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

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


	for (var i = 0; i < arrayOfFasta.length; i++)	{
		
		newProtein = getSequenceFromFasta (arrayOfFasta[i]);
		title = getTitleFromFasta (arrayOfFasta[i]);
		newProtein = removeNonProteinAllowDegen(newProtein);
	
		outputWindow.document.write(getFastaTitleFromTitleAndSequence(title, newProtein));

		writeOneToThree(newProtein);

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

function writeOneToThree (proteinSequence)	{ 
	proteinSequence = proteinSequence.toLowerCase();
	proteinSequence = proteinSequence.replace(/(.)/g, 
                    function (str, p1, offset, s) {
                      return " " + p1 + " ";
                   }
                );

	proteinSequence = proteinSequence.replace(/a/g, "ALA");
	proteinSequence = proteinSequence.replace(/b/g, "ASX");
	proteinSequence = proteinSequence.replace(/c/g, "CYS");
	proteinSequence = proteinSequence.replace(/d/g, "ASP");
	proteinSequence = proteinSequence.replace(/e/g, "GLU");
	proteinSequence = proteinSequence.replace(/f/g, "PHE");
	proteinSequence = proteinSequence.replace(/g/g, "GLY");
	proteinSequence = proteinSequence.replace(/h/g, "HIS");
	proteinSequence = proteinSequence.replace(/i/g, "ILE");
	proteinSequence = proteinSequence.replace(/k/g, "LYS");
	proteinSequence = proteinSequence.replace(/l/g, "LEU");
	proteinSequence = proteinSequence.replace(/m/g, "MET");
	proteinSequence = proteinSequence.replace(/n/g, "ASN");
	proteinSequence = proteinSequence.replace(/p/g, "PRO");
	proteinSequence = proteinSequence.replace(/q/g, "GLN");
	proteinSequence = proteinSequence.replace(/r/g, "ARG");
	proteinSequence = proteinSequence.replace(/s/g, "SER");
	proteinSequence = proteinSequence.replace(/t/g, "THR");
	proteinSequence = proteinSequence.replace(/v/g, "VAL");
	proteinSequence = proteinSequence.replace(/w/g, "TRP");
	proteinSequence = proteinSequence.replace(/x/g, "XAA");
	proteinSequence = proteinSequence.replace(/y/g, "TYR");
	proteinSequence = proteinSequence.replace(/z/g, "GLX");
	proteinSequence = proteinSequence.replace(/\*/g, "***");

	proteinSequence = proteinSequence.replace(/\s*(.)(.)(.)\s*/g,
                    function (str, p1, p2, p3, offset, s) {
                      return p1 + p2.toLowerCase() + p3.toLowerCase();
                   }
                );
	
	outputWindow.document.write (addReturns(proteinSequence));
	return true;		
}