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

function translate (theDocument) {	

	var newDna = "";
	var title = "";
	var maxInput = 200000;

	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;
	}

	var rfText = theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value;
	if ((theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value).match(/^\d+$/)) {
		rfText++;
	}
	else {
		rfText = '"' + theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value + '"';
	}	

	openWindow("Translate");
	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('&gt;rf ' + rfText + ' ' + title + '\n');
		writeTranslation(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 writeTranslation (dnaSequence, geneticCode, startPos, strand)	{
	var geneticCodeMatchExp = getGeneticCodeMatchExp (geneticCode);
	var geneticCodeMatchResult = getGeneticCodeMatchResult (geneticCode);

	if (strand == "reverse")	{
		dnaSequence = reverse(complement(dnaSequence));
	}	
	if (startPos == "uppercase")	{
		dnaSequence = dnaSequence.replace(/[a-z]/g,"");
	}
	else	{
		dnaSequence = dnaSequence.substring(parseInt(startPos), dnaSequence.length);
	}

	//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/g, "");
	outputWindow.document.write(addReturns(dnaSequence));
	return true;
}