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

function proteinMw (theDocument) {	
	var newProtein = "";
	var maxInput = 200000;

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

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

	//the weights below have water subtracted
	var arrayOfMw = ["/A/ (A)71.08", "/C/ (C)103.14", "/D/ (D)115.09", "/E/ (E)129.12"," /F/ (F)147.18", "/G/ (G)57.06", "/H/ (H)137.15", "/I/ (I)113.17", "/K/ (K)128.18", "/L/ (L)113.17", "/M/ (M)131.21", "/N/ (N)114.11", "/P/ (P)97.12", "/Q/ (Q)128.41", "/R/ (R)156.20", "/S/ (S)87.08", "/T/ (T)101.11", "/V/ (V)99.14", "/W/ (W)186.21", "/Y/ (Y)163.18"];

	openWindow("Protein Molecular Weight");
	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 = removeNonProteinStrict(newProtein);
	
		outputWindow.document.write(getInfoFromTitleAndSequence(title, newProtein));

		writeProtMw(newProtein, arrayOfMw, theDocument.forms[0].elements[4].options[theDocument.forms[0].elements[4].selectedIndex].value, theDocument.forms[0].elements[5].options[theDocument.forms[0].elements[5].selectedIndex].value);

		outputWindow.document.write ('<br />\n<br />\n');
	}
	closeWindow();
	return true;
}

function writeProtMw (proteinSequence, arrayOfMw, copies, fusion)	{ //calculates molecular weight of protein.
	var water = 18.015;
	var result = 0;
	copies = parseInt(copies);
	for (var j = 0; j < copies; j++)	{
		proteinSequence = proteinSequence + fusion;
	}
	for (var j = 0; j < (arrayOfMw.length); j++)	{

		var tempNumber = 0;
		var matchExp = arrayOfMw[j].match(/\/[^\/]+\//) + "gi";
		matchExp = eval(matchExp);
		if (proteinSequence.search(matchExp) != -1)	{
			tempNumber = ((proteinSequence.match(matchExp)).length);	
		}
		result = result + tempNumber * parseFloat( arrayOfMw[j].match(/[\d\.]+/).toString() );
	}

	if (result == 0)	{
		outputWindow.document.write(result + ' kD');
	}
	else	{
		result = result + water; //add the weight of water for the ends of the protein.
		result = result/1000;	//convert to kilodaltons.
		result = result.toFixed(2);
		outputWindow.document.write(result + ' kD');
	}
	return true;
}