//Written by Paul Stothard, University of Alberta, Canada
//Modified output by George Waldon

function restMap (theDocument) {	

	var newDna = "";
	var title = "";
	var maxInput = 100000;

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

	var restrictionSiteCollection;

	var geneticCode = getGeneticCodeString(theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value);

	var restrictionSites = getRestrictionSiteString(theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].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(/,/);
    // not valid anymore with new enzyme file
	//if (checkRestPatterns(restrictionSites) == false)	{
	//	return false;
	//}

	openWindow("Restriction Map");	
	outputWindow.document.write(RestrictionSiteTypetoString(theDocument.forms[0].elements[8].options[theDocument.forms[0].elements[8].selectedIndex].value));
	outputWindow.document.write("<br /><br />\n");
    outputWindow.document.write("<span class=\"one\">" + "cuts once" + "</span><br />\n");
	outputWindow.document.write("<span class=\"two\">" + "cuts twice" + "</span><br />\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);
		openPre();
		outputWindow.document.write(getInfoFromTitleAndSequenceAndTopology(title, newDna, theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value));

		restrictionSiteCollection = findRestrictionSites(newDna, restrictionSites, theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);
		restrictionSiteCollection.sortRestrictionSites();

		layoutRestTrans (newDna, geneticCode, restrictionSiteCollection, theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
		
		outputWindow.document.write ('\n');
		closePre();	
				
		writeRestrictionSites (newDna, restrictionSites, theDocument.forms[0].elements[7].options[theDocument.forms[0].elements[7].selectedIndex].value);
		outputWindow.document.write ('<br />\n<br />\n');
	}


	closeWindow();
	return true;
}	

function layoutRestTrans (dnaSequence, geneticCode, restrictionSiteCollection, 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 translation = new TranslationComponent();
		translation.setCharacters("  " + translate(dnaSequence.substring(2, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		translation.setFrame(3);
		textLayout.addComponent(translation);
	}

	if ((readingFrame == "2") || (readingFrame == "all_three")) {
		var translation = new TranslationComponent();
		translation.setCharacters(" " + translate(dnaSequence.substring(1, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		translation.setFrame(2);
		textLayout.addComponent(translation);
	}

	if ((readingFrame == "1") || (readingFrame == "all_three")) {
		var translation = new TranslationComponent();
		translation.setCharacters(translate(dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		translation.setFrame(1);
		textLayout.addComponent(translation);
	}

	if (readingFrame == "uppercase") {
		var translation = new UppercaseTranslationComponent();
		translation.setCharacters(uppercaseTranslate(dnaSequence, geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}
		
	var dna = new DnaComponent();
	dna.setCharacters(dnaSequence);
	textLayout.addComponent(dna);

	var ruler = new RulerComponent();
       	ruler.setCharacters(dnaSequence);
	ruler.buildRuler();
	textLayout.addComponent(ruler);

	dna = new DnaComplementComponent();
	dna.setCharacters(complement(dnaSequence));
	textLayout.addComponent(dna);
	
	var empty = new EmptyComponent();
	textLayout.addComponent(empty);

	var sitesInRange = 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);

		//reversing gives better appearance
		sitesInRange.reverse();

		for (var j = 0; j < sitesInRange.length; j++) {
			//9 is added because of indent to dna sequence

			if (sitesInRange[j].numberOfCuts == 1) {
				outputWindow.document.write(spaceString.substring(0, sitesInRange[j].position - i + 9) + "<span class=\"one\">" + sitesInRange[j].label + "</span>\n");
			}

			else if (sitesInRange[j].numberOfCuts == 2) {
				outputWindow.document.write(spaceString.substring(0, sitesInRange[j].position - i + 9) + "<span class=\"two\">" + sitesInRange[j].label + "</span>\n");
			}

			else if (sitesInRange[j].numberOfCuts == 3) {
				outputWindow.document.write(spaceString.substring(0, sitesInRange[j].position - i + 9) + "<span class=\"three\">" + sitesInRange[j].label + "</span>\n");
			}

			else {
				outputWindow.document.write(spaceString.substring(0, sitesInRange[j].position - i + 9) + sitesInRange[j].label + "\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 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++)	{

		matchExp = arrayOfItems[i].match(/\/.+\//) + "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)));
			}				
		}
		
		
		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 setFrame method
function setFrame (readingFrame) {
    this.frame = readingFrame;
}

//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;
}

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

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

//------------------------------------ TranslationComponent Class extend LayoutComponent Class
//constructor
function TranslationComponent () {
	this.characters = new Array();
    this.frame = 0;
}

TranslationComponent.prototype = new LayoutComponent();

//override writeLayoutComponent
TranslationComponent.prototype.writeLayoutComponent = function (start, stop) {
    outputWindow.document.write ('<SPAN class="translation">');
    if(this.frame>=0)
        outputWindow.document.write (rightNumNSign (this.frame, "+", 8, ""));
    else
        outputWindow.document.write (rightNumNSign (this.frame, "-", 8, ""));
    outputWindow.document.write (this.characters.slice(start, stop).join("") + "\n");
    outputWindow.document.write ('</SPAN>');
	this.positionLabel = this.positionLabel + (stop - start) / 3;
}

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

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

UppercaseTranslationComponent.prototype = new LayoutComponent ();

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

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

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

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

//override writeLayoutComponent
DnaComplementComponent.prototype.writeLayoutComponent = function (start, stop) {
    var ind = this.characters.length- this.positionLabel +1;
	outputWindow.document.write (rightNum (ind, "", 8, ""));
	outputWindow.document.write (this.characters.slice(start, stop).join("") + "\n");
	this.positionLabel = this.positionLabel + (stop - start);
}
//------------------------------------

//------------------------------------ RulerComponent Class extend LayoutComponent Class
//constructor
function RulerComponent () {
	this.characters = new Array();
}
RulerComponent.prototype = new LayoutComponent ();

//override writeLayoutComponent
RulerComponent.prototype.writeLayoutComponent = function (start, stop) {
	outputWindow.document.write (rightNum ("", "", 8, ""));
	var text = this.characters.slice(start, stop).join("");
	text = text.replace(/^(\d+)/g, 
                 function (str, p1, offset, s) {		     
		     return p1.replace(/./g," ");
                 }
    	);
	text = text.replace(/(\d+)$/g, 
                 function (str, p1, offset, s) {		     
		     return p1.replace(/./g," ");
                 }
    	);
        outputWindow.document.write (text + "\n");
}

//RulerComponent buildRuler method
function buildRuler () {
    //do something
    var sequence = this.characters.join("");
    var count = 0;
    var spacing = "         ";
    sequence = sequence.replace(/(.{1,10})/g, 
                 function (str, p1, offset, s) {
		     var ruler = count + spacing;
		     if (count == 0) {
			 ruler = spacing;
		     }
		     count = count + 10;
		     return ruler.substring(0,10);
                 }
    );
    this.characters = sequence.match(/./g)
}

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

//define object methods
RulerComponent.prototype.buildRuler = buildRuler;

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

//------------------------------------ EmptyComponent Class extend LayoutComponent Class
//constructor
function EmptyComponent () {
	this.positionLabel = 1;
}
EmptyComponent.prototype = new LayoutComponent ();

//override writeLayoutComponent
EmptyComponent.prototype.writeLayoutComponent = function (start, stop) {
	outputWindow.document.write (rightNum ("", "", 8, ""));
	for(i=start;i<stop;i++)
		outputWindow.document.write (" ");
	outputWindow.document.write ("\n");
	this.positionLabel = this.positionLabel + (stop - start);
}
//------------------------------------

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