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

function combineFasta (theDocument) {	

	var maxInput = 500000;
	var sequenceCount = 0;
	var sequences = new Array();

	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 arrayOfFasta = getArrayOfFasta (theDocument.forms[0].elements[0].value);

	for (var i = 0; i < arrayOfFasta.length; i++)	{
		sequences.push(removeNonLetters(getSequenceFromFasta (arrayOfFasta[i])));
	}

	var sequence = sequences.join("");
	openWindow("Combine FASTA");
	openPre();
	if (sequences.length == 1) {
		outputWindow.document.write("&gt;results for " + sequence.length + " residue sequence made from " + sequences.length + " records, starting \"" + sequence.substring(0,10) + "\"\n");
	}
	else if (sequences.length > 1) {
		outputWindow.document.write("&gt;results for " + sequence.length + " residue sequence made from " + sequences.length + " records, starting \"" + sequence.substring(0,10) + "\"\n");
	}
	else {
		outputWindow.document.write("<div class=\"info\">No sequence records were read</div>\n");
	}
	outputWindow.document.write(addReturns(sequence) + "\n");		
	closePre();
	closeWindow();
	return true;
	
}