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

function filterDna (theDocument) {

    	var newDna = "";
    	var maxInput = 500000;

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

    	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkTextLength(theDocument.forms[0].elements[0].value, maxInput) == false))	{
		return false;
    	}	        
	
    	var re = new RegExp (theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value,"g");
    	newDna = theDocument.forms[0].elements[0].value.replace(re,theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
    	if (theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value == "uppercase")	{
		newDna = newDna.toUpperCase();
    	}
    	else {
		if (theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value == "lowercase")	{
	    		newDna = newDna.toLowerCase();
		}
    	}

	openWindow("Filter DNA");
	openPre();
	outputWindow.document.write ('>filtered DNA sequence consisting of ' + newDna.length + ' bases.\n');
	outputWindow.document.write (addReturns(newDna));
	outputWindow.document.write ("\n");	
	closePre();
	closeWindow();
    	return true;
}