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

function threeToOne (theDocument) {	
	var newProtein = "";
	var maxInput = 100000;

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

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

	openWindow("Three to One");
	openPre();
	var arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);


	for (var i = 0; i < arrayOfFasta.length; i++)	{
		
		newProtein = getTripletSequenceFromFasta(arrayOfFasta[i]);
		title = getFastaTitleFromTriplets(arrayOfFasta[i]);
		newProtein = filterTriplets(newProtein);
	
		outputWindow.document.write(getInfoFromTitleAndSequenceTriplets(title, newProtein));

		writeThreeToOne(newProtein);

		outputWindow.document.write ('\n\n');
	}
	
	closePre();
	closeWindow();
	return true;
}

function writeThreeToOne (proteinSequence)	{ 
	
	proteinSequence = proteinSequence.replace(/(.)(.)(.)/g,
                    function (str, p1, p2, p3, offset, s) {
                      return p1.toUpperCase() + p2.toLowerCase() + p3.toLowerCase();
                   }
                );
	proteinSequence = proteinSequence.replace(/Ala/g, " A ");
	proteinSequence = proteinSequence.replace(/Cys/g, " C ");
	proteinSequence = proteinSequence.replace(/Asp/g, " D ");
	proteinSequence = proteinSequence.replace(/Glu/g, " E ");
	proteinSequence = proteinSequence.replace(/Phe/g, " F ");
	proteinSequence = proteinSequence.replace(/Gly/g, " G ");
	proteinSequence = proteinSequence.replace(/His/g, " H ");
	proteinSequence = proteinSequence.replace(/Ile/g, " I ");
	proteinSequence = proteinSequence.replace(/Lys/g, " K ");
	proteinSequence = proteinSequence.replace(/Leu/g, " L ");
	proteinSequence = proteinSequence.replace(/Met/g, " M ");
	proteinSequence = proteinSequence.replace(/Asn/g, " N ");
	proteinSequence = proteinSequence.replace(/Pro/g, " P ");
	proteinSequence = proteinSequence.replace(/Gln/g, " Q ");
	proteinSequence = proteinSequence.replace(/Arg/g, " R ");
	proteinSequence = proteinSequence.replace(/Ser/g, " S ");
	proteinSequence = proteinSequence.replace(/Thr/g, " T ");
	proteinSequence = proteinSequence.replace(/Val/g, " V ");
	proteinSequence = proteinSequence.replace(/Trp/g, " W ");
	proteinSequence = proteinSequence.replace(/Tyr/g, " Y ");
	proteinSequence = proteinSequence.replace(/\*\*\*/g, " Z ");

	proteinSequence = proteinSequence.replace(/\s/g, "");
	
	outputWindow.document.write (addReturns(proteinSequence));
	return true;		
}

function filterTriplets (tripletSequence)	{
	tripletSequence = tripletSequence.replace (/\s|\d/gi,"");
	return tripletSequence;
}

function getFastaTitleFromTriplets (tripletSequence)	{
	fastaSequenceTitle = "Untitled";
	if (tripletSequence.search(/\>[^\f\n\r]+[\f\n\r]/) != -1)	{
		fastaSequenceTitle = (tripletSequence.match(/\>[^\f\n\r]+[\f\n\r]/,"")).toString();
		fastaSequenceTitle = fastaSequenceTitle.replace(/\>|[\f\n\r]/g,"");
		fastaSequenceTitle = filterFastaTitle(fastaSequenceTitle);
	}
	return fastaSequenceTitle;
}

function getTripletSequenceFromFasta (tripletSequence)	{
	
	if (tripletSequence.search(/\>[^\f\n\r]+[\f\n\r]/) != -1)	{
		tripletSequence = tripletSequence.replace(/\>[^\f\n\r]+[\f\n\r]/,"");
	}
	return tripletSequence;
}

function getInfoFromTitleAndSequenceTriplets (fastaSequenceTitle, sequence)	{
	var stringToReturn = '&gt;results for sequence ';
	if (fastaSequenceTitle.search(/[^\s]/) != -1)	{
		stringToReturn = stringToReturn + '"' + fastaSequenceTitle + '"';
	}
	stringToReturn = stringToReturn + ' starting "' + sequence.substring(0,12) + '"';
	return stringToReturn + '\n';
}