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

function sampleProtein (theDocument) {

	var maxInput = 100000;

	if (testScript() == false) {
		return false;
	}
	
	var enteredNumber = (theDocument.forms[0].elements[0].value).replace(/[^\d]/g,"");
	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (verifyMaxDigits (enteredNumber, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false) || (checkSequenceLength(theDocument.forms[0].elements[1].value, maxInput) == false))	{
		return false;
	}

	var seqNum = parseInt(theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);

	var newProtein = getSequenceFromFasta (theDocument.forms[0].elements[1].value);
	var title = getTitleFromFasta (theDocument.forms[0].elements[1].value);
	newProtein = removeNonProteinAllowDegen(newProtein);

	var components = new Array(newProtein.length);
	if (newProtein.search(/./) != -1)	{
		components = newProtein.match(/./g);
	}	

	openWindow("Sample Protein");
	openPre();
	for (var i=1; i <= seqNum; i++) {
		outputWindow.document.write ('&gt;' + 'sampled sequence ' + i + ' consisting of ' + enteredNumber + ' residues.\n');
		writeRandomSequence(components, enteredNumber);
		outputWindow.document.write ("\n");
	}
	closePre();
	closeWindow();
    	return true;
}