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

function transMap (theDocument) {	

	var newDna = "";
	var title = "";
	var maxInput = 500000;

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

	var geneticCode = getGeneticCodeString(theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].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;
	}

	openWindow("Translation Map");
	openPre();	
	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(getInfoFromTitleAndSequence(title, newDna));

		layoutTranslation (newDna, geneticCode, 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\n');
	}


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

function layoutTranslation (dnaSequence, geneticCode, basesPerLine, readingFrame)	{

	basesPerLine = parseInt(basesPerLine);

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

	var textLayout = new TextLayout();

	if ((readingFrame == "3") || (readingFrame == "all_three")) {
		var translation = new TranslationComponent();
		translation.setCharacters("  " + translate(dnaSequence.substring(2, dnaSequence.length), geneticCodeMatchExp, geneticCodeMatchResult));
		textLayout.addComponent(translation);
	}

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

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

	for (var i = 0; i < dnaSequence.length; i = i + basesPerLine) {
		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;	
}


//------------------------------------ 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;
}

//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;
}

TranslationComponent.prototype = new LayoutComponent();

//override writeLayoutComponent
TranslationComponent.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) / 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);
}
//------------------------------------


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

//override writeLayoutComponent
RulerComponent.prototype.writeLayoutComponent = function (start, stop) {
	outputWindow.document.write (rightNum (this.positionLabel, "", 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");
	this.positionLabel = this.positionLabel + (stop - start);
}

//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;

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