) == false)	{
		return false;
	}

	restrictionSites = restrictionSites.split(/,/);
	if (checkRestPatterns(restrictionSites) == false)	{
		return false;
	}
	var mutatedRestrictionSites = buildMutatedRestrictionSites(restrictionSites);

	openWindow("Mutate for Digest");
	openPre();
	outputWindow.document.write("<span class=\"mutated_sequence\">" + "sequence and translations for mutated version" + "</span>\n");
	outputWindow.document.write("<span class=\"current_sequence\">" + "sequence and translations for non-mutated version" + "</span>\n");
	outputWindow.document.write("\n");			
	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);

		outputWindow.document.write(getInfoFromTitleAndSequenceAndTopology(title, newDna, TOPOLOGY));

		restrictionSiteCollection = findRestrictionSites(newDna, restrictionSites, TOPOLOGY);
		restrictionSiteCollection.sortRestrictionSites();

		//build restrictionSiteCollection from mutated sites
		mutatedRestrictionSiteCollection = findRestrictionSites(newDna, mutatedRestrictionSites, TOPOLOGY);

		mutatedRestrictionSiteCollection = removeNormalMatchesFromMutantSites(mutatedRestrictionSiteCollection, restrictionSiteCollection);

		mutatedRestrictionSiteCollection = removeOverlappingMatchesFromMutantSites(mutatedRestrictionSiteCollection);

		//use these sites to build mutatedDna
		//modify call below once these are available
		mutatedDna = buildMutatedDna(newDna, mutatedRestrictionSiteCollection);

		layoutRestTrans (newDna, mutatedDna, geneticCode, restrictionSiteCollection, mutatedRestrictionSiteCollection, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value, theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value);
		
		outputWindow.document.write ('\n\n');
	}


	closePre();
	closeWindow();
	return true;
}	

function layoutRestTrans (dnaSequence, mutatedDnaSequence, geneticCode, restrictionSiteCollection, mutatedRestrictionSiteCollection, basesPerLine, readingFrame)	{

	basesPerLine = parseInt(basesPerLine);

	var geneticCodeMatchExp = getGeneticCodeMatchExp (geneticCode);
	var geneticCodeMatchResult = getGeneticCodeMatchResult (geneticCode);
	var spaceString = "                                                                                                                                  ";	

	var textLayout = new TextLayout();

	if ((readingFrame == "3") || (readingFrame == "all_three")) {

		var translationMut = new TranslationComponent();
		translationMut.spanStart = "<span class=\"mutated_sequence\">";
		translationMut.spanEnd = "</span>";
		translationMut.setCharacters("  " + translate(mutatedDnaSequence.substring(2, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translationMut);

		var translation = new TranslationComponent();
		translation.spanStart = "<span class=\"current_sequence\">";
		translation.spanEnd = "</span>";
		translation.setCharacters("  " + translate(dnaSequence.substring(2, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}

	if ((readingFrame == "2") || (readingFrame == "all_three")) {

		var translationMut = new TranslationComponent();
		translationMut.spanStart = "<span class=\"mutated_sequence\">";
		translationMut.spanEnd = "</span>";
		translationMut.setCharacters(" " + translate(mutatedDnaSequence.substring(1, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translationMut);

		var translation = new TranslationComponent();
		translation.spanStart = "<span class=\"current_sequence\">";
		translation.spanEnd = "</span>";
		translation.setCharacters(" " + translate(dnaSequence.substring(1, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}

	if ((readingFrame == "1") || (readingFrame == "all_three")) {

		var translationMut = new TranslationComponent();
		translationMut.spanStart = "<span class=\"mutated_sequence\">";
		translationMut.spanEnd = "</span>";
		translationMut.setCharacters(translate(mutatedDnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translationMut);

		var translation = new TranslationComponent();
		translation.spanStart = "<span class=\"current_sequence\">";
		translation.spanEnd = "</span>";
		translation.setCharacters(translate(dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}

	if (readingFrame == "uppercase") {

		var translationMut = new UppercaseTranslationComponent();
		translationMut.spanStart = "<span class=\"mutated_sequence\">";
		translationMut.spanEnd = "</span>";
		translationMut.setCharacters(uppercaseTranslate(mutatedDnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translationMut);

		var translation = new UppercaseTranslationComponent();
		translation.spanStart = "<span class=\"current_sequence\">";
		translation.spanEnd = "</span>";
		translation.setCharacters(uppercaseTranslate(dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}

	var dnaMut = new DnaComponent();
	dnaMut.spanStart = "<span class=\"mutated_sequence\">";
	dnaMut.spanEnd = "</span>";
	dnaMut.setCharacters(mutatedDnaSequence);
	textLayout.addComponent(dnaMut);
		
	var dna = new DnaComponent();
	dna.spanStart = "<span class=\"current_sequence\">";
	dna.spanEnd = "</span>";
	dna.setCharacters(dnaSequence);
	textLayout.addComponent(dna);

	var sitesInRange = new Array();
	var sitesInRangeMut = new Array();

	for (var i = 0; i < dnaSequence.length; i = i + basesPerLine) {
		//first get restriction sites in this range
		sitesInRange = restrictionSiteCollection.getSitesInRange(i, i + basesPerLine);
		sitesInRangeMut = mutatedRestrictionSiteCollection.getSitesInRange(i, i + basesPerLine);
		//reversing gives better appearance
		sitesInRange.reverse();
		sitesInRangeMut.reverse();

		for (var j = 0; j < sitesInRangeMut.length; j++) {
			//9 is added because of indent to dna sequence
			outputWindow.document.write(spaceString.substring(0, sitesInRangeMut[j].position - i + 9) + "<span class=\"mutated_sequence\">" + sitesInRangeMut[j].label + "</span>\n");
		}

		for (var j = 0; j < sitesInRange.length; j++) {
			//9 is added because of indent to dna sequence
			outputWindow.document.write(spaceString.substring(0, sitesInRange[j].position - i + 9) + "<span class=\"current_sequence\">" + sitesInRange[j].label + "</span>\n");
		}

		textLayout.writeLayout(i, i + basesPerLine);
	}

	return true;
}

function translate (dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult) {

	//don't translate if fewer than three bases
	if (dnaSequence.replace(/[^A-Za-z]/g, "").length < 3) {
		return "";
	}

	dnaSequence = dnaSequence.replace(/(...)/g, 
                    function (str, p1, offset, s) {
                      	return " " + p1 + " ";
                   }
        );	
	
	for (var i = 0; i < geneticCodeMatchExp.length; i++)	{
		dnaSequence = dnaSequence.replace(geneticCodeMatchExp[i], geneticCodeMatchResult[i]);
	}

	dnaSequence = dnaSequence.replace(/\S{3}/g, "X");
	dnaSequence = dnaSequence.replace(/\s\S{1,2}$/, "");
	dnaSequence = dnaSequence.replace(/^\s/, "");
	return dnaSequence;	
}

function uppercaseTranslate (dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult) {

	dnaSequence = dnaSequence.replace(/[a-z]/g, " ");

	//don't translate if fewer than three bases
	if (dnaSequence.replace(/[^A-Za-z]/g, "").length < 3) {
		return "";
	}

	dnaSequence = dnaSequence.replace(/([A-Z])(\s*)([A-Z])(\s*)([A-Z])(\s*)/g, 
                    function (str, p1, p2, p3, p4, p5, p6, offset, s) {
                      	return " " + p1 + p3 + p5 + " " + p2 + p4 + p6;
                   }
        );

	dnaSequence = dnaSequence.replace(/\s\S{1,2}\s/g, "");

	for (var i = 0; i < geneticCodeMatchExp.length; i++)	{
		dnaSequence = dnaSequence.replace(geneticCodeMatchExp[i], geneticCodeMatchResult[i]);
	}

	dnaSequence = dnaSequence.replace(/\S{3}/g, "X");
	dnaSequence = dnaSequence.replace(/^\s/, "");

	return dnaSequence;	
}

function buildMutatedRestrictionSites (restrictionSites) {
	var mutatedRestrictionSites = new Array();
	for (var i = 0; i < (restrictionSites.length); i++)	{
		var site = ((restrictionSites[i].match(/\/.+\//)).toString()).replace(/[\/\\]/g,"").toLowerCase();
		var label = (restrictionSites[i].match(/\([^\(]+\)/)).toString();
		var cutDistance = parseFloat((restrictionSites[i].match(/\)\D*\d+/)).toString().replace(/\)\D*/,""));
		var singleDegenSites = new Array();
		var doubleDegenSites = new Array();
		for (var j = 0; j < (site.length); j++)	{
			if ((site.charAt(j) != "n") && (site.charAt(j) != "N")) {
				var pre = site.substring(0, j);
				var post = site.substring(j + 1, site.length);
				var newSite = pre + "N" + post;
				singleDegenSites.push(newSite);				
			}
		}

		if (site.length > 6) {					
			for (var j = 0; j < (singleDegenSites.length); j++)	{
				for (var k = 0; k < (singleDegenSites[j].length); k++)	{
					if ((singleDegenSites[j].charAt(k) != "n") && (singleDegenSites[j].charAt(k) != "N")) {
						var pre = singleDegenSites[j].substring(0, k);
						var post = singleDegenSites[j].substring(k + 1, singleDegenSites[j].length);
						var newSite = pre + "N" + post;
						doubleDegenSites.push(newSite);				
					}				
				}	
			}
		}

		for (var j = 0; j < (singleDegenSites.length); j++)	{
			mutatedRestrictionSites.push("/" + singleDegenSites[j] + "/" + " " + label + cutDistance);
		}

		for (var j = 0; j < (doubleDegenSites.length); j++)	{
			mutatedRestrictionSites.push("/" + doubleDegenSites[j] + "/" + " " + label + cutDistance);
		}
	}
	return mutatedRestrictionSites;	
}

function removeNormalMatchesFromMutantSites (mutatedRestrictionSiteCollection, restrictionSiteCollection) {
	var originalMutatedRestrictionSites = new Array();
	for (var i = 0; i < (mutatedRestrictionSiteCollection.restrictionSites.length); i++)	{
		var mutatedSite = mutatedRestrictionSiteCollection.restrictionSites[i];
		var isOriginal = true;
		for (var j = 0; j < (restrictionSiteCollection.restrictionSites.length); j++)	{
			var normalSite = restrictionSiteCollection.restrictionSites[j];
			if (normalSite.position == mutatedSite.position) {
				isOriginal = false;
				break;
			}
		}
		if (isOriginal) {
			originalMutatedRestrictionSites.push(mutatedSite);
		}		
	}
	mutatedRestrictionSiteCollection.restrictionSites = originalMutatedRestrictionSites;
	return mutatedRestrictionSiteCollection;
}

function removeOverlappingMatchesFromMutantSites (mutatedRestrictionSiteCollection) {
	var originalMutatedRestrictionSites = new Array();
	for (var i = 0; i < (mutatedRestrictionSiteCollection.restrictionSites.length); i++)	{
		var mutatedSite = mutatedRestrictionSiteCollection.restrictionSites[i];
		var isOriginal = true;
		for (var j = 0; j < (originalMutatedRestrictionSites.length); j++)	{	
			var mutatedSiteJ = originalMutatedRestrictionSites[j];
			//don't want one site to alter protein translation under another site
			var startRangeJ = mutatedSiteJ.position + mutatedSiteJ.cutDistance - mutatedSiteJ.iupacPattern.length - 2;
			var endRangeJ = mutatedSiteJ.position + mutatedSiteJ.cutDistance - 1 + 2;

			var startRange = mutatedSite.position + mutatedSite.cutDistance - mutatedSite.iupacPattern.length;
			var endRange = mutatedSite.position + mutatedSite.cutDistance - 1;

			if ((startRange <= startRangeJ) && (endRange >= startRangeJ)) {
				isOriginal = false;
				break;
			}

			if ((startRange <= endRangeJ) && (endRange >= endRangeJ)) {
				isOriginal = false;
				break;
			}

			if ((startRange <= startRangeJ) && (endRange >= endRangeJ)) {
				isOriginal = false;
				break;
			}

			if ((startRange >= startRangeJ) && (endRange <= endRangeJ)) {
				isOriginal = false;
				break;
			}

		}
		if (isOriginal) {
			originalMutatedRestrictionSites.push(mutatedSite);
		}		
	}
	mutatedRestrictionSiteCollection.restrictionSites = originalMutatedRestrictionSites;
	return mutatedRestrictionSiteCollection;
}

function buildMutatedDna (originalDna, mutatedRestrictionSiteCollection) {
	var mutatedDna = originalDna;
	var mutatedDnaArray = new Array();
	mutatedRestrictionSiteCollection.sortRestrictionSites();
	mutatedRestrictionSiteCollection.restrictionSites.reverse();
	for (var i = 0; i < (mutatedRestrictionSiteCollection.restrictionSites.length); i++)	{
		var mutatedSite = mutatedRestrictionSiteCollection.restrictionSites[i];
		var siteStart = mutatedSite.position + mutatedSite.cutDistance - mutatedSite.iupacPattern.length;
		var siteEnd = mutatedSite.position + mutatedSite.cutDistance - 1;
		var siteLength = siteEnd - siteStart;

		mutatedDnaArray.push(mutatedDna.substring(0,siteStart) + replaceMutatedDnaSegment(mutatedDna.substring(siteStart, siteEnd + 1), mutatedSite.iupacPattern, mutatedSite.label));
		mutatedDnaArray.push(mutatedDna.substring(siteEnd + 1, mutatedDna.length));
		
		mutatedDna = mutatedDnaArray.join("");
		mutatedDnaArray = new Array();	
	}
	mutatedRestrictionSiteCollection.restrictionSites.reverse();
	return mutatedDna;
}

function replaceMutatedDnaSegment(originalSegment, iupacPattern, label) {
	var newSegment = "";
	var genericSite;
	//determine genericSite from label
	genericSite = ((label.match(/[a-z\|]+\s\d+/)).toString()).replace(/\||\s\d+/g,"");
	var isUpperCase;
	var charToAdd;
	for (var i = 0; i < originalSegment.length; i++)	{
		if (((originalSegment.charAt(i)).toString()).search(/[A-Z]/) == -1) {
			isUpperCase = false;
		}
		else {
			isUpperCase = true;
		}

		if (originalSegment.charAt(i) == genericSite.charAt(i)) {
			charToAdd = originalSegment.charAt(i);
		}
		else if (iupacPattern.charAt(i) == "N") {
			charToAdd = genericSite.charAt(i);
		}
		else {
			charToAdd = originalSegment.charAt(i);
		}
		
		if (isUpperCase) {
			newSegment = newSegment + charToAdd.toString().toUpperCase();
		}	
		else {
			newSegment = newSegment + charToAdd.toString().toLowerCase();		
		}		
	}
	
	return newSegment;
}

function findRestrictionSites (sequence, arrayOfItems, dnaConformation)	{	

	var lookAhead = 50;
	var lowerLimit = 0;
	var upperLimit = sequence.length;
	var shiftValue = 0;
	var cutDistance;
	var matchExp;
	var matchPosition;
	var matchArray;
	var label;
	var timesFound = 0;
	var tempArray = new Array();

	var restrictionSiteCollection = new RestrictionSiteCollection();

	if (dnaConformation == "circular")	{
		shiftValue = (sequence.substring(0, lookAhead)).length;
		sequence = sequence.substring(sequence.length - lookAhead,sequence.length) + sequence + sequence.substring(0,lookAhead);
		lowerLimit = 0 + shiftValue;
		upperLimit = upperLimit + shiftValue;
	}

	for (var i = 0; i < (arrayOfItems.length); i++)	{
		var iupacPattern = ((arrayOfItems[i].match(/\/.+\//)).toString()).replace(/[\/\\]/g,"");
		matchExp = "/" + convertDegenerates(iupacPattern) + "/" + "gi";
		matchPosition = 0;
		matchExp = eval(matchExp);
		cutDistance = parseFloat((arrayOfItems[i].match(/\)\D*\d+/)).toString().replace(/\)\D*/,""));
		label = ((arrayOfItems[i].match(/\([^\(]+\)/)).toString()).replace(/\(|\)/g,"");

		while (matchArray = matchExp.exec(sequence)) {
			timesFound++;
			matchPosition = matchExp.lastIndex;
			matchPosition = matchPosition - cutDistance;
			if ((matchPosition >= lowerLimit) && (matchPosition < upperLimit))	{	
				tempArray.push(new RestrictionSite(label + " " + (matchPosition - shiftValue + 1), (matchPosition - shiftValue), cutDistance, iupacPattern));
			}				
		}
		
		
		for (var j = 0; j < tempArray.length; j++) {
			tempArray[j].numberOfCuts = timesFound;
			restrictionSiteCollection.addRestrictionSite(tempArray[j]);
		}
		timesFound = 0;	
		tempArray = new Array();
	}
	
	return restrictionSiteCollection;
}


//------------------------------------ TextLayout Class
//TextLayout writeLayout method
function writeLayout (start, stop) {
	for (var i = 0; i < this.components.length; i++)	{
		this.components[i].writeLayoutComponent(start, stop);
	}	
}

//TextLayout addComponent method
function addComponent(component) {
	this.components.push(component);
}

//TextLayout class
function TextLayout () {
   	this.components = new Array();
}

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

//define object methods
TextLayout.prototype.writeLayout = writeLayout;
TextLayout.prototype.addComponent = addComponent;
//------------------------------------


//------------------------------------ LayoutComponent Abstract Class
//LayoutComponent writeLayoutComponent method
function writeLayoutComponent(start, stop) {
	//abstract method
}

//LayoutComponent setCharacters method
function setCharacters (text) {
	if (text.search(/./) != -1)	{
		this.characters = text.match(/./g);
	}
}

//LayoutComponent isRoom method
function isRoom (start, stop) {
	//return true if nothing in characters array in this range
	var rangeToCheck = this.characters.slice(start, stop);
	rangeToCheck = rangeToCheck.join("");
	if (rangeToCheck.search(/\w/) == -1) {
		return true;
	}
	else {
		return false;
	}
}

//LayoutComponent class
function LayoutComponent() {
	this.characters = new Array();
	this.positionLabel = 1;
	this.spanStart = "";
	this.spanEnd = "";
}

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

//define object methods
LayoutComponent.prototype.writeLayoutComponent = writeLayoutComponent;
LayoutComponent.prototype.setCharacters = setCharacters;
LayoutComponent.prototype.isRoom = isRoom;
//------------------------------------

//------------------------------------ TranslationComponent Class extend LayoutComponent Class
//constructor
function TranslationComponent () {
	this.characters = new Array();
	this.positionLabel = 1;
	this.spanStart = "";
	this.spanEnd = "";
}

TranslationComponent.prototype = new LayoutComponent();

//override writeLayoutComponent
TranslationComponent.prototype.writeLayoutComponent = function (start, stop) {
	outputWindow.document.write (rightNum (this.positionLabel, "", 8, ""));
	outputWindow.document.write (this.spanStart);
	outputWindow.document.write (this.characters.slice(start, stop).join(""));
	outputWindow.document.write (this.spanEnd + "\n");
	this.positionLabel = this.positionLabel + (stop - start) / 3;
}

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

//------------------------------------ UppercaseTranslationComponent Class extend LayoutComponent Class
//constructor
function UppercaseTranslationComponent () {
	this.characters = new Array();
	this.positionLabel = 1;
	this.spanStart = "";
	this.spanEnd = "";
}

UppercaseTranslationComponent.prototype = new LayoutComponent ();

//override writeLayoutComponent
UppercaseTranslationComponent.prototype.writeLayoutComponent = function (start, stop) {
	var textToWrite = this.characters.slice(start, stop).join("");
	if (textToWrite.search(/\w/) != -1) {
		outputWindow.document.write (rightNum (this.positionLabel, "", 8, ""));
		outputWindow.document.write (this.spanStart);
		this.positionLabel = this.positionLabel + ((textToWrite.match(/[A-Z]/g)).length);
		outputWindow.document.write (textToWrite);
		outputWindow.document.write (this.spanEnd + "\n");
	}
}
//------------------------------------

//------------------------------------ DnaComponent Class extend LayoutComponent Class
//constructor
function DnaComponent () {
	this.characters = new Array();
	this.positionLabel = 1;
	this.spanStart = "";
	this.spanEnd = "";
}
DnaComponent.prototype = new LayoutComponent ();

//override writeLayoutComponent
DnaComponent.prototype.writeLayoutComponent = function (start, stop) {
	outputWindow.document.write (rightNum (this.positionLabel, "", 8, ""));
	outputWindow.document.write (this.spanStart);
	outputWindow.document.write (this.characters.slice(start, stop).join(""));
	outputWindow.document.write (this.spanEnd + "\n");
	this.positionLabel = this.positionLabel + (stop - start);
}
//------------------------------------

//------------------------------------ RestrictionSite class
//RestrictionSite class
function RestrictionSite(label, position, cutDistance, iupacPattern) {
	this.label = label;
	this.position = position;
	this.cutDistance = cutDistance;
	this.iupacPattern = iupacPattern;
	this.numberOfCuts;
}
//------------------------------------

//------------------------------------ RestrictionSiteCollection class
//RestrictionSiteCollection addRestrictionSite method
function addRestrictionSite (restrictionSite) {
	this.restrictionSites.push(restrictionSite);	
}

//RestrictionSiteCollection sortRestrictionSites method
function sortRestrictionSites () {
	this.restrictionSites.sort(restrictionSiteSorter);	
}

//RestrictionSiteCollection getSitesInRange method
function getSitesInRange (start, stop) {
	var arrayToReturn = new Array();
	//start at end
	for (var i = this.restrictionSites.length - 1; i >= 0; i--)	{
		if ((this.restrictionSites[i].position >= start) && (this.restrictionSites[i].position < stop)) {
			arrayToReturn.push(this.restrictionSites.pop());
		}
		else {
			break;
		}
	}	
	return arrayToReturn;
}

//RestrictionSiteCollection class
function RestrictionSiteCollection () {
   	this.restrictionSites = new Array();
}

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

//define object methods
RestrictionSiteCollection.prototype.addRestrictionSite = addRestrictionSite;
RestrictionSiteCollection.prototype.sortRestrictionSites = sortRestrictionSites;
RestrictionSiteCollection.prototype.getSitesInRange = getSitesInRange;

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

//sort so first ones at end
function restrictionSiteSorter (a, b) {
   	if (a.position < b.position) {
      		return 1;
	}
   	if (a.position > b.position) {
      		return -1;
	}
	else {
		return 0;
	}
}