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

function identSim (theDocument) {

	var maxInput = 20000;	
	var theAlignment = "";
	var alignArray = new Array();
	var groupString = "";
	var arrayOfGroups = new Array();

	var titleArray = new Array();
	var sequenceArray = new Array();

	var longestTitle;

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

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

	theAlignment = "X" + theDocument.forms[0].elements[0].value;
	alignArray = theAlignment.split(/[>%]/);

	if (earlyCheckAlign (alignArray) == false)	{
		return false;
	}

	for (var i = 1; i < alignArray.length; i++)	{
		titleArray[i-1] = alignArray[i].match(/[^\f\n\r]+[\f\n\r]/);
		titleArray[i-1] = filterFastaTitle(titleArray[i-1].toString()).replace(/[\f\n\r]/g, "");
		titleArray[i-1] = titleArray[i-1].substring(0, 20);
		if (i == 1) {
			longestTitle = titleArray[i-1].length;
		}
		else if (titleArray[i-1].length > longestTitle)	{
			longestTitle = titleArray[i-1].length;
		}
		sequenceArray[i-1] = alignArray[i].replace(/[^\f\n\r]+[\f\n\r]/,"");
		sequenceArray[i-1] = filterAlignSeq (sequenceArray[i-1]);
	}

	if (checkAlign (titleArray, sequenceArray) == false)	{
		return false;
	}

	groupString = (theDocument.forms[0].elements[1].value.replace(/\s/g,"")).toUpperCase();
	arrayOfGroups = groupString.split(/,/);
	if (checkGroupInput (arrayOfGroups) == false)	{
		return false;
	}


	openWindowAlign("Ident and Sim");
	openPre();
	writeIdentAndSim (titleArray, sequenceArray, arrayOfGroups);
	closePre();
	closeWindow();
	return true;
}

function writeIdentAndSim (titleArray, sequenceArray, arrayOfGroups)	{
	var identical = 0;
	var similar = 0;
	var alignLength = 0;
	for (var k = 0; k < sequenceArray.length; k++)	{
		for (var m = k + 1; m < sequenceArray.length; m++)	{
			for (var i = 0; i < sequenceArray[0].length; i++)	{
				alignLength = alignLength + 1;
				if ((sequenceArray[k].charAt(i).toUpperCase() == sequenceArray[m].charAt(i).toUpperCase()) && (sequenceArray[k].charAt(i).toUpperCase() != "X"))	{
					if ((sequenceArray[k].charAt(i) != "-") && (sequenceArray[k].charAt(i) != "."))	{
						identical = identical + 1;
					}
					else	{
						alignLength = alignLength - 1;
					}
				}
				else	{
					for (var j = 0; j < arrayOfGroups.length; j++)	{
						if (arrayOfGroups[j].search(sequenceArray[k].charAt(i).toUpperCase()) != -1 && arrayOfGroups[j].search(sequenceArray[m].charAt(i).toUpperCase()) != -1)	{
							similar = similar + 1;
							break;
						}
					}
				}
			}
		outputWindow.document.write('<b>Results for ' + titleArray[k] + ' vs ' + titleArray[m] + ':</b>\n');
		outputWindow.document.write("  Alignment length: " + alignLength + "\n");
		outputWindow.document.write("Identical residues: " + identical + "\n");
		outputWindow.document.write("  Similar residues: " + similar + "\n");
		if (identical == 0)	{
			outputWindow.document.write("  Percent identity: " + 0 + "\n");
		}
		else	{
			outputWindow.document.write("  Percent identity: " + ((identical/alignLength)*100).toFixed(2) + "\n");
		}
		if ((similar == 0) && (identical == 0))	{
			outputWindow.document.write("Percent similarity: " + 0 + "\n");
		}
		else	{
			outputWindow.document.write("Percent similarity: " + (((identical + similar)/alignLength)*100).toFixed(2) + "\n");
		}
		outputWindow.document.write("\n");
		identical = 0;
		similar = 0;
		alignLength = 0;
		}
	}
	return true;
}