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

function filterProtein (theDocument) {

    	var newProtein = "";
    	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");
    	newProtein = 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")	{
		newProtein = newProtein.toUpperCase();
    	}
    	else {
		if (theDocument.forms[0].elements[6].options[theDocument.forms[0].elements[6].selectedIndex].value == "lowercase")	{
	    		newProtein = newProtein.toLowerCase();
		}
    	}

	openWindow("Filter Protein");
	openPre();
	outputWindow.document.write ('>filtered protein sequence consisting of ' + newProtein.length + ' residues.\n');
	outputWindow.document.write (addReturns(newProtein));
	outputWindow.document.write ("\n");	
	closePre();
	closeWindow();
    	return true;
}