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

function emblFasta (theDocument) {

    	var newDna = "";
    	var maxInput = 200000;

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

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

	openWindow("EMBL to FASTA");
	openPre();
	emblToFasta(theDocument.forms[0].elements[0].value);	
	closePre();
	closeWindow();
	return true;
}

function emblToFasta (emblFile)	{
	var title;
	emblFile = "_" + emblFile + "_";
	var recordArray = emblFile.split(/ID\s\s\s[^\f\n\r]*/);
	for (var i=1; i < recordArray.length; i++) {
		var mainArray = recordArray[i].split (/[\f\n\r]\s*FH   Key             Location\/Qualifiers[\f\n\r]+\s*FH|[\f\n\r]\s*XX[\s]*[\f\n\r]\s*SQ[^\f\n\r]*/);
		if ((mainArray[0].search(/[\f\n\r]\s*DE[^\f\n\r]+/) != -1)) {
			title = ((mainArray[0].match(/[\f\n\r]\s*DE[^\f\n\r]+/)).toString()).replace(/[\f\n\r]\s*DE\s*/, "");
		}
		else {
			title = "Untitled";
		}
		title = filterFastaTitle(title.replace(/[\f\n\r\t]+$/g, "")) + "\n";
		dnaArray = mainArray[2].split (/\/{2}/);
		if (dnaArray.length == 1) {
			alert ("The entire EMBL file may not have been processed.");
			outputWindow.focus();
		}
		dnaSequence = removeNonDna(dnaArray[0]);
		outputWindow.document.write ("&gt;" + title + addReturns(dnaSequence) + "\n\n");
	}
	return true;
}