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

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

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

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

	openWindow("Shuffle Protein");
	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));

		writeShuffledSequence(newProtein);
		
		outputWindow.document.write ('\n\n');
	}


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