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

function randomProteinRegions (theDocument) {	
	var newProtein = "";
	var title = "";
	var maxInput = 500000;
	var matchFound = false;
	var ranges = new Array();

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

	if ((checkFormElement (theDocument.forms[0].elements[0]) == false) || (checkSequenceLength(theDocument.forms[0].elements[0].value, maxInput) == false) || (checkFormElement (theDocument.forms[0].elements[1]) == false))	{
		return false;
	}

	var arrayOfRanges = theDocument.forms[0].elements[1].value.split(/,/);
	var arrayOfStartAndEnd;
	for (var i=0; i < arrayOfRanges.length; i++) {
		arrayOfStartAndEnd = arrayOfRanges[i].split(/\.\.|\-/);
		if ((arrayOfStartAndEnd.length == 1) && (arrayOfStartAndEnd[0].search(/\d/) != -1)) {
			matchFound = true;
			ranges.push(new Range(arrayOfStartAndEnd[0], arrayOfStartAndEnd[0]));
		}
		else if ((arrayOfStartAndEnd.length == 2) && (arrayOfStartAndEnd[0].search(/\d/) != -1) && (arrayOfStartAndEnd[1].search(/\d/) != -1)) {
			matchFound = true;
			ranges.push(new Range(arrayOfStartAndEnd[0], arrayOfStartAndEnd[1]));
		}				
	}
	if (matchFound == false) {
		alert ("No ranges were entered.");
		return false;
	}
	
	openWindow("Random Protein Regions");
	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));

		writeSequenceRanges(newProtein, ranges, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);
		
		outputWindow.document.write ('\n\n');
	}

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