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

function revComp (theDocument) {	
	var newDna = "";
	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("Reverse Complement");
	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));
	
		if (theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value == "reverse-complement")	{
	                outputWindow.document.write(">" + title + " reverse complement\n");
			newDna = reverse(complement(newDna));
		}
		else if (theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value == "reverse")	{
	                outputWindow.document.write(">" + title + " reverse\n");
			newDna = reverse(newDna);
		}
		else if (theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value == "complement")	{
	                outputWindow.document.write(">" + title + " complement\n");
			newDna = complement(newDna);
		}

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